NPC1

NameSynonymsFull NameRefSeq IDDescription (.pdf)IGV-img (humangenome)Sashimi-img (humangenome)UCSC-img (humangenome)IGV-img (batgenome)
NPC1 Niemann-Pick disease, type C1 NM_000271 pdf

Download all snapshots for IGV, UCSC and Sashimi (zip archive)

Description

This gene encodes a large protein that resides in the limiting membrane of endosomes and lysosomes and mediates intracellular cholesterol trafficking via binding of cholesterol to its N-terminal domain. It is predicted to have a cytoplasmic C-terminus, 13 transmembrane domains, and 3 large loops in the lumen of the endosome - the last loop being at the N-terminus. This protein transports low-density lipoproteins to late endosomal/lysosomal compartments where they are hydrolized and released as free cholesterol. Defects in this gene cause Niemann-Pick type C disease, a rare autosomal recessive neurodegenerative disorder characterized by over accumulation of cholesterol and glycosphingolipids in late endosomal/lysosomal compartments.

The NPC1 appears to be essential for Ebola and Marburg virus infection \citesearchit. The NPC1 is moderately expressed in human cells samples and not detectable in bat cells samples. In human cells samples the expression is upregulated over time. Interestingly, on the opposite strand the open reading frame 8 on chromosome 18 (C18orf8) seems to be co-regulated. Additionally the C18orf8 shows unique alternative splicing events during Ebola and Marburg virus infection.

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Maximum read counts and DESeq normalized read counts for human and bat cell lines

Source Species Mapping on Mock3h Mock7h Mock23h EBOV3h EBOV7h EBOV23h MARV3h MARV7h MARV23h
Read_Max
humanH. sapiensGenome179 277 336 191 343 505 233 345 279
Read_Max
batR. aegyptiacusTranscriptome 6 4 2 5 1 2 3 4 6
Read_Max
bat_genomeR. aegyptiacusGenome 101 72 53 83 61 38 61 136 74
DESeq
humanH. sapiensGenome 3193.52 4164.12 4494.52 3012.4 3816.99 7260.94 3057.18 4089.68 4739.66
DESeq
batR. aegyptiacusTranscriptome 14.44 22.78 9.55 11.99 10.86 9.98 15.46 19.18 7.12
DESeq
bat_genomeR. aegyptiacusGenome 1545.18 1197.44 1057.76 1550.35 1202.08 1173.56 1445.02 1374.18 872.46

Human Condition Comparisons

human Mock EBOV MARV FCMock_EBOV FCMock_MARV FCEBOV_MARV
3h 3193.52 3012.4 3057.18 -0.08 -0.06 0.02
7h 4164.12 3816.99 4089.68 -0.13 -0.03 0.1
23h 4494.52 7260.94 4739.66 0.69 0.08 -0.62

Human Time Point Comparisons

human 3h 7h 23h FC3h_7h FC3h_23h FC7h_23h
Mock 3193.52 4164.12 4494.52 0.38 0.49 0.11
Ebov 3012.4 3816.99 7260.94 0.34 1.27 0.93
Marv 3057.18 4089.68 4739.66 0.42 0.63 0.21

Bat Condition Comparisons

bat Mock EBOV MARV FCMock_EBOV FCMock_MARV FCEBOV_MARV
3h 14.44 11.99 15.46 -0.27 0.1 0.37
7h 22.78 10.86 19.18 -1.07 -0.25 0.82
23h 9.55 9.98 7.12 0.06 -0.42 -0.49

Bat Time Point Comparisons

bat 3h 7h 23h FC3h_7h FC3h_23h FC7h_23h
Mock 14.44 22.78 9.55 0.66 -0.6 -1.25
Ebov 11.99 10.86 9.98 -0.14 -0.26 -0.12
Marv 15.46 19.18 7.12 0.31 -1.12 -1.43