COL8A1 (collagen type VIII alpha 1 chain) - Rat Genome Database

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Gene: COL8A1 (collagen type VIII alpha 1 chain) Sus scrofa
Analyze
Symbol: COL8A1
Name: collagen type VIII alpha 1 chain
RGD ID: 14164418
Description: INVOLVED IN camera-type eye morphogenesis (ortholog); endothelial cell proliferation (ortholog); positive regulation of cell-substrate adhesion (ortholog); PARTICIPATES IN syndecan signaling pathway; ASSOCIATED WITH Congenital Abnormalities (ortholog); diastolic heart failure (ortholog); genetic disease (ortholog); FOUND IN collagen trimer (inferred); extracellular region (inferred)
Type: protein-coding
RefSeq Status: MODEL
Previously known as: collagen alpha-1(VIII) chain; collagen alpha-1(VIII) chain pseudogene; collagen VIII alpha 1; type VIII collagen alpha 1 chain
RGD Orthologs
Human
Mouse
Rat
Chinchilla
Bonobo
Dog
Squirrel
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Sscrofa11.1 - Pig Sscrofa11.1 Assembly
Position:
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl13159,216,144 - 159,374,576 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.113159,216,138 - 159,374,718 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.213169,086,122 - 169,094,141 (+)NCBISscrofa10.2Sscrofa10.2susScr3
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References
Additional References at PubMed
PMID:22301074  


Genomics

Comparative Map Data
COL8A1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl13159,216,144 - 159,374,576 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.113159,216,138 - 159,374,718 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.213169,086,122 - 169,094,141 (+)NCBISscrofa10.2Sscrofa10.2susScr3
COL8A1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38399,638,594 - 99,799,217 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl399,638,475 - 99,799,226 (+)EnsemblGRCh38hg38GRCh38
GRCh37399,357,438 - 99,518,061 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 363100,840,144 - 100,997,848 (+)NCBINCBI36Build 36hg18NCBI36
Build 343100,840,143 - 100,997,848NCBI
Celera397,746,575 - 97,904,287 (+)NCBICelera
Cytogenetic Map3q12.1NCBI
HuRef396,725,773 - 96,884,050 (+)NCBIHuRef
CHM1_1399,320,440 - 99,478,624 (+)NCBICHM1_1
T2T-CHM13v2.03102,343,632 - 102,504,274 (+)NCBIT2T-CHM13v2.0
Col8a1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391657,444,619 - 57,575,100 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1657,444,621 - 57,575,100 (-)EnsemblGRCm39 Ensembl
GRCm381657,624,256 - 57,754,737 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1657,624,258 - 57,754,737 (-)EnsemblGRCm38mm10GRCm38
MGSCv371657,624,369 - 57,754,850 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361657,548,056 - 57,553,783 (-)NCBIMGSCv36mm8
Celera1657,949,273 - 58,079,512 (-)NCBICelera
Cytogenetic Map16C1.1NCBI
cM Map1634.22NCBI
Col8a1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81156,245,998 - 56,378,586 (+)NCBIGRCr8
mRatBN7.21142,776,851 - 42,906,432 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1142,777,628 - 42,906,424 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1151,533,937 - 51,662,714 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01144,195,524 - 44,324,293 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01143,324,116 - 43,452,883 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01144,877,690 - 45,006,203 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1144,877,859 - 45,007,891 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01148,073,158 - 48,201,421 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41143,604,994 - 43,733,870 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11143,785,922 - 43,791,642 (+)NCBI
Celera1142,573,892 - 42,702,340 (+)NCBICelera
Cytogenetic Map11q12NCBI
Col8a1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554271,187,550 - 1,335,794 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554271,187,550 - 1,335,794 (+)NCBIChiLan1.0ChiLan1.0
COL8A1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2297,584,157 - 97,744,951 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1397,589,413 - 97,749,735 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0396,732,445 - 96,892,726 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.13103,416,557 - 103,573,617 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl3103,521,159 - 103,573,617 (+)Ensemblpanpan1.1panPan2
COL8A1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1336,285,742 - 6,428,172 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl336,285,415 - 6,425,414 (+)EnsemblCanFam3.1canFam3CanFam3.1
Col8a1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405602150,545,175 - 150,692,760 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049366303,443,068 - 3,590,516 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049366303,443,085 - 3,590,430 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
COL8A1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12281,094,127 - 81,242,801 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2281,091,493 - 81,242,763 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604185,334,932 - 85,484,882 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Col8a1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462478912,962,144 - 13,130,492 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in COL8A1
2982 total Variants

Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system hemolymphoid system musculoskeletal system nervous system renal system reproductive system respiratory system
High
Medium 2 1
Low 8 4 3 5 2 22 2 1 1
Below cutoff 1 1

Sequence


RefSeq Acc Id: ENSSSCT00000013101   ⟹   ENSSSCP00000012756
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.1 Ensembl13159,216,142 - 159,374,504 (-)Ensembl
RefSeq Acc Id: ENSSSCT00000046576   ⟹   ENSSSCP00000039945
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.1 Ensembl13159,216,145 - 159,374,576 (-)Ensembl
RefSeq Acc Id: ENSSSCT00000081405   ⟹   ENSSSCP00000070722
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.1 Ensembl13159,218,475 - 159,227,450 (-)Ensembl
RefSeq Acc Id: ENSSSCT00000086899   ⟹   ENSSSCP00000063419
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.1 Ensembl13159,216,144 - 159,374,504 (-)Ensembl
RefSeq Acc Id: XM_001926443   ⟹   XP_001926478
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.113159,216,138 - 159,374,718 (-)NCBI
Sequence:
RefSeq Acc Id: XM_005670255   ⟹   XP_005670312
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.113159,216,138 - 159,374,628 (-)NCBI
Sequence:
RefSeq Acc Id: XP_001926478   ⟸   XM_001926443
- Peptide Label: isoform X2
- UniProtKB: F1SKX7 (UniProtKB/TrEMBL),   A0A8D0PXW0 (UniProtKB/TrEMBL),   A0A287A7T8 (UniProtKB/TrEMBL),   A0A5G2R2Z9 (UniProtKB/TrEMBL),   A0A8D0VZ59 (UniProtKB/TrEMBL),   A0A8D1NCJ8 (UniProtKB/TrEMBL),   A0A8D1RI04 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_005670312   ⟸   XM_005670255
- Peptide Label: isoform X1
- UniProtKB: A0A8D0VWK5 (UniProtKB/TrEMBL),   A0A5G2R2Z9 (UniProtKB/TrEMBL),   A0A8D0VZ59 (UniProtKB/TrEMBL),   A0A8D1NCJ8 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSSSCP00000012756   ⟸   ENSSSCT00000013101
RefSeq Acc Id: ENSSSCP00000039945   ⟸   ENSSSCT00000046576
RefSeq Acc Id: ENSSSCP00000070722   ⟸   ENSSSCT00000081405
RefSeq Acc Id: ENSSSCP00000063419   ⟸   ENSSSCT00000086899
Protein Domains
C1q


Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSSSCG00000011973 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
  ENSSSCG00005024551 UniProtKB/TrEMBL
  ENSSSCG00015073472 UniProtKB/TrEMBL
  ENSSSCG00025016113 UniProtKB/TrEMBL
  ENSSSCG00030020229 UniProtKB/TrEMBL
  ENSSSCG00035070802 UniProtKB/TrEMBL
  ENSSSCG00040031566 UniProtKB/TrEMBL
  ENSSSCG00045003779 UniProtKB/TrEMBL
  ENSSSCG00050060562 UniProtKB/TrEMBL
  ENSSSCG00055021493 UniProtKB/TrEMBL
  ENSSSCG00060001175 UniProtKB/TrEMBL
  ENSSSCG00065000599 UniProtKB/TrEMBL
Ensembl Transcript ENSSSCT00000046576 ENTREZGENE
  ENSSSCT00000046576.3 UniProtKB/TrEMBL
  ENSSSCT00000081405.1 UniProtKB/TrEMBL
  ENSSSCT00000086899.1 UniProtKB/TrEMBL
  ENSSSCT00005038927.1 UniProtKB/TrEMBL
  ENSSSCT00005038976.1 UniProtKB/TrEMBL
  ENSSSCT00005038983.1 UniProtKB/TrEMBL
  ENSSSCT00005039012.1 UniProtKB/TrEMBL
  ENSSSCT00005039024.1 UniProtKB/TrEMBL
  ENSSSCT00015098820.1 UniProtKB/TrEMBL
  ENSSSCT00015098866.1 UniProtKB/TrEMBL
  ENSSSCT00015098914.1 UniProtKB/TrEMBL
  ENSSSCT00015098986.1 UniProtKB/TrEMBL
  ENSSSCT00025021611.1 UniProtKB/TrEMBL
  ENSSSCT00025021630.1 UniProtKB/TrEMBL
  ENSSSCT00025021677.1 UniProtKB/TrEMBL
  ENSSSCT00030027967.1 UniProtKB/TrEMBL
  ENSSSCT00030027977.1 UniProtKB/TrEMBL
  ENSSSCT00030027984.1 UniProtKB/TrEMBL
  ENSSSCT00030027999.1 UniProtKB/TrEMBL
  ENSSSCT00035095684.1 UniProtKB/TrEMBL
  ENSSSCT00035095695.1 UniProtKB/TrEMBL
  ENSSSCT00035095711.1 UniProtKB/TrEMBL
  ENSSSCT00040042425.1 UniProtKB/TrEMBL
  ENSSSCT00040042473.1 UniProtKB/TrEMBL
  ENSSSCT00040042533.1 UniProtKB/TrEMBL
  ENSSSCT00045006266.1 UniProtKB/TrEMBL
  ENSSSCT00045006268.1 UniProtKB/TrEMBL
  ENSSSCT00045006274.1 UniProtKB/TrEMBL
  ENSSSCT00045006283.1 UniProtKB/TrEMBL
  ENSSSCT00050082504.1 UniProtKB/TrEMBL
  ENSSSCT00050082506.1 UniProtKB/TrEMBL
  ENSSSCT00050082509.1 UniProtKB/TrEMBL
  ENSSSCT00050082514.1 UniProtKB/TrEMBL
  ENSSSCT00055042210.1 UniProtKB/TrEMBL
  ENSSSCT00055042266.1 UniProtKB/TrEMBL
  ENSSSCT00055042331.1 UniProtKB/TrEMBL
  ENSSSCT00060001430.1 UniProtKB/TrEMBL
  ENSSSCT00060001431.1 UniProtKB/TrEMBL
  ENSSSCT00060001432.1 UniProtKB/TrEMBL
  ENSSSCT00065000682.1 UniProtKB/TrEMBL
  ENSSSCT00065000687.1 UniProtKB/TrEMBL
  ENSSSCT00065000693.1 UniProtKB/TrEMBL
Gene3D-CATH 2.60.120.40 UniProtKB/TrEMBL
InterPro C1q_dom UniProtKB/TrEMBL
  Collagen UniProtKB/TrEMBL
  Tumour_necrosis_fac-like_dom UniProtKB/TrEMBL
KEGG Report ssc:397430 UniProtKB/TrEMBL
NCBI Gene COL8A1 ENTREZGENE
PANTHER COLLAGEN ALPHA UniProtKB/TrEMBL
  COLLAGEN ALPHA-1(IV) CHAIN UniProtKB/TrEMBL
  COLLAGEN ALPHA-1(X) CHAIN UniProtKB/TrEMBL
  EMILIN ELASTIN MICROFIBRIL INTERFACE-LOCATED PROTEIN ELASTIN MICROFIBRIL INTERFACER UniProtKB/TrEMBL
Pfam C1q UniProtKB/TrEMBL
  Collagen UniProtKB/TrEMBL
PRINTS COMPLEMNTC1Q UniProtKB/TrEMBL
PROSITE C1Q UniProtKB/TrEMBL
SMART C1Q UniProtKB/TrEMBL
Superfamily-SCOP SSF49842 UniProtKB/TrEMBL
UniProt A0A287A7T8 ENTREZGENE
  A0A5G2R2Z9 ENTREZGENE
  A0A8D0PXW0 ENTREZGENE, UniProtKB/TrEMBL
  A0A8D0VWK5 ENTREZGENE, UniProtKB/TrEMBL
  A0A8D0VZ59 ENTREZGENE, UniProtKB/TrEMBL
  A0A8D1E677_PIG UniProtKB/TrEMBL
  A0A8D1GJ20_PIG UniProtKB/TrEMBL
  A0A8D1NCJ8 ENTREZGENE, UniProtKB/TrEMBL
  A0A8D1RI04 ENTREZGENE, UniProtKB/TrEMBL
  F1SKX7 ENTREZGENE
UniProt Secondary A0A287A7T8 UniProtKB/TrEMBL
  A0A5G2QGJ6 UniProtKB/TrEMBL
  A0A5G2R2Z9 UniProtKB/TrEMBL
  F1SKX7 UniProtKB/TrEMBL
VGNC ID VGNC:86880 ENTREZGENE