If you use our data please cite: Mostajo, Nelly F., et al. "A comprehensive annotation and differential expression analysis of short and long non-coding RNAs in 16 bat genomes." NAR Genomics and Bioinformatics 2.1 (2019): lqz006.

README: How to navigate through and work with this supplement

Contents



All genome, annotation (GTF), and intermediate files can be additionally found in the Open Science Framework. Code is available at GitHub.

Table S1: Assembly statistics by QUAST

back to top

Assembly statistics for all 16 investigated bat genomes calculated with QUAST.

Full QUAST report: HTML, TEX

Icarus genome browser: HTML

Table S2: Bat RNA-Seq data

back to top

Bat RNA-Seq data used for validation of the extended non-coding RNA annotation.

RNA-Seq Label Bat species Tissue # Samples Read length (bp) # Reads (mio) Lib type Seq setup Accession Ref Study topic
1 Field-2015 M. lucifugus Wing skin tissue 11 101 15,1-19,4 polyA+ pe/ss SRP055976 Field (2015) White-nose syndrome (WNS) caused by a psychrophilic fungus Pseudogymnoascus destructans in hibernating bats
2 Eckalbar-2016 M. natalensis forelimb/hindlimb tissue 18 100 30,9-82,7 polyA+ pe/ss SRP051253 Eckalbar (2016) Developing bat wing by investigating forelimb and hindlimb autopods at sequential embryonic stages
3 Hölzer-2016 R. aegyptiacus R06E-J primary embryonic cell line 9 100 18,7-25,1 rRNA- pe/not-ss SRP128545 Hölzer (2016) Ebola and Marburg virus infection in human and bat cells at three time points
4 Field-2018 M. lucifugus Wing skin tissue 24 50 30,8-49,9 rRNA- se/ss SRP111376 Field (2018) Comparison of fungus-infected (P. destructans) wing tissue (causing WNS) between torpor/warm hibernating bats
5 Hölzer-2019 M. daubentonii MyDauNi/2c kidney cell line 18 50 66,2-72,0 rRNA- se/ss GSE121301 Hölzer (2019) Comparison of an IFN-inducing virus (RVFV; Clone 13) or treatment with IFN at two time points
6 Weber-2019 M. daubentonii MyDauNi/2c kidney cell line 18 50 8,6-12,5 sRNA se/ss GSE132336 This study Comparison of an IFN-inducing virus (RVFV; Clone 13) or treatment with IFN at two time points



Table S3: rRNAs

back to top

Download table data

CSV: rRNA.csv - XLSX: rRNA.xlsx

Selection menu

Table
rRNA PVA PAL RAE EHE ESP HAR RSI RFE MLY DRO PPA MLU MBR MDA EFU MNA
FASTA FASTA FASTA FASTA FASTA FASTA FASTA FASTA FASTA FASTA FASTA FASTA FASTA FASTA FASTA FASTA
GFF GFF GFF GFF GFF GFF GFF GFF GFF GFF GFF GFF GFF GFF GFF GFF
GTF GTF GTF GTF GTF GTF GTF GTF GTF GTF GTF GTF GTF GTF GTF GTF
18s_rRNA 1 1 19 1 15 - - 1 - - 1 6 3 1 - -
28s_rRNA 2 - 12 1 13 - - 1 1 - 2 13 10 3 2 -
8s_rRNA 17919 585 14038 12853 17278 194 128 106 259 351 393 146 142 162 169 51



Table S4: tRNAs

back to top

Download table data

CSV: tRNAs.csv - XLSX: tRNAs.xlsx

Selection menu

Table
tRNA PVA PAL RAE EHE ESP HAR RSI RFE MLY DRO PPA MLU MBR MDA EFU MNA
GTF GTF GTF GTF GTF GTF GTF GTF GTF GTF GTF GTF GTF GTF GTF GTF
TRNASCAN-SE TRNASCAN-SE TRNASCAN-SE TRNASCAN-SE TRNASCAN-SE TRNASCAN-SE TRNASCAN-SE TRNASCAN-SE TRNASCAN-SE TRNASCAN-SE TRNASCAN-SE TRNASCAN-SE TRNASCAN-SE TRNASCAN-SE TRNASCAN-SE TRNASCAN-SE
Ala_AGC 10 9 8 8 11 9 13 11 29 12 22 14 12 9 12 15
Ala_CGC 9 6 6 5 6 2 6 4 46 3 7 6 8 7 9 11
Ala_GGC 3 1 1 6 1 1 13 9 2217 3 8 2 3 4 2 7
Ala_TGC 149 138 95 116 107 7 5 8 32 8 15 25 15 14 15 15
Arg_ACG 4 5 5 4 6 5 6 5 4 7 10 16 10 15 16 9
Arg_CCG 2 2 2 2 2 4 4 2 4 6 4 3 2 3 7 3
Arg_CCT 4 5 5 5 5 78 108 91 15 4 13 11 13 9 8 8
Arg_GCG - - - - - - - - 10 13 2 70 64 63 68 17
Arg_TCG 5 5 5 4 5 4 3 4 22 5 8 12 13 14 12 8
Arg_TCT 6 5 8 5 5 27 12 9 18 5 6 8 5 6 6 5
Asn_ATT 2 4 - 1 2 5 20 16 14 2 2 4 7 4 2 1
Asn_GTT 8 6 11 5 9 31 27 17 138 11 27 13 10 12 11 12
Asp_ATC - - - 1 - - - 1 358 - - 4 3 5 2 2
Asp_GTC 7 8 9 7 9 8 9 8 5253 11 18 10 11 14 7 7
Cys_ACA 2 1 1 3 1 1 - 1 2 31 36 18 15 17 12 11
Cys_GCA 21 19 20 18 20 22 21 17 18 80 54 83 88 95 78 62
Gln_CTG 8 7 10 7 5 77 40 27 146 6 18 15 14 19 18 12
Gln_TTG 2 3 4 3 5 5 10 4 27 2 7 10 9 15 15 10
Glu_CTC 7 9 12 10 9 16 117 91 7098 8 16 14 9 12 12 13
Glu_TTC 22 18 16 23 23 6 6 4 404 4 6 6 6 6 5 5
Gly_ACC 1 1 2 1 - - 2 2 8 - 4 1 3 4 2 1
Gly_CCC 3 3 7 6 3 3 10 9 200 7 5 8 7 8 8 11
Gly_GCC 10 11 9 9 9 11 8 7 77 10 26 11 12 11 13 16
Gly_TCC 25 28 25 29 29 7 4 3 25 5 6 7 7 8 6 6
His_ATG - - - - - 5 3 - 6 6 5 212 198 197 167 45
His_GTG 6 5 5 5 5 8 6 6 53 36 18 112 110 118 92 46
Ile_AAT 6 6 8 4 6 192 1599 1038 8 81 87 93 96 88 77 99
Ile_GAT - - 1 - - 1737 805 657 17 157 123 121 137 106 126 159
Ile_TAT 182 179 128 123 124 32 34 40 4 19 14 24 21 21 17 23
Leu_AAG 4 4 5 3 5 16 21 22 7 4 9 7 11 16 8 18
Leu_CAA 4 3 4 3 5 92 10 7 26 10 9 13 16 11 9 11
Leu_CAG 7 5 6 4 6 13 15 10 8 6 11 16 12 17 11 25
Leu_GAG - - - - - 16 15 6 6 8 5 12 18 26 15 28
Leu_TAA 15 17 14 14 15 2 6 5 4 4 6 3 4 3 2 9
Leu_TAG 16 15 9 8 10 3 3 5 4 4 5 4 3 5 2 98
Lys_CTT 10 7 9 9 8 671 321 272 332 17 19 31 18 17 14 16
Lys_TTT 7 9 7 6 9 22 19 14 28 11 11 6 11 8 6 12
Met_CAT 15 14 15 15 12 335 301 240 14 71 64 112 120 96 86 119
Phe_AAA - - - - - 5 15 15 - 3 5 2 1 2 4 2
Phe_GAA 6 6 5 5 6 27 14 12 5 12 25 11 14 15 11 10
Pro_AGG 6 6 6 6 6 6 7 6 13 9 16 16 19 26 14 144
Pro_CGG 1 1 2 1 2 3 4 1 13 2 1 8 5 6 8 5
Pro_GGG - - - 4 - - 10 10 58 7 6 12 12 16 11 26
Pro_TGG 6 5 4 5 4 4 5 3 65 2 6 7 9 4 12 22
SeC(e)_TCA 1 1 1 1 1 1 1 1 1 1 1 - 1 1 1 1
SeC_TCA - - - 2 1 9 25 28 315 145 68 469 493 441 498 325
Ser_ACT - - - - - 7 41 45 1 2 4 6 5 2 5 10
Ser_AGA 5 5 3 5 5 5 5 7 6 7 14 9 12 11 7 13
Ser_CGA 3 3 2 3 2 4 3 3 31 4 7 7 8 10 6 4
Ser_GCT 6 5 5 5 5 75 37 27 26 13 15 19 15 16 11 11
Ser_GGA - - 1 - - 1 5 8 34 2 6 7 8 4 6 5
Ser_TGA 3 2 4 4 2 4 3 6 8 2 5 10 7 5 5 11
Sup_CTA - - 3 - - 11 7 4 65 2 2 4 2 1 1 3
Sup_TTA 5 6 8 12 13 2 2 6 8 1 3 1 - 1 1 -
Thr_AGT 5 5 5 4 5 21 149 126 4 19 21 25 26 17 17 25
Thr_CGT 3 4 3 2 3 21 57 57 3 15 10 19 18 21 21 26
Thr_GGT - - - - - 84 515 421 626 11 10 10 18 15 17 23
Thr_TGT 15 11 10 8 10 21 34 28 20 14 17 23 26 29 17 26
Trp_CCA 4 5 6 5 6 4 5 6 9 13 14 8 14 13 8 12
Tyr_ATA 2 1 1 1 1 3 3 2 5 8 9 11 15 16 13 6
Tyr_GTA 6 8 10 9 17 8 9 9 85 24 22 21 16 15 15 12
Val_AAC 9 9 18 11 14 15 54 56 8 13 31 9 11 11 9 9
Val_CAC 52 52 61 29 49 31 17 15 43 17 14 29 25 30 30 25
Val_GAC 6 9 11 11 10 34 23 18 93 12 13 9 6 10 4 8
Val_TAC 2405 2347 1764 1400 1788 4 5 4 8 4 8 7 5 7 5 5



Table S5: snoRNAs

back to top

SnoRNA alignments were hand-curated and divided into H/ACA and C/D box snoRNAs, if possible.

Download table data

CSV: snoRNA_gorap.csv - XLSX: snoRNA_gorap.xlsx

Selection menu

Table
snoRNA_gorap RFam_ID class FASTA STK PVA PAL RAE EHE ESP HAR RSI RFE MLY DRO PPA MLU MBR MDA EFU MNA
GTF GTF GTF GTF GTF GTF GTF GTF GTF GTF GTF GTF GTF GTF GTF GTF
ACA64 RF01225 Unclassified FASTA STK 1 1 1 1 1 - - - - 2 3 3 2 1 3 2
SCARNA1 RF00553 H/ACA FASTA STK 2 2 2 2 1 1 1 1 1 3 4 3 3 3 5 4
SCARNA11 RF00564 H/ACA FASTA STK 1 1 1 1 1 1 1 1 1 12 8 5 6 5 4 5
SCARNA13 RF00231 H/ACA FASTA STK 1 1 1 1 1 1 1 1 1 2 2 1 3 2 1 1
SCARNA14 RF00582 H/ACA FASTA STK 1 1 1 1 1 1 1 1 1 3 2 3 3 2 4 2
SCARNA15 RF00426 H/ACA FASTA STK 1 1 1 1 1 1 2 1 1 3 2 2 2 2 1 1
SCARNA16 RF00424 H/ACA FASTA STK 1 1 2 1 1 1 1 1 1 3 - 1 2 3 2 1
SCARNA18 RF00283 C/D FASTA STK 1 1 1 1 1 3 1 1 1 1 1 3 2 3 3 2
SCARNA2 RF01268 C/D FASTA STK 1 1 1 1 1 1 1 1 - 2 1 1 1 - 1 1
SCARNA20 RF00601 H/ACA FASTA STK 1 1 1 1 1 1 1 1 2 2 2 2 3 4 4 4
SCARNA21 RF00602 H/ACA FASTA STK 2 2 2 2 2 1 1 1 5 1 1 1 1 1 1 1
SCARNA23 RF00427 H/ACA FASTA STK 1 1 1 1 1 1 1 1 1 3 - 1 1 2 2 1
SCARNA24 RF00422 H/ACA FASTA STK 2 2 2 1 2 1 1 1 - 6 2 10 9 12 5 5
SCARNA3 RF00565 H/ACA FASTA STK 1 1 2 2 2 2 2 2 2 1 2 2 2 2 2 2
SCARNA4 RF00423 H/ACA FASTA STK 1 1 1 1 1 2 1 1 1 3 1 3 4 4 4 2
SCARNA6 RF00478 Unclassified FASTA STK 1 2 1 2 2 1 1 1 1 1 1 1 1 1 1 1
SCARNA7 RF01295 Unclassified FASTA STK 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
SCARNA8 RF00286 H/ACA FASTA STK 1 1 1 1 1 1 1 1 1 1 1 5 6 5 3 2
SNORA1 RF00408 H/ACA FASTA STK 2 2 3 2 1 1 2 1 1 3 6 3 4 5 5 1
SNORA11 RF00614 H/ACA FASTA STK 6 5 4 5 6 5 5 4 2 5 5 19 29 12 7 7
SNORA12 RF00586 H/ACA FASTA STK 2 2 2 1 2 1 1 1 1 1 1 2 2 2 2 1
SNORA13 RF00396 H/ACA FASTA STK 2 2 2 2 2 1 1 1 1 3 3 3 2 2 1 2
SNORA15 RF00398 H/ACA FASTA STK 2 2 2 2 2 2 2 3 2 5 2 3 1 2 1 2
SNORA16 RF00190 H/ACA FASTA STK 2 2 2 3 2 1 1 1 1 3 4 7 10 8 4 2
SNORA18 RF00425 H/ACA FASTA STK 4 4 4 2 3 4 7 4 5 1 2 6 7 5 4 1
SNORA19 RF00413 H/ACA FASTA STK 5 2 2 3 2 3 2 2 3 4 5 4 5 5 3 3
SNORA22 RF00414 H/ACA FASTA STK 1 1 1 1 1 2 2 2 1 3 6 5 4 4 6 3
SNORA25 RF00402 H/ACA FASTA STK 5 5 4 4 5 5 6 6 7 10 9 15 15 12 14 9
SNORA26 RF00568 H/ACA FASTA STK 2 2 2 2 1 1 3 4 2 3 4 9 7 6 10 5
SNORA27 RF00443 H/ACA FASTA STK 3 2 2 2 2 1 3 2 2 4 2 2 2 2 3 5
SNORA28 RF00400 H/ACA FASTA STK 5 4 3 4 3 1 2 2 4 1 1 1 - 1 2 -
SNORA29 RF00429 H/ACA FASTA STK 2 2 2 2 1 2 2 2 1 5 7 11 13 15 11 6
SNORA33 RF00438 H/ACA FASTA STK 3 3 2 3 3 1 2 1 2 13 11 9 11 11 14 8
SNORA35 RF00566 H/ACA FASTA STK 1 1 1 1 1 1 1 1 2 1 2 2 2 2 2 2
SNORA38 RF00428 H/ACA FASTA STK 3 4 4 4 3 3 3 4 2 11 10 11 13 12 19 6
SNORA40 RF00561 H/ACA FASTA STK - - - - - - - - - 1 2 - - - - -
SNORA41 RF00403 H/ACA FASTA STK 1 1 1 2 1 2 2 2 2 7 7 5 3 3 4 2
SNORA42 RF00406 H/ACA FASTA STK 9 8 5 4 6 9 4 4 5 27 21 31 33 26 32 25
SNORA43 RF00416 H/ACA FASTA STK 3 3 2 3 2 1 1 1 1 1 3 5 6 5 7 1
SNORA44 RF00405 H/ACA FASTA STK 1 1 1 1 1 2 1 1 2 7 7 6 11 6 7 4
SNORA46 RF00404 H/ACA FASTA STK 1 1 1 1 1 1 - - 1 2 1 1 1 1 2 1
SNORA47 RF01234 H/ACA FASTA STK 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 1
SNORA48 RF00554 H/ACA FASTA STK 3 3 2 4 5 5 4 4 4 7 8 65 60 67 65 13
SNORA50 RF00407 H/ACA FASTA STK 1 1 1 1 1 1 1 1 - 2 2 2 2 2 2 1
SNORA52 RF00419 H/ACA FASTA STK 6 5 3 4 4 1 2 1 1 4 2 - 1 1 3 2
SNORA55 RF00431 H/ACA FASTA STK 1 1 1 1 1 1 1 1 1 1 1 2 3 3 1 1
SNORA56 RF00417 H/ACA FASTA STK 1 1 1 1 1 1 1 1 1 2 1 2 2 2 2 1
SNORA57 RF00191 H/ACA FASTA STK 4 3 2 3 2 2 4 4 - 7 4 8 12 8 9 7
SNORA58 RF00418 H/ACA FASTA STK 1 1 - 1 1 1 1 1 1 1 3 8 5 6 5 2
SNORA61 RF00420 H/ACA FASTA STK 4 3 2 3 2 1 2 2 2 15 8 11 11 12 12 1
SNORA63 RF00092 H/ACA FASTA STK 5 5 4 5 5 5 5 5 4 7 5 8 7 5 5 4
SNORA66 RF00155 H/ACA FASTA STK 2 1 1 1 1 1 1 1 1 8 11 10 8 14 10 5
SNORA68 RF00263 H/ACA FASTA STK 1 1 1 1 1 1 1 1 1 2 5 2 3 3 3 1
SNORA69 RF00265 H/ACA FASTA STK 1 1 1 1 1 2 1 - - 6 2 3 1 2 2 1
SNORA7 RF00409 H/ACA FASTA STK 2 2 1 2 2 - 1 1 1 6 4 3 4 4 4 1
SNORA70 RF00156 H/ACA FASTA STK 5 4 6 6 5 2 3 2 2 2 1 6 3 6 5 2
SNORA72 RF00139 H/ACA FASTA STK 4 4 3 2 3 1 1 3 1 2 1 4 4 4 3 1
SNORA73 RF00045 H/ACA FASTA STK 4 3 3 4 3 4 4 3 3 8 9 12 8 10 7 7
SNORA74 RF00090 H/ACA FASTA STK 2 1 2 1 1 2 2 2 2 1 1 3 3 1 2 2
SNORA75 RF00072 H/ACA FASTA STK 1 1 1 1 1 - 1 1 1 3 5 2 2 2 2 2
SNORA76 RF00598 H/ACA FASTA STK 2 1 1 1 1 2 1 1 1 1 2 3 3 3 1 1
SNORA77 RF00599 H/ACA FASTA STK 1 1 1 1 1 2 1 2 2 3 5 4 4 3 3 2
SNORA79 RF00600 H/ACA FASTA STK 2 3 3 3 3 2 3 3 2 13 3 4 5 4 4 3
SNORA81 RF01241 H/ACA FASTA STK 2 1 3 1 3 3 3 3 1 2 3 2 5 1 2 1
SNORA84 RF01229 H/ACA FASTA STK 1 1 - 1 1 1 1 1 1 - 1 - - - - -
SNORA9 RF00411 H/ACA FASTA STK 2 2 2 2 2 1 1 1 1 1 2 5 6 7 3 1
SNORD10 RF01290 C/D FASTA STK 1 1 1 1 1 1 1 1 1 1 1 1 1 1 - 1
SNORD100 RF00609 C/D FASTA STK 5 5 4 8 2 6 2 4 2 4 3 6 35 3 2 4
SNORD101 RF00186 C/D FASTA STK 2 2 1 1 2 1 2 1 3 2 2 2 3 2 2 1
SNORD102 RF00187 C/D FASTA STK 1 2 1 1 2 1 1 1 1 2 1 1 1 1 1 2
SNORD103 RF00188 C/D FASTA STK 6 5 3 3 5 4 2 2 3 7 5 5 4 2 3 5
SNORD105 RF00584 C/D FASTA STK 2 1 4 4 2 1 3 1 3 2 2 3 1 3 3 4
SNORD107 RF01164 C/D FASTA STK 8 8 4 7 6 - 5 4 3 2 7 5 3 2 3 6
SNORD108 RF01158 Unclassified FASTA STK 1 3 2 1 1 1 1 1 2 - - 1 2 1 1 2
SNORD109A RF01278 C/D FASTA STK 3 2 1 1 1 3 2 2 2 2 6 1 - 2 2 3
SNORD11 RF01182 C/D FASTA STK 1 1 2 3 1 1 2 1 - 2 2 2 2 3 1 3
SNORD110 RF00610 C/D FASTA STK 3 3 4 1 4 1 3 3 3 1 2 3 3 2 1 1
SNORD112 RF01169 C/D FASTA STK 60 68 57 57 41 60 73 72 21 29 37 30 36 25 29 40
SNORD116 RF00108 C/D FASTA STK 3 4 3 4 5 19 20 17 17 17 23 37 16 21 3 29
SNORD11B RF01192 C/D FASTA STK 4 2 2 2 2 2 1 3 4 1 1 1 2 2 2 2
SNORD121A RF01191 C/D FASTA STK 5 4 3 3 4 4 6 4 1 2 5 5 4 4 4 4
SNORD123 RF01156 C/D FASTA STK 1 2 1 1 1 4 3 2 1 2 3 2 1 3 2 3
SNORD124 RF01211 C/D FASTA STK 1 1 2 1 1 2 1 2 1 1 2 1 1 1 1 1
SNORD125 RF01200 C/D FASTA STK 1 1 1 2 3 2 1 1 2 1 1 3 3 3 2 1
SNORD126 RF01168 C/D FASTA STK 1 2 1 2 3 3 2 1 2 2 1 1 2 1 1 2
SNORD127 RF01186 C/D FASTA STK 3 5 4 5 4 1 1 2 2 2 1 1 1 1 2 1
SNORD14 RF00016 C/D FASTA STK 6 6 11 9 10 12 9 11 8 11 11 7 12 6 9 15
SNORD17 RF00567 C/D FASTA STK 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
SNORD19 RF00569 C/D FASTA STK 2 2 2 2 4 3 1 2 2 3 2 2 2 2 2 3
SNORD19B RF01183 C/D FASTA STK 1 1 1 1 1 1 1 1 2 1 1 1 1 1 1 1
SNORD2 RF01299 C/D FASTA STK 7 8 5 7 5 9 5 4 3 4 4 2 4 2 3 2
SNORD20 RF00217 C/D FASTA STK 3 2 1 3 1 - 3 2 3 1 3 2 2 2 1 1
SNORD22 RF00099 C/D FASTA STK 4 4 5 4 6 8 9 5 6 8 8 6 7 5 7 5
SNORD23 RF00603 C/D FASTA STK 3 1 2 - 3 2 3 4 - 3 - 4 6 1 4 2
SNORD24 RF00069 C/D FASTA STK 7 6 4 4 6 4 4 4 3 3 5 5 2 3 5 4
SNORD26 RF00087 C/D FASTA STK 8 9 5 5 3 10 5 7 5 7 4 4 4 4 3 5
SNORD27 RF00086 C/D FASTA STK 2 1 7 3 3 4 7 3 2 4 2 9 8 3 6 4
SNORD28 RF00085 C/D FASTA STK 2 2 2 2 2 1 1 1 1 3 1 3 2 2 2 1
SNORD30 RF00088 C/D FASTA STK 1 2 2 2 2 1 1 1 1 2 2 1 1 1 1 1
SNORD31 RF00089 C/D FASTA STK 5 5 7 9 9 2 6 7 7 3 4 2 6 4 13 5
SNORD33 RF00133 C/D FASTA STK 4 3 3 3 2 2 2 4 3 2 4 3 4 3 4 3
SNORD36 RF00049 C/D FASTA STK 4 4 5 4 4 4 7 5 4 3 3 2 2 3 2 4
SNORD39 RF00157 C/D FASTA STK 2 1 2 3 2 2 3 3 3 3 4 2 2 4 2 4
SNORD41 RF00588 C/D FASTA STK 2 2 2 2 1 2 2 3 1 2 3 4 2 2 3 2
SNORD47 RF00281 C/D FASTA STK 6 5 3 7 3 2 5 4 1 4 2 3 2 4 4 1
SNORD48 RF00282 C/D FASTA STK 1 1 2 1 2 2 1 1 3 3 3 2 1 2 1 2
SNORD49 RF00277 C/D FASTA STK 2 2 2 2 2 2 2 2 1 2 2 5 2 4 2 2
SNORD5 RF01161 C/D FASTA STK 2 2 3 1 1 1 1 2 1 1 5 2 3 2 1 2
SNORD50 RF00278 C/D FASTA STK 5 7 2 3 2 2 4 3 6 5 7 7 7 8 7 7
SNORD51 RF00280 C/D FASTA STK 2 2 3 2 2 1 2 2 1 1 1 2 1 1 1 1
SNORD52 RF00276 C/D FASTA STK 6 6 4 10 5 8 3 3 7 6 7 7 7 4 6 6
SNORD57 RF00274 C/D FASTA STK 1 1 3 4 1 3 4 2 3 3 4 4 3 6 2 5
SNORD58 RF00151 C/D FASTA STK 7 9 8 10 9 9 12 9 8 15 12 13 9 6 7 10
SNORD59 RF00273 C/D FASTA STK 5 5 4 3 5 7 3 3 3 4 2 4 5 5 2 3
SNORD60 RF00271 C/D FASTA STK 2 2 3 3 4 5 1 1 3 3 3 2 1 2 3 3
SNORD61 RF00270 C/D FASTA STK 1 1 1 1 1 2 2 1 - 1 1 2 2 3 1 1
SNORD62 RF00153 C/D FASTA STK 3 3 2 2 2 4 2 3 4 3 5 5 4 4 2 3
SNORD63 RF00154 C/D FASTA STK 5 4 3 7 7 3 3 6 6 2 3 1 3 3 3 3
SNORD64 RF00570 C/D FASTA STK 2 2 1 4 3 1 3 2 2 3 2 4 3 4 2 3
SNORD65 RF00571 C/D FASTA STK 1 1 1 1 1 1 1 1 2 1 1 3 3 1 1 2
SNORD66 RF00572 C/D FASTA STK 4 4 6 7 6 4 3 6 4 5 5 4 3 5 5 4
SNORD67 RF00573 C/D FASTA STK 1 1 2 2 1 3 2 2 3 1 3 2 1 1 1 1
SNORD69 RF00574 C/D FASTA STK 2 1 1 1 2 1 1 2 1 4 2 2 2 2 2 3
SNORD70 RF00575 C/D FASTA STK 2 2 3 2 2 2 2 3 2 2 3 2 3 2 2 2
SNORD71 RF00576 C/D FASTA STK 1 1 1 1 1 2 1 1 1 1 1 1 1 1 1 1
SNORD72 RF00577 C/D FASTA STK 1 1 2 1 1 1 1 1 1 2 2 2 2 2 2 3
SNORD73 RF00071 C/D FASTA STK 5 4 5 4 7 5 4 4 3 3 5 5 5 3 3 3
SNORD74 RF00284 C/D FASTA STK 12 7 6 6 6 6 7 5 7 8 4 6 4 6 7 4
SNORD77 RF00591 C/D FASTA STK 1 2 2 2 1 2 1 1 1 3 2 1 1 1 1 2
SNORD78 RF00592 C/D FASTA STK 7 7 5 5 4 3 2 2 3 2 2 5 5 3 4 1
SNORD79 RF00152 C/D FASTA STK 5 2 4 1 1 1 3 3 3 3 4 2 1 2 2 4
SNORD81 RF00136 C/D FASTA STK 2 1 1 1 1 1 1 1 1 1 1 1 1 2 1 2
SNORD82 RF00158 C/D FASTA STK 4 4 2 5 3 - 5 1 1 3 2 4 3 3 3 2
SNORD87 RF00439 C/D FASTA STK 4 3 2 1 2 2 2 1 2 2 3 1 1 1 1 1
SNORD88 RF00604 C/D FASTA STK 6 5 6 1 6 5 4 3 4 5 5 11 10 9 7 4
SNORD89 RF00578 C/D FASTA STK 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
SNORD90 RF00579 C/D FASTA STK 1 1 1 1 1 1 1 1 2 1 2 1 1 1 1 1
SNORD91 RF00580 C/D FASTA STK 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 1
SNORD93 RF00606 C/D FASTA STK 1 2 1 1 2 3 3 1 1 1 2 2 2 2 2 1
SNORD94 RF00613 C/D FASTA STK 1 1 2 2 1 1 2 1 1 1 1 1 1 1 1 1
SNORD97 RF01291 Unclassified FASTA STK 3 3 3 2 3 1 5 4 2 2 3 2 3 3 1 2
SNORD98 RF00607 C/D FASTA STK 2 2 6 3 3 1 4 2 5 2 3 3 3 4 5 4
SNORD99 RF00608 C/D FASTA STK 1 1 2 2 2 1 2 2 3 1 3 1 2 2 3 2
SNORND104 RF00289 C/D FASTA STK 2 3 2 6 5 3 6 3 5 3 1 3 2 2 3 6
U3 RF00012 C/D FASTA STK 5 6 5 6 4 32 13 13 8 38 18 20 18 14 8 7
snoMBII-202 RF00324 C/D FASTA STK 7 6 3 8 5 5 8 7 5 4 6 6 7 6 6 4
snoR38 RF00213 C/D FASTA STK 4 3 5 2 4 3 5 6 5 2 4 5 4 5 5 4
snoU105B RF01173 Unclassified FASTA STK - 1 1 1 1 2 1 - - 2 1 1 1 1 1 1
snoU109 RF01233 Unclassified FASTA STK 3 3 3 3 3 1 3 3 2 3 1 7 6 3 7 3
snoU13 RF01210 Unclassified FASTA STK 26 25 24 23 26 65 71 61 60 35 28 20 21 23 17 21
snoU18 RF01159 Unclassified FASTA STK 2 2 - 1 2 - - 1 1 - - 2 1 - 2 -
snoU2-30 RF00493 C/D FASTA STK 7 6 9 5 6 6 6 6 5 3 3 6 5 5 6 3
snoU54 RF01277 Unclassified FASTA STK 4 3 8 4 3 1 2 4 4 1 3 2 3 3 3 3
snoU6-53 RF00377 C/D FASTA STK 3 4 6 3 6 3 7 5 3 3 3 1 1 1 1 5
snoU82P RF01151 Unclassified FASTA STK 1 1 1 1 1 1 1 1 1 2 2 2 3 2 2 1
snoU83B RF00593 C/D FASTA STK 6 6 4 5 4 2 3 4 1 2 1 4 2 3 2 3
snoU85 RF01296 Unclassified FASTA STK 1 1 1 1 1 1 1 1 1 1 2 1 1 1 1 1
snoU89 RF01294 Unclassified FASTA STK 1 1 1 1 1 1 1 - 1 1 - 1 1 1 1 1
snoZ17 RF00266 C/D FASTA STK 2 2 2 3 2 2 2 2 - 3 2 2 2 3 2 2
snoZ30 RF00288 C/D FASTA STK 1 3 5 2 1 6 1 2 5 6 7 3 1 4 5 1
snoZ39 RF00341 C/D FASTA STK 1 2 2 2 2 1 1 1 1 1 1 1 1 1 1 1
snosnR61 RF00476 C/D FASTA STK 1 4 4 3 3 3 4 3 3 2 5 3 4 2 2 4



Table S6: miRNAs (structure/sequence-based)

back to top

These miRNA hits were hand-curated and produced by a structure/sequence-based search using RFAM alignments as templates.

Download table data

CSV: miRNA_gorap.csv - XLSX: miRNA_gorap.xlsx

Selection menu

Table
miRNA_gorap RFam_ID FASTA STK PVA PAL RAE EHE ESP HAR RSI RFE MLY DRO PPA MLU MBR MDA EFU MNA
GTF GTF GTF GTF GTF GTF GTF GTF GTF GTF GTF GTF GTF GTF GTF GTF
let-7 RF00027 FASTA STK 11 11 10 8 10 9 10 9 6 9 7 6 7 6 7 10
mir-1 RF00103 FASTA STK 1 4 4 4 4 4 4 4 2 3 2 4 4 5 4 4
mir-101 RF00253 FASTA STK 2 2 2 2 2 2 2 2 2 3 2 2 2 2 2 2
mir-103 RF00129 FASTA STK 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3
mir-105 RF00670 FASTA STK 4 3 3 3 1 3 3 4 5 3 3 3 3 3 2 4
mir-122 RF00684 FASTA STK 1 1 1 1 2 1 1 1 1 1 1 1 1 1 1 1
mir-1224 RF00942 FASTA STK 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
mir-1225 RF00946 FASTA STK 1 1 1 1 1 1 1 1 - 1 - 1 1 1 1 1
mir-124 RF00239 FASTA STK 2 2 3 2 3 3 3 3 1 2 2 2 2 2 3 2
mir-1249 RF01918 FASTA STK 1 1 1 1 1 1 1 1 - 1 1 1 1 1 1 1
mir-126 RF00701 FASTA STK 1 1 1 1 1 1 1 1 - 1 - - 1 - 1 1
mir-128 RF00649 FASTA STK 2 1 2 1 2 2 2 2 1 2 1 2 2 2 2 2
mir-1287 RF02015 FASTA STK 1 1 1 1 1 1 1 1 - 1 1 1 2 1 1 1
mir-130 RF00258 FASTA STK 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
mir-1302 RF00951 FASTA STK 217 232 175 206 162 236 221 199 113 124 118 132 126 105 119 184
mir-1306 RF01014 FASTA STK 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
mir-1307 RF01038 FASTA STK 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
mir-132 RF00662 FASTA STK 2 2 2 1 2 2 2 1 - 2 - 2 - - 2 2
mir-133 RF00446 FASTA STK 2 3 3 2 2 3 3 2 2 3 2 3 3 3 3 3
mir-134 RF00699 FASTA STK 1 1 1 - 1 1 1 1 - - - - - - - 1
mir-135 RF00246 FASTA STK 3 3 3 3 4 3 3 3 2 3 2 3 4 2 3 3
mir-136 RF00687 FASTA STK 1 1 1 1 1 1 1 1 1 1 - 1 1 1 1 1
mir-137 RF00694 FASTA STK 1 1 1 1 1 1 1 - - 1 - - - 1 1 1
mir-138 RF00671 FASTA STK 2 2 2 1 2 2 2 2 1 2 2 2 2 2 2 2
mir-1388 RF01945 FASTA STK 1 1 1 1 1 1 1 1 - 1 - 1 1 1 1 1
mir-139 RF00703 FASTA STK 1 1 1 1 1 1 1 - - 1 - 1 1 1 1 1
mir-140 RF00678 FASTA STK 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
mir-142 RF01896 FASTA STK 1 1 1 - 1 1 1 1 - 1 - 1 1 1 1 1
mir-143 RF00683 FASTA STK - 1 1 1 1 1 1 1 - 1 1 1 1 1 1 1
mir-144 RF00682 FASTA STK 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
mir-145 RF00675 FASTA STK 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
mir-146 RF00691 FASTA STK 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
mir-147 RF00693 FASTA STK 5 4 3 3 3 5 4 3 4 4 3 2 2 2 2 2
mir-149 RF00829 FASTA STK 1 1 1 - 1 1 1 1 - - - 1 1 1 1 1
mir-15 RF00455 FASTA STK 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
mir-150 RF00767 FASTA STK 1 1 1 1 1 1 1 1 1 1 - 1 1 1 1 1
mir-153 RF00650 FASTA STK 2 2 2 2 2 2 2 2 1 2 1 2 2 2 2 2
mir-154 RF00641 FASTA STK 51 50 51 48 52 53 56 52 36 41 39 44 45 40 45 45
mir-155 RF00731 FASTA STK 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
mir-181 RF00076 FASTA STK 3 3 3 3 3 3 3 3 2 3 3 3 3 3 4 3
mir-182 RF00702 FASTA STK 1 1 1 1 1 1 1 1 - 1 1 1 1 1 1 1
mir-183 RF00663 FASTA STK 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
mir-184 RF00657 FASTA STK 1 1 1 1 1 1 1 1 - 1 - - - 1 - 1
mir-185 RF00771 FASTA STK 1 1 1 1 1 1 1 1 1 1 1 2 1 1 1 1
mir-186 RF00697 FASTA STK 3 3 2 3 3 2 4 2 2 3 3 3 3 3 3 2
mir-187 RF00674 FASTA STK 1 1 1 1 1 1 1 1 - 1 1 1 1 1 1 1
mir-188 RF01897 FASTA STK 3 3 3 3 3 3 4 4 3 3 3 3 3 3 3 3
mir-19 RF00245 FASTA STK 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3
mir-190 RF00672 FASTA STK 2 2 2 2 2 2 2 2 1 2 2 2 2 2 2 2
mir-191 RF00764 FASTA STK 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
mir-1912 RF02017 FASTA STK - - - - - 1 - 1 1 - 1 1 1 1 1 1
mir-192 RF00130 FASTA STK 2 2 2 2 2 2 2 2 2 2 1 1 2 2 2 2
mir-193 RF01895 FASTA STK 2 2 2 2 2 2 2 2 2 2 1 2 2 2 2 2
mir-194 RF00257 FASTA STK 3 3 3 3 2 3 3 3 2 3 2 3 3 3 3 3
mir-196 RF00256 FASTA STK 3 3 3 3 3 3 3 3 2 3 3 3 3 3 3 3
mir-197 RF00707 FASTA STK - - - - - 1 1 1 - - - - - - - -
mir-198 RF00681 FASTA STK - - - - - - - 1 - - - - - - - -
mir-199 RF00144 FASTA STK 3 3 3 2 3 3 3 3 2 3 1 2 3 3 3 3
mir-202 RF00705 FASTA STK 1 1 1 1 1 1 1 1 - 1 - 1 1 1 1 1
mir-203 RF00696 FASTA STK - - 1 - 1 1 1 - - - - - - - - -
mir-204 RF00646 FASTA STK 1 2 2 2 2 2 2 2 2 2 2 3 2 2 2 2
mir-205 RF00656 FASTA STK 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
mir-207 RF00802 FASTA STK - - - 1 - - - - - - - - - - - -
mir-208 RF00749 FASTA STK 2 3 2 2 2 2 2 - - 2 1 2 2 2 2 2
mir-21 RF00658 FASTA STK 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
mir-210 RF00679 FASTA STK 1 1 1 1 1 1 1 - - 1 - - - 1 1 1
mir-214 RF00660 FASTA STK 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
mir-216 RF00654 FASTA STK 3 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
mir-217 RF00673 FASTA STK 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
mir-218 RF00255 FASTA STK 2 2 2 2 2 2 2 2 1 2 1 2 2 2 2 2
mir-219 RF00251 FASTA STK 2 2 2 1 2 2 2 1 - 2 1 1 1 1 2 1
mir-22 RF00653 FASTA STK 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
mir-221 RF00651 FASTA STK 2 2 2 2 2 2 2 2 2 2 1 2 2 2 2 2
mir-223 RF00664 FASTA STK 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
mir-224 RF00680 FASTA STK 1 1 1 1 1 1 1 1 1 1 - 1 1 1 1 1
mir-23 RF00642 FASTA STK 2 2 2 2 2 3 2 2 1 2 2 1 2 2 2 2
mir-24 RF00178 FASTA STK 2 - 2 2 2 3 2 1 - 2 2 1 2 1 2 2
mir-25 RF02020 FASTA STK 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
mir-27 RF00644 FASTA STK 2 2 2 2 2 3 2 2 1 2 2 1 2 2 2 2
mir-28 RF00655 FASTA STK 3 3 3 3 3 3 3 2 3 4 3 3 3 3 3 3
mir-290 RF00665 FASTA STK 3 3 3 3 3 4 4 5 4 3 3 12 17 7 4 4
mir-296 RF00733 FASTA STK 1 1 1 - 1 1 - - - - - - - - - -
mir-2968 RF02093 FASTA STK 1 1 1 1 1 1 1 1 - - - 1 - - 1 1
mir-2985-2 RF02095 FASTA STK 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3
mir-299 RF00756 FASTA STK 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
mir-30 RF00131 FASTA STK 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7
mir-301 RF02061 FASTA STK 2 2 2 2 2 2 2 2 2 2 3 2 3 2 2 3
mir-302 RF00668 FASTA STK 5 4 4 5 3 4 6 5 5 6 7 5 5 5 4 5
mir-31 RF00661 FASTA STK 1 1 1 1 1 1 1 1 1 1 1 2 1 1 1 1
mir-32 RF00666 FASTA STK 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
mir-322 RF00737 FASTA STK 1 1 1 1 1 1 1 1 - 1 - 1 1 1 1 -
mir-326 RF00719 FASTA STK 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
mir-328 RF00772 FASTA STK 1 1 1 1 1 1 1 1 - 1 - 1 1 1 1 1
mir-33 RF00667 FASTA STK 2 2 2 2 2 2 2 2 1 2 1 1 1 1 2 2
mir-330 RF00770 FASTA STK 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
mir-331 RF00769 FASTA STK 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
mir-335 RF00766 FASTA STK 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
mir-337 RF00765 FASTA STK 1 1 1 - 1 1 1 1 1 1 1 - 1 1 1 1
mir-338 RF00686 FASTA STK 1 1 1 - 1 1 1 1 - 1 - - 1 2 1 1
mir-339 RF00763 FASTA STK 1 1 1 - 1 1 1 1 - 1 - 1 - 2 1 1
mir-340 RF00761 FASTA STK 3 3 3 2 1 2 4 4 3 2 2 4 4 3 3 2
mir-342 RF00760 FASTA STK - 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
mir-345 RF01044 FASTA STK 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
mir-346 RF00758 FASTA STK 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
mir-350 RF00806 FASTA STK 2 1 1 - 1 1 - 1 1 1 1 1 1 1 1 -
mir-361 RF00744 FASTA STK 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
mir-363 RF01898 FASTA STK 1 1 1 1 1 1 2 1 1 1 1 1 1 1 1 1
mir-365 RF00659 FASTA STK 2 2 2 2 2 2 2 2 1 2 2 2 3 2 2 2
mir-367 RF00735 FASTA STK 1 1 1 1 1 1 1 1 - 1 1 1 1 1 1 1
mir-370 RF00740 FASTA STK 1 1 1 1 1 1 1 1 - 1 - 1 1 1 1 1
mir-374 RF00840 FASTA STK 1 1 1 1 1 1 2 2 3 - - 1 1 - - -
mir-375 RF00700 FASTA STK 1 1 1 1 1 1 1 1 - 1 1 1 1 - 1 1
mir-378 RF00741 FASTA STK 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
mir-383 RF00715 FASTA STK 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
mir-384 RF00841 FASTA STK 4 4 3 3 2 4 2 2 - 4 3 1 1 - 1 2
mir-412 RF00762 FASTA STK 1 1 1 1 1 1 1 - 1 1 1 1 1 1 1 1
mir-423 RF00870 FASTA STK 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
mir-425 RF00803 FASTA STK 1 1 1 1 1 1 1 1 1 - - - - - 1 1
mir-431 RF00718 FASTA STK 1 - 1 - 1 1 1 1 - 1 - 1 1 1 1 1
mir-433 RF00748 FASTA STK 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
mir-448 RF00723 FASTA STK 1 1 1 2 1 2 1 1 1 1 2 2 2 2 2 2
mir-449 RF00711 FASTA STK 3 3 3 3 3 5 3 4 3 2 2 - 2 1 2 1
mir-450 RF00708 FASTA STK 3 3 3 3 3 2 2 2 2 3 3 3 3 3 3 3
mir-451 RF00722 FASTA STK 1 1 1 1 1 2 2 2 2 2 2 2 2 2 2 1
mir-452 RF00839 FASTA STK 1 1 1 1 1 1 1 1 1 1 - 1 1 1 1 1
mir-454 RF00746 FASTA STK 1 1 1 1 1 1 1 1 1 1 1 - - - - -
mir-484 RF00783 FASTA STK 1 1 1 1 1 1 1 1 - 1 1 1 1 1 1 1
mir-486 RF00784 FASTA STK 1 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1
mir-488 RF00861 FASTA STK 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
mir-489 RF00698 FASTA STK 1 1 1 1 1 1 1 1 1 - 1 - - - - 1
mir-490 RF00792 FASTA STK 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
mir-491 RF00862 FASTA STK 1 1 - 1 - 1 1 1 1 - - 1 1 1 1 1
mir-492 RF00989 FASTA STK - - - - - 1 1 1 - 7 1 1 2 1 - 2
mir-497 RF00793 FASTA STK 1 1 1 1 1 1 1 1 1 1 1 - 1 1 1 1
mir-499 RF00745 FASTA STK 1 1 1 1 1 1 1 1 1 1 - 1 1 1 1 1
mir-503 RF00753 FASTA STK 1 1 1 1 1 1 1 1 - 1 - 1 1 1 1 1
mir-504 RF00939 FASTA STK 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
mir-505 RF00781 FASTA STK 1 1 1 1 1 1 1 1 1 1 1 1 1 1 - 1
mir-541 RF00777 FASTA STK 1 1 1 1 1 1 1 1 1 1 - - - - - -
mir-542 RF00755 FASTA STK 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
mir-544 RF01045 FASTA STK 231 224 151 185 141 160 192 188 85 86 100 77 91 65 80 139
mir-551 RF00892 FASTA STK 1 1 2 1 1 2 2 2 1 2 1 1 2 2 1 3
mir-563 RF01003 FASTA STK 1 1 1 1 1 1 1 1 1 1 1 - - - - -
mir-567 RF01036 FASTA STK - - - - - 1 1 1 1 - 1 1 1 1 1 -
mir-569 RF01018 FASTA STK - - 1 - 1 1 1 1 - 1 1 1 1 1 1 1
mir-574 RF00929 FASTA STK 1 1 1 1 1 1 1 - - 1 - 2 1 - 4 1
mir-582 RF00927 FASTA STK 1 1 - 1 1 1 1 1 1 1 1 1 1 1 1 1
mir-584 RF01016 FASTA STK 34 39 31 33 36 55 61 66 14 20 24 26 31 26 20 31
mir-590 RF00928 FASTA STK 2 2 2 2 2 2 2 2 2 1 1 2 2 2 2 2
mir-592 RF00877 FASTA STK 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
mir-598 RF01059 FASTA STK 2 1 - - - 1 1 - - 2 2 1 1 1 3 1
mir-599 RF00991 FASTA STK 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
mir-611 RF01022 FASTA STK 1 1 1 - - 1 - - - - - - - - 1 1
mir-612 RF00959 FASTA STK - - - 1 - - - - - - - 1 1 - 1 -
mir-615 RF00879 FASTA STK 1 1 1 - 1 1 1 1 - 1 - 1 1 - 1 1
mir-626 RF00968 FASTA STK 1 1 1 1 1 - - - - 1 1 1 1 1 1 1
mir-628 RF01012 FASTA STK 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
mir-632 RF01010 FASTA STK 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
mir-638 RF00978 FASTA STK - - 1 - 1 1 1 - - - - - - 1 - -
mir-639 RF01031 FASTA STK 1 1 - - 1 - 1 - - - - 1 1 1 1 -
mir-652 RF00872 FASTA STK 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
mir-653 RF00937 FASTA STK 1 1 1 1 1 1 1 1 1 1 1 - - - - 1
mir-662 RF00983 FASTA STK - - - - - 1 1 1 1 1 1 1 1 1 1 1
mir-663 RF00957 FASTA STK - - - - - - 1 - - 1 - 4 2 1 3 -
mir-665 RF00921 FASTA STK 1 1 1 - 1 1 1 1 - 1 - - 1 1 1 1
mir-668 RF00890 FASTA STK 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
mir-672 RF00911 FASTA STK 1 1 1 1 1 1 1 1 1 - - - 1 1 - -
mir-675 RF00897 FASTA STK - - - - - 1 - - - - - - - - - -
mir-676 RF00966 FASTA STK 1 1 - 1 - - 1 1 - 1 1 1 1 - 1 1
mir-684 RF00876 FASTA STK 7 6 5 5 6 14 14 9 14 22 12 25 26 24 27 16
mir-7 RF00053 FASTA STK 4 3 4 3 3 3 3 3 2 3 2 3 3 3 3 3
mir-708 RF00917 FASTA STK 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
mir-744 RF00936 FASTA STK 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
mir-761 RF01939 FASTA STK 1 1 1 1 1 1 - 1 1 1 1 1 1 1 1 1
mir-764 RF01920 FASTA STK - - - - - - - - 1 - - 1 1 1 1 1
mir-767 RF01033 FASTA STK - - - - - - - - - 1 1 1 1 1 1 1
mir-770 RF00888 FASTA STK - - - - - 1 - - - - - - - - - -
mir-8 RF00241 FASTA STK 5 5 4 3 5 5 5 5 - 5 - 5 4 5 5 5
mir-802 RF00887 FASTA STK 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
mir-872 RF00918 FASTA STK - - - - - - - 1 - 1 1 - - - - 1
mir-873 RF00910 FASTA STK 1 1 2 1 1 1 1 1 1 1 1 1 1 1 1 1
mir-874 RF00919 FASTA STK 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
mir-875 RF00933 FASTA STK 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
mir-876 RF00935 FASTA STK 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
mir-877 RF00912 FASTA STK - - - 1 - 1 1 1 1 - - - - - - -
mir-885 RF01015 FASTA STK 1 1 - 1 - 1 1 - - 1 1 1 1 1 1 1
mir-9 RF00237 FASTA STK 3 2 3 1 3 3 3 2 1 2 1 1 1 1 3 2
mir-92 RF00464 FASTA STK 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
mir-922 RF01019 FASTA STK - - - - - 1 1 1 1 1 - 1 1 1 1 1
mir-936 RF01002 FASTA STK 1 2 1 - - - - 1 - - - - - - - -
mir-937 RF01039 FASTA STK 1 1 1 - 1 1 1 1 - - - - - - 1 -
mir-940 RF01023 FASTA STK - - - - - 1 1 1 - - 1 1 1 - - -
mir-96 RF00669 FASTA STK 1 1 1 1 1 1 1 1 1 1 - 1 1 1 1 1



Table S7: miRNAs (RNA-Seq-based)

back to top

These miRNA hits were predicted based on smallRNA-Seq data using miRDeep2.

Download table data

CSV: miRNA_mirdeep.csv - XLSX: miRNA_mirdeep.xlsx

Selection menu

Table
miRNA_mirDeep gene_biotype PVA PAL RAE EHE ESP HAR RSI RFE MLY DRO PPA MLU MBR MDA EFU MNA
HTML HTML HTML HTML HTML HTML HTML HTML HTML HTML HTML HTML HTML HTML HTML HTML
de novo mirdeep2 miRNA 450 394 440 349 458 440 431 384 368 467 387 2148 2159 2464 1991 444



Table S8: Other ncRNAs

back to top

Numbers and linked files (FASTA, GTF, STK) are based on the hand-corrected results.

Download table data

CSV: other_gorap.csv - XLSX: other_gorap.xlsx

Selection menu

Table
other_gorap RFam_ID FASTA STK PVA PAL RAE EHE ESP HAR RSI RFE MLY DRO PPA MLU MBR MDA EFU MNA
GTF GTF GTF GTF GTF GTF GTF GTF GTF GTF GTF GTF GTF GTF GTF GTF
7SK RF00100 FASTA STK 9 7 9 11 6 22 4 5 2 7 6 6 5 2 5 7
ACEA_U3 RF01848 FASTA STK - - - - - - - - - - 1 - - - - -
Antizyme_FSE RF00381 FASTA STK 2 2 2 2 2 2 2 2 3 4 5 7 11 10 7 2
CAESAR RF00172 FASTA STK 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
CDKN2B-AS RF01909 FASTA STK 1 1 1 1 1 1 1 1 - 1 1 1 1 1 1 1
CDKN2B-AS_3 RF02045 FASTA STK 1 1 1 1 1 1 1 1 - - - - 1 1 1 1
CLRN1-AS1 RF02089 FASTA STK 2 2 1 1 - 1 1 1 - - - 1 1 1 1 1
CPEB3_ribozyme RF00622 FASTA STK 1 1 1 1 1 - 1 1 1 1 1 1 1 - - 1
CoTC_ribozyme RF00621 FASTA STK 1 1 1 1 1 1 1 1 1 1 1 - - - - -
DAOA-AS1_1 RF02090 FASTA STK 1 1 1 1 1 - 1 1 1 1 1 1 1 1 1 1
DAOA-AS1_2 RF02091 FASTA STK 1 1 1 1 1 - 1 1 1 1 1 1 1 1 1 1
DLEU1_1 RF02103 FASTA STK 2 1 1 1 1 1 1 1 1 1 - 1 1 1 1 1
DLEU1_2 RF02104 FASTA STK 1 1 1 1 1 1 1 1 1 - - - - - - 1
DLEU2_1 RF02105 FASTA STK 2 2 2 1 2 3 3 3 1 2 2 1 1 1 1 2
DLEU2_2 RF02106 FASTA STK 1 1 1 1 1 2 2 2 1 - 2 1 1 1 1 1
DLEU2_3 RF02107 FASTA STK 1 1 1 1 1 2 2 2 1 1 1 1 1 1 1 1
DLEU2_4 RF02108 FASTA STK 3 3 3 2 3 2 2 2 1 1 1 1 1 1 1 1
DLEU2_5 RF02109 FASTA STK 3 3 3 3 3 2 2 2 1 1 1 1 1 1 1 1
DLEU2_6 RF02110 FASTA STK 3 3 3 3 3 2 2 2 - 2 1 1 1 1 2 2
DLG2-AS1_1 RF02112 FASTA STK 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
DLG2-AS1_2 RF02113 FASTA STK 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 -
DLX6-AS1_1 RF01887 FASTA STK 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
DLX6-AS1_2 RF01888 FASTA STK 1 1 1 1 1 1 1 1 1 - 1 1 1 1 1 1
DPB RF01455 FASTA STK 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 1
Evf-2_5p RF01778 FASTA STK 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
FAM13A-AS1_1 RF02114 FASTA STK 1 1 1 1 1 - - - 1 1 - 1 1 1 1 -
FAM13A-AS1_2 RF02115 FASTA STK - - - - - 1 1 1 1 2 1 1 1 1 1 1
FAS-AS1 RF02116 FASTA STK 1 1 1 1 1 - 1 1 1 1 - 1 1 1 1 1
FMR1-AS1_1 RF02117 FASTA STK 1 1 1 1 1 1 1 - 1 1 1 1 1 1 1 1
FMR1-AS1_2 RF02118 FASTA STK 1 1 1 - 1 1 1 1 - - - 1 1 1 1 1
FTX_1 RF02119 FASTA STK - - - - - - - - - 1 1 - - - - -
FTX_2 RF02120 FASTA STK - - - - - - - - - 1 1 - - - - -
FTX_3 RF02121 FASTA STK - - - - - - - - - 1 - - - - - 1
FTX_4 RF02123 FASTA STK - - - 1 - 1 1 1 1 1 1 - - - - 1
FTX_5 RF02122 FASTA STK - - 1 - - 1 1 1 - 1 1 - - - - -
G-CSF_SLDE RF00183 FASTA STK 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
GABA3 RF01803 FASTA STK 6 6 5 5 6 5 7 7 6 7 6 7 6 6 5 6
GHRLOS RF02126 FASTA STK 1 1 1 1 1 1 1 1 - - 1 - - - - -
GNAS-AS1_1 RF02127 FASTA STK - 1 1 - 1 1 1 1 - 1 - 1 1 1 1 1
GNAS-AS1_2 RF02128 FASTA STK - - - - - 1 1 1 1 1 1 1 1 1 1 1
GNAS-AS1_3 RF02129 FASTA STK 1 1 2 1 1 1 1 - - - 1 - - - - 1
GNAS-AS1_4 RF02130 FASTA STK 1 1 2 1 1 1 1 1 1 1 1 1 1 1 1 1
GNAS-AS1_5 RF02131 FASTA STK 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
H19_1 RF01972 FASTA STK 1 1 - - 1 1 1 1 - 1 - - - 1 - 1
H19_2 RF01973 FASTA STK 1 1 1 - 1 1 1 - - 1 - - 1 - 1 1
HAR1A RF00635 FASTA STK - - 1 - 1 1 1 1 - 1 - 1 1 1 1 1
HOTAIRM1_1 RF01975 FASTA STK 1 1 1 1 1 1 1 - - 1 - 1 - - - -
HOTAIRM1_2 RF01976 FASTA STK 1 1 1 1 1 1 1 1 - 1 1 1 1 1 1 1
HOTAIRM1_3 RF01977 FASTA STK 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
HOTAIRM1_4 RF01978 FASTA STK 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
HOTAIRM1_5 RF01979 FASTA STK 1 1 1 1 1 1 1 1 1 1 1 1 1 2 1 1
HOTAIR_1 RF01904 FASTA STK 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
HOTAIR_2 RF01905 FASTA STK 1 1 1 1 1 1 1 1 - 1 1 1 1 1 1 1
HOTAIR_3 RF01906 FASTA STK 1 1 1 1 1 1 1 1 1 1 1 - - - 1 1
HOTTIP_1 RF02040 FASTA STK - 1 1 1 1 - - - - 1 - 1 1 1 1 -
HOTTIP_2 RF02041 FASTA STK 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
HOTTIP_3 RF02042 FASTA STK 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
HOTTIP_4 RF02043 FASTA STK 1 1 1 1 1 1 1 1 - 1 1 1 1 1 1 1
HOXA11-AS1_1 RF02137 FASTA STK 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 -
HOXA11-AS1_2 RF02138 FASTA STK 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
HOXA11-AS1_3 RF02139 FASTA STK 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
HOXA11-AS1_4 RF02140 FASTA STK 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
HOXA11-AS1_5 RF02141 FASTA STK 1 1 1 1 1 1 1 1 - 1 - 1 1 1 1 1
HOXA11-AS1_6 RF02142 FASTA STK 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
HOXB13-AS1_1 RF02132 FASTA STK 1 1 1 1 1 1 1 1 1 1 1 - 1 1 1 -
HOXB13-AS1_2 RF02133 FASTA STK 1 1 1 1 1 1 1 1 1 - 1 - - - - 1
HULC RF02101 FASTA STK 1 1 1 1 1 1 1 1 - 1 1 1 1 1 1 1
HYMAI RF02143 FASTA STK 1 1 1 1 1 1 1 1 1 1 - 1 1 1 1 -
Hammerhead_HH10 RF02277 FASTA STK 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
Hammerhead_HH9 RF02275 FASTA STK 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
Histone3 RF00032 FASTA STK 153 157 166 129 177 149 164 154 123 137 129 147 146 132 126 150
IRES_Bag1 RF00222 FASTA STK 1 1 1 1 1 1 1 1 - 1 - 1 - - 1 1
IRES_HIF1 RF00449 FASTA STK 1 - 1 - 1 1 1 1 - 1 - 1 1 - - -
IRES_IGF2 RF00483 FASTA STK 1 1 1 1 1 1 1 1 - 1 1 - - - 1 1
IRES_L-myc RF00261 FASTA STK 1 1 1 - 1 1 1 - - 1 - 1 - - 1 -
IRES_TrkB RF00547 FASTA STK - 1 1 - 1 1 1 1 - - - 1 1 1 1 1
IRES_VEGF_A RF00461 FASTA STK 1 1 1 - 1 1 1 - - 1 - 1 - - 1 -
IRES_mnt RF00457 FASTA STK 1 1 1 1 1 1 1 1 - 1 - 1 - 1 1 1
IRE_I RF00037 FASTA STK 31 30 19 23 18 42 27 25 20 83 52 335 345 295 298 108
IRE_II RF02253 FASTA STK 13 12 16 11 12 9 9 9 16 8 9 8 8 10 12 8
JPX_1 RF02124 FASTA STK - - - - - 1 1 1 1 2 1 1 1 1 1 1
JPX_2 RF02125 FASTA STK - - - - - 1 1 - - 1 - 1 1 1 1 1
KCNQ1OT1_1 RF01946 FASTA STK 1 1 1 - 1 1 1 1 - 1 - - 1 1 1 1
KCNQ1OT1_2 RF01947 FASTA STK 1 1 1 - 1 1 1 1 - 1 - 1 - 1 1 1
KCNQ1OT1_3 RF01948 FASTA STK 1 1 1 - 1 1 1 1 - 1 - 1 1 1 1 1
KCNQ1OT1_5 RF01950 FASTA STK 1 1 1 1 1 1 1 1 1 1 - - 1 1 - 1
KRAS_3UTR RF02584 FASTA STK 1 1 1 1 1 1 1 1 1 1 1 - - - - 1
K_chan_RES RF00485 FASTA STK 17 18 17 17 17 18 17 17 13 17 16 15 17 18 18 17
LINC00901 RF01884 FASTA STK 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
MALAT1 RF01871 FASTA STK 1 1 1 1 1 1 1 1 1 1 - 1 1 1 1 1
MAT2A_A RF02260 FASTA STK 1 1 1 1 1 1 1 1 1 1 2 1 1 1 1 1
MAT2A_B RF02261 FASTA STK 1 1 1 1 1 2 1 1 1 1 2 1 1 1 1 2
MAT2A_C RF02262 FASTA STK 2 2 2 2 2 2 1 1 1 1 2 1 1 1 1 2
MAT2A_D RF02263 FASTA STK 2 3 2 4 4 4 2 3 2 1 3 1 1 1 1 3
MAT2A_E RF02264 FASTA STK 1 2 1 2 1 5 3 3 1 1 2 1 1 1 1 2
MAT2A_F RF02265 FASTA STK 2 2 1 1 1 5 2 3 1 1 2 1 1 1 1 2
MEG3_2 RF01872 FASTA STK 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
MEG8_1 RF02145 FASTA STK 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
MEG8_2 RF02146 FASTA STK 1 1 1 - 1 1 1 1 - - 1 1 1 1 1 1
MEG8_3 RF02147 FASTA STK 1 1 1 - 1 - - - - - - - - - - 1
MESTIT1_1 RF02148 FASTA STK 2 1 1 1 1 1 1 1 1 1 1 - - - - -
MESTIT1_2 RF02149 FASTA STK 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
MESTIT1_3 RF02150 FASTA STK 1 1 1 1 1 1 1 1 - 1 1 1 1 1 1 1
MIAT_exon1 RF01874 FASTA STK 1 1 1 1 1 1 1 1 - 1 1 1 1 1 1 1
MIAT_exon5_1 RF01875 FASTA STK 1 1 1 1 1 1 1 1 1 3 1 1 1 1 1 1
MIAT_exon5_2 RF01876 FASTA STK 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
MIAT_exon5_3 RF01877 FASTA STK 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
MIMT1_1 RF02151 FASTA STK 1 1 1 1 1 1 1 1 1 - - - - 1 1 -
Metazoa_SRP RF00017 FASTA STK 37 34 39 39 33 22 11 13 40 34 18 20 17 21 14 9
Mico1 RF01928 FASTA STK 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
NBR2 RF02153 FASTA STK 2 2 1 2 2 2 2 1 1 1 1 1 1 1 1 1
NCRUPAR_1 RF02154 FASTA STK 1 1 - 1 - 1 1 1 - 1 1 1 1 1 1 1
NCRUPAR_2 RF02155 FASTA STK 1 1 - 1 1 - 1 - 1 - - - - - 1 -
NEAT1_1 RF01955 FASTA STK 2 2 2 2 2 1 1 2 2 2 1 - 1 - 3 2
NEAT1_2 RF01956 FASTA STK 2 2 2 2 2 1 1 1 2 2 1 1 2 2 4 2
NEAT1_3 RF01957 FASTA STK 2 2 2 2 2 1 1 2 2 3 1 3 3 3 5 2
NPPA-AS1_1 RF02156 FASTA STK 1 1 1 1 1 1 1 1 1 - - 2 1 1 1 1
NPPA-AS1_3 RF02158 FASTA STK 1 1 1 1 1 1 1 1 1 1 1 2 1 1 - -
NRF2_IRES RF02531 FASTA STK 1 1 1 - 1 1 1 - - 1 1 - - - 1 -
NRON RF00636 FASTA STK 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
ODC_IRES RF02535 FASTA STK 2 2 2 2 2 5 3 3 2 5 5 8 9 6 6 2
PART1_1 RF02159 FASTA STK 1 1 2 1 1 1 1 1 1 1 1 1 1 1 1 1
PART1_2 RF02160 FASTA STK 1 1 2 1 1 1 1 1 1 1 1 1 1 1 1 1
PCA3_2 RF01894 FASTA STK 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
PCGEM1 RF01981 FASTA STK 1 1 1 1 1 1 1 1 1 1 1 1 2 1 1 1
PISRT1 RF01873 FASTA STK 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
PVT1_1 RF02164 FASTA STK 1 1 1 - 1 1 1 - - 1 - 1 - - 1 -
PVT1_2 RF02165 FASTA STK 2 1 1 1 1 1 1 1 - 1 1 1 1 1 1 1
PVT1_3 RF02166 FASTA STK 2 2 2 2 2 1 2 2 1 2 2 2 2 2 2 1
PVT1_4 RF02167 FASTA STK 1 1 - - - 1 1 1 - 1 - 1 - - 1 1
PVT1_5 RF02168 FASTA STK 1 1 1 1 1 1 1 1 1 1 1 1 1 1 - 1
PVT1_6 RF02169 FASTA STK 1 1 1 1 1 - - - - - - - - - - -
PVT1_7 RF02170 FASTA STK 1 1 1 1 1 1 1 1 - 1 - - - - - -
Phe_leader RF01859 FASTA STK - - - - - - - - - - - - - 1 - 1
PhotoRC-II RF01717 FASTA STK - - 2 - - - - - - - 1 - - - - 1
Pinc RF01983 FASTA STK 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
Prion_pknot RF00523 FASTA STK 10 8 4 8 7 9 5 3 3 13 9 17 9 12 17 5
Protozoa_SRP RF01856 FASTA STK - - - - - 1 6 - - 1 2 - - - - -
RF_site4 RF01090 FASTA STK 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
RF_site5 RF01093 FASTA STK 2 2 1 2 2 2 2 2 2 2 1 1 2 1 2 2
RMST_1 RF01962 FASTA STK 1 1 1 1 1 1 1 1 1 1 1 1 2 1 1 1
RMST_10 RF01971 FASTA STK 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
RMST_2 RF01963 FASTA STK 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 -
RMST_3 RF01964 FASTA STK 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
RMST_4 RF01965 FASTA STK 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 -
RMST_5 RF01966 FASTA STK 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
RMST_6 RF01967 FASTA STK 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
RMST_7 RF01968 FASTA STK 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
RMST_8 RF01969 FASTA STK 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
RMST_9 RF01970 FASTA STK 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
RNase_MRP RF00030 FASTA STK 1 1 1 1 1 2 1 1 1 1 1 1 1 1 1 1
SECIS_1 RF00031 FASTA STK 14 12 9 10 10 9 7 12 9 10 9 14 12 9 9 9
SMAD5-AS1_1 RF02173 FASTA STK 1 1 1 1 1 - 1 1 1 1 1 1 1 1 1 -
SMAD5-AS1_2 RF02174 FASTA STK 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
SMAD5-AS1_3 RF02175 FASTA STK 1 1 1 1 1 1 1 1 - 1 1 1 1 1 1 1
SMAD5-AS1_4 RF02176 FASTA STK 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
SMCR2_1 RF02177 FASTA STK - - - - - 1 1 - - - - - 1 - - -
SMCR2_2 RF02178 FASTA STK - - - - - 1 1 - - 1 1 - 1 - 1 1
SOX2OT_exon1 RF01951 FASTA STK 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
SOX2OT_exon2 RF01952 FASTA STK 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
SOX2OT_exon3 RF01953 FASTA STK 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
SOX2OT_exon4 RF01954 FASTA STK 1 1 1 1 1 1 1 1 1 1 - 2 2 2 1 1
SPRY4-IT1_1 RF02038 FASTA STK 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
SPRY4-IT1_2 RF02039 FASTA STK 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
ST7-AS1_1 RF02179 FASTA STK 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
ST7-AS1_2 RF02180 FASTA STK 1 1 1 1 1 1 1 1 1 1 1 - - - 1 1
ST7-OT3_1 RF02183 FASTA STK 1 1 1 1 1 - 1 1 - 1 1 2 2 2 1 3
ST7-OT3_3 RF02185 FASTA STK 1 1 1 1 1 1 1 1 - 1 1 1 1 1 1 1
ST7-OT4_1 RF02187 FASTA STK 1 1 1 1 1 1 1 1 1 1 1 - - - - 1
ST7-OT4_2 RF02188 FASTA STK 1 1 1 1 1 1 1 1 1 1 1 1 1 1 - 1
ST7-OT4_3 RF02189 FASTA STK 1 1 1 1 1 1 1 1 1 1 1 1 1 - - 1
ST7-OT4_4 RF02190 FASTA STK 1 1 1 1 1 1 1 1 - 1 1 1 1 2 1 1
Six3os1_1 RF02246 FASTA STK 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
Six3os1_2 RF02247 FASTA STK 1 1 1 1 1 1 1 1 - 1 1 1 1 1 1 -
Six3os1_3 RF02248 FASTA STK 1 1 1 - 1 1 1 1 - 1 - 1 1 1 1 -
Six3os1_4 RF02249 FASTA STK 1 1 1 - 1 1 1 - - 1 - 1 1 1 1 -
Six3os1_5 RF02250 FASTA STK 1 1 1 1 1 1 1 1 - 1 1 1 1 1 1 1
TB8Cs3H1 RF01550 FASTA STK - - - 1 - - - - - - - - - - - -
TB9Cs1H3 RF01553 FASTA STK - - - - - - - - - - 1 - 1 1 - 2
TB9Cs2H1 RF01554 FASTA STK - 1 - - - - - - - - - - - - - -
TCL6_1 RF02191 FASTA STK 2 1 1 1 - 1 1 1 - - - - - - - -
TCL6_2 RF02192 FASTA STK 1 1 2 1 1 1 1 1 - 1 1 - - - - -
TP53TG1_1 RF02195 FASTA STK 1 1 1 - 1 1 1 1 1 1 - - - - - -
TP53TG1_2 RF02196 FASTA STK 1 1 1 - 1 1 1 1 - 1 - - - - 1 -
TPP RF00059 FASTA STK - - - - - - - - - - 2 - - - - -
TTC28-AS1_1 RF02198 FASTA STK 1 1 1 - 1 1 1 1 - 1 - 1 - - 1 1
TTC28-AS1_2 RF02199 FASTA STK 1 1 1 1 - 1 1 1 - - - - - - - -
TTC28-AS1_3 RF02200 FASTA STK 1 1 1 1 - 1 1 1 - - 1 1 1 1 1 -
TTC28-AS1_4 RF02201 FASTA STK 1 1 1 1 1 1 1 1 1 1 - - - - - 1
TUG1_1 RF01882 FASTA STK 1 1 1 1 1 1 1 1 1 1 1 - - - 1 1
TUG1_2 RF01883 FASTA STK 1 1 1 1 1 1 1 1 1 - - - - - - -
TUG1_3 RF01891 FASTA STK 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
TUG1_4 RF01892 FASTA STK 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
TUSC7 RF01879 FASTA STK 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
Telomerase-vert RF00024 FASTA STK 2 2 2 2 1 2 1 2 - 2 - 1 - - 1 1
Twister-P5 RF02684 FASTA STK - - - - - 1 - - - - - - - - - -
U11 RF00548 FASTA STK 4 4 4 3 4 6 3 2 4 10 11 23 24 21 15 17
U12 RF00007 FASTA STK 2 2 2 2 2 2 1 2 2 3 3 2 4 4 4 4
U1A_PIE RF00460 FASTA STK 1 2 2 2 2 1 1 1 1 3 2 3 3 2 4 3
U4 RF00015 FASTA STK 4 5 4 3 5 15 15 15 26 14 11 12 19 11 10 5
U4atac RF00618 FASTA STK 1 1 1 1 1 2 2 3 1 4 6 3 4 3 6 3
U5 RF00020 FASTA STK 8 7 8 6 6 8 9 8 11 14 12 11 12 10 10 10
U6 RF00026 FASTA STK 449 383 380 354 342 621 483 442 564 698 625 933 951 875 774 501
U6atac RF00619 FASTA STK 14 11 10 13 15 23 18 19 25 18 16 12 18 14 10 8
U7 RF00066 FASTA STK 5 4 4 6 6 13 9 6 6 8 8 22 22 23 26 8
U8 RF00096 FASTA STK 3 4 4 3 3 12 4 4 4 2 2 4 4 2 3 1
VIS1 RF01992 FASTA STK 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
Vault RF00006 FASTA STK 2 2 2 3 3 2 2 2 3 4 7 5 7 6 6 9
Vax2os1_3 RF02272 FASTA STK 1 1 1 1 1 1 1 1 - 1 1 - 1 1 1 1
Vimentin3 RF00109 FASTA STK 6 7 3 6 3 4 3 4 3 3 6 1 2 1 2 4
WT1-AS_1 RF02203 FASTA STK 1 1 1 1 1 1 1 1 1 1 1 1 2 1 1 -
WT1-AS_2 RF02204 FASTA STK 1 1 1 1 1 1 1 1 - 1 1 1 2 1 1 1
WT1-AS_3 RF02205 FASTA STK 1 1 1 1 1 1 1 1 1 1 1 1 2 1 - -
WT1-AS_6 RF02208 FASTA STK 1 1 1 1 1 1 1 1 - 1 1 1 1 1 1 1
WT1-AS_7 RF02209 FASTA STK 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
WT1-AS_8 RF02210 FASTA STK 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
XIST_A_REPEAT RF02162 FASTA STK 6 6 4 6 5 8 6 5 1 6 7 6 12 6 5 7
XIST_intron RF02266 FASTA STK 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
Xist_exon1 RF01880 FASTA STK 1 1 1 1 1 2 1 1 - 1 2 1 1 - 1 -
Xist_exon4 RF01881 FASTA STK 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
Y_RNA RF00019 FASTA STK 8 9 7 8 9 8 10 8 30 12 7 9 9 12 15 9
ZEB2_AS1_1 RF01984 FASTA STK 1 1 1 1 1 1 1 1 1 1 1 1 1 1 - 1
ZEB2_AS1_2 RF01985 FASTA STK 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
ZEB2_AS1_3 RF01986 FASTA STK 1 1 1 - 1 1 - 1 - 1 1 - 1 - 1 -
ZEB2_AS1_4 RF01987 FASTA STK 1 1 1 1 1 - 1 1 1 1 1 1 1 1 1 1
ZFAT-AS1_2 RF02212 FASTA STK 1 1 1 1 1 1 1 1 1 1 1 - - - - 1
ZNFX1-AS1_1 RF02215 FASTA STK 1 1 1 1 1 1 1 1 - 1 - 1 2 1 1 1
ZNFX1-AS1_2 RF02216 FASTA STK 1 1 1 1 - - 1 1 - 1 - 3 3 3 3 1
ZNRD1-AS1_2 RF02219 FASTA STK 2 2 2 3 2 3 4 3 2 - 1 1 2 1 1 2
mascRNA-menRNA RF01684 FASTA STK 2 2 2 2 2 2 2 2 3 2 2 2 2 2 2 2
p27_CRE RF00454 FASTA STK 1 1 1 1 1 1 1 - - - - 1 - 1 1 -
pRNA RF01518 FASTA STK - 1 15 1 13 - - - - - 1 - 1 1 1 -
sn2524 RF01212 FASTA STK 2 2 - 1 - - - - 1 - 1 - 1 - 1 1
snR41 RF01218 FASTA STK 1 2 2 1 2 - 2 1 1 - - 1 1 - 1 3
snR47 RF01203 FASTA STK - - - - - - - - - 1 - 1 - 1 2 -
snR51 RF01214 FASTA STK - - 1 - - - - - - - - - - - - -
snR56 RF01188 FASTA STK 3 3 - - - - - - - - 2 - - - - -
snR75 RF01185 FASTA STK - - - - - - - - 1 - - - - - - -
snR76 RF01209 FASTA STK 1 1 1 3 1 2 1 1 4 1 1 - 1 2 1 3
snR77 RF01181 FASTA STK 1 - - - 1 1 1 1 - 1 1 - - - 2 1
snR78 RF01176 FASTA STK 1 1 1 1 2 - 1 - - - 1 - 1 - 1 1
tmRNA RF00023 FASTA STK - - - - - - - - - - 1 - - - - -
uc_338 RF02271 FASTA STK 3 3 3 3 2 3 4 3 2 2 2 3 3 3 3 3
whalefall-1 RF01762 FASTA STK - - - - - - - - - - - - - - 1 -



Table S9: lncRNAs

back to top

Long ncRNAs were annotated using a high confidence data set comprising 107,039 human transcript annotations of potential lncRNAs from the LNCipedia (v5.2) data base as input for a BLASTn search.

Attention, the table is huge (49MB) and might load longer!

Open lncRNA HTML

Download CSV (14MB)

Download XLSX (5.8MB)

All blast and annotation (GTF) files can be as well found in the Open Science Framework




Figure S1: lncRNA assembly quality vs. annotation

back to top



Amount of annotated lncRNAs and lncRNA hot spots in relation to assembly quality

The amount of long non-coding RNAs (lncRNAs; left) and lncRNA hot spots (right) annotated in bat genome assemblies ordered by assembly quality (N50). The most left assembly (M. lyra; MLY) has the lowest N50.




Table S10: mtDNA

back to top

Annotations of full mitochondrial genomes were done with MITOS

Download table data: CSV: Mitochondrial_annotation.csv - XLSX: Mitochondrial_annotation.xlsx
Mitochondrial annotation gene_biotype PVA PAL RAE EHE (rearranged) HAR RFE DRO PPA MLU MBR MDA
GTF GTF GTF GTF, unarranged GTF GTF GTF GTF GTF GTF GTF
mitogenome mitogenome mitogenome mitogenome, unarranged mitogenome mitogenome mitogenome mitogenome mitogenome mitogenome mitogenome
annotation plot annotation plot annotation plot annotation plot, unarranged annotation plot annotation plot annotation plot annotation plot annotation plot annotation plot annotation plot
ncRNA annotation plot ncRNA annotation plot ncRNA annotation plot ncRNA annotation plot, unarranged ncRNA annotation plot ncRNA annotation plot ncRNA annotation plot ncRNA annotation plot ncRNA annotation plot ncRNA annotation plot ncRNA annotation plot
RNA sequences RNA sequences RNA sequences RNA sequences, unarranged RNA sequences RNA sequences RNA sequences RNA sequences RNA sequences RNA sequences RNA sequences
protein coding annotation plot protein coding annotation plot protein coding annotation plot protein coding annotation plot, unarranged protein coding annotation plot protein coding annotation plot protein coding annotation plot protein coding annotation plot protein coding annotation plot protein coding annotation plot protein coding annotation plot
protein coding sequences protein coding sequences protein coding sequences protein coding sequences protein coding sequences protein coding sequences protein coding sequences protein coding sequences protein coding sequences protein coding sequences protein coding sequences
atp6 protein_coding 1 1 1 1 1 1 1 1 1 1 1
atp8 protein_coding 1 1 1 1 1 1 1 1 1 1 1
cob protein_coding 1 1 1 1 1 1 1 1 1 1 1
cox1 protein_coding 1 1 1 1 1 1 1 1 1 1 1
cox2 protein_coding 1 1 1 1 1 1 1 1 1 1 1
cox3 protein_coding 1 1 1 1 1 1 1 1 1 1 1
nad1 protein_coding 1 1 1 1 1 1 1 1 1 1 1
nad2 protein_coding 1 1 1 1 1 1 1 1 1 1 1
nad3 protein_coding 1 1 1 1 1 1 1 1 1 1 1
nad4 protein_coding 1 1 1 1 1 1 1 1 1 1 1
nad4l protein_coding 1 1 1 1 1 1 1 1 1 1 1
nad5 protein_coding 1 1 1 1 1 1 1 1 1 1 1
nad6 protein_coding 1 1 1 1 1 1 1 1 1 1 1
rrnL rRNA 1 1 1 1 1 1 1 1 1 1 1
rrnS rRNA 1 1 1 1 1 1 1 1 1 1 1
trnA(gca) tRNA 1 1 1 1 1 1 1 1 1 1 1
trnC(tgc) tRNA 1 1 1 1 1 1 1 1 1 1 1
trnD(gac) tRNA 1 1 1 1 1 1 1 1 1 1 1
trnE(gaa) tRNA 1 1 1 1 1 1 1 1 1 1 1
trnF(ttc) tRNA 1 1 1 1 1 1 1 1 1 1 1
trnG(gga) tRNA 1 1 1 1 1 1 1 1 1 1 1
trnH(cac) tRNA 1 1 1 1 1 1 1 1 1 1 1
trnI(atc) tRNA 1 1 1 1 1 1 1 1 1 1 1
trnK(aaa) tRNA 1 1 1 1 1 1 1 1 1 1 1
trnL1(cta) tRNA 1 1 1 1 1 1 1 1 1 1 1
trnL2(tta) tRNA 1 1 1 1 1 1 1 1 1 1 1
trnM(atg) tRNA 1 1 1 1 1 1 1 1 1 1 1
trnN(aac) tRNA 1 1 1 1 1 1 1 1 1 1 1
trnP(cca) tRNA 1 1 1 1 1 1 1 1 1 1 1
trnQ(caa) tRNA 1 1 1 1 1 1 1 1 1 1 1
trnR(cga) tRNA 1 1 1 1 1 1 1 1 1 1 1
trnS1(agc) tRNA 1 1 1 1 1 1 1 1 1 1 1
trnS2(tca) tRNA 1 1 1 1 1 1 1 1 1 1 1
trnT(aca) tRNA 1 1 1 1 1 1 1 1 1 1 1
trnV(gta) tRNA 1 1 1 1 1 1 1 1 1 1 1
trnW(tga) tRNA 1 1 1 1 1 1 1 1 1 1 1
trnY(tac) tRNA 1 1 1 1 1 1 1 1 1 1 1



Files S1: Final merged annotation GTFs (full NCBI + new ncRNAs)

back to top

For each bat species we merged the known NCBI annotations (protein- and non-coding) with our new ncRNA annotations in two steps to provide extended full annotations directly usable for further computational analyses.

First, for each bat species we merged our new ncRNA annoations using a custom script (merge_gtf_global_ids.py). After reading in all features and asserting correct file structure, overlaps were resolved in the following manner: (1) exons are considered overlapping if more than 50 % of the shorter one is covered by the larger one. (2) if only one of the overlapping set is of biotype protein-coding, remove all others. (3) for further ties, keep only the exon that is highest on a priority list based on annotation source. (4) for further ties, keep only the longest of the exons. For each exon to be removed the corresponding transcript is deleted, and gene records that lost all transcript are also deleted.

Second, we converted and filtered the NCBI annotations to a compatible format with a custom script (format_ncbi.py) and then combined the results with our merged novel ncRNA annotations using the same strategy to resolve overlaps as above, but imposing less strict format rules (merge_gtf_ncbi.py).

Download all final GTFs (130 MB)

All annotation (GTF) files were additionally uploaded to the Open Science Framework.