COL7A1 (collagen type VII alpha 1 chain) - Rat Genome Database

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Gene: COL7A1 (collagen type VII alpha 1 chain) Chlorocebus sabaeus
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Symbol: COL7A1
Name: collagen type VII alpha 1 chain
RGD ID: 18623364
Description: ENCODES a protein that exhibits identical protein binding (ortholog); INVOLVED IN endodermal cell differentiation (ortholog); PARTICIPATES IN syndecan signaling pathway; ASSOCIATED WITH Aicardi-Goutieres Syndrome 1 (ortholog); amelogenesis imperfecta (ortholog); autosomal dominant dystrophic epidermolysis bullosa (ortholog); FOUND IN basement membrane (ortholog)
Type: protein-coding
RefSeq Status: MODEL
Previously known as: collagen alpha-1(VII) chain
RGD Orthologs
Human
Mouse
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: ChlSab1.1 - Green Monkey 1.1 Assembly
Position:
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1229,964,652 - 9,996,785 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl229,964,651 - 9,996,626 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_023666041157,089,010 - 157,121,213 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Pathway Annotations     Click to see Annotation Detail View
References
Additional References at PubMed
PMID:22301074   PMID:30032202  


Genomics

Comparative Map Data
COL7A1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1229,964,652 - 9,996,785 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl229,964,651 - 9,996,626 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_023666041157,089,010 - 157,121,213 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
COL7A1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38348,564,073 - 48,595,329 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl348,564,073 - 48,595,329 (-)EnsemblGRCh38hg38GRCh38
GRCh37348,601,506 - 48,632,762 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36348,576,510 - 48,607,597 (-)NCBINCBI36Build 36hg18NCBI36
Build 34348,576,509 - 48,607,689NCBI
Celera348,557,241 - 48,588,335 (-)NCBICelera
Cytogenetic Map3p21.31NCBI
HuRef348,659,828 - 48,690,843 (-)NCBIHuRef
CHM1_1348,553,813 - 48,584,903 (-)NCBICHM1_1
T2T-CHM13v2.0348,593,030 - 48,624,289 (-)NCBIT2T-CHM13v2.0
Col7a1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm399108,782,654 - 108,813,943 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl9108,782,654 - 108,813,943 (+)EnsemblGRCm39 Ensembl
GRCm389108,953,586 - 108,984,875 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl9108,953,586 - 108,984,875 (+)EnsemblGRCm38mm10GRCm38
MGSCv379108,855,790 - 108,886,920 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv369108,810,682 - 108,841,812 (+)NCBIMGSCv36mm8
Celera9108,511,705 - 108,542,813 (+)NCBICelera
Cytogenetic Map9F2NCBI
cM Map959.63NCBI
Col7a1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr88118,483,364 - 118,515,736 (+)NCBIGRCr8
mRatBN7.28109,604,877 - 109,637,249 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl8109,604,861 - 109,637,252 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx8115,222,418 - 115,254,812 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.08113,421,605 - 113,453,999 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.08111,264,400 - 111,296,794 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.08117,694,441 - 117,726,844 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl8117,694,605 - 117,726,844 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.08117,046,218 - 117,078,589 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.48113,971,207 - 114,003,445 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.18113,990,661 - 114,022,897 (+)NCBI
Celera8108,898,754 - 108,930,986 (+)NCBICelera
Cytogenetic Map8q32NCBI
Col7a1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_004955532650,913 - 681,186 (-)NCBIChiLan1.0ChiLan1.0
COL7A1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2248,538,744 - 48,570,837 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1348,543,509 - 48,574,722 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0348,485,922 - 48,518,036 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1349,567,831 - 49,599,027 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl349,568,163 - 49,598,919 (-)Ensemblpanpan1.1panPan2
COL7A1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12040,519,121 - 40,550,305 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2040,519,378 - 40,552,935 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2040,436,737 - 40,467,232 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02041,004,719 - 41,035,678 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2041,004,749 - 41,038,309 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12040,242,306 - 40,272,806 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02040,647,074 - 40,677,568 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02040,928,007 - 40,958,502 (+)NCBIUU_Cfam_GSD_1.0
Col7a1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440560263,588,441 - 63,621,451 (-)NCBIHiC_Itri_2
SpeTri2.0NW_004936529348,938 - 381,701 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
COL7A1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.11331,262,750 - 31,295,112 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21334,507,211 - 34,539,557 (-)NCBISscrofa10.2Sscrofa10.2susScr3
Col7a1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247302,569,510 - 2,599,959 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2


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

endocrine system hemolymphoid system nervous system
High
Medium
Low 36 16 56
Below cutoff 2 4

Sequence


RefSeq Acc Id: ENSCSAT00000013637   ⟹   ENSCSAP00000011629
Type: CODING
Position:
Green Monkey AssemblyChrPosition (strand)Source
ChlSab1.1 Ensembl229,964,651 - 9,996,626 (-)Ensembl
RefSeq Acc Id: XM_007984132   ⟹   XP_007982323
Type: CODING
Position:
Green Monkey AssemblyChrPosition (strand)Source
ChlSab1.1229,964,652 - 9,996,780 (-)NCBI
Vero_WHO_p1.0NW_023666041157,089,011 - 157,121,213 (+)NCBI
Sequence:
RefSeq Acc Id: XM_038003980   ⟹   XP_037859908
Type: CODING
Position:
Green Monkey AssemblyChrPosition (strand)Source
Vero_WHO_p1.0NW_023666041157,089,011 - 157,121,213 (+)NCBI
RefSeq Acc Id: XM_038003981   ⟹   XP_037859909
Type: CODING
Position:
Green Monkey AssemblyChrPosition (strand)Source
Vero_WHO_p1.0NW_023666041157,089,010 - 157,121,213 (+)NCBI
RefSeq Acc Id: XM_038003982   ⟹   XP_037859910
Type: CODING
Position:
Green Monkey AssemblyChrPosition (strand)Source
Vero_WHO_p1.0NW_023666041157,089,010 - 157,114,993 (+)NCBI
RefSeq Acc Id: XR_005242109
Type: NON-CODING
Position:
Green Monkey AssemblyChrPosition (strand)Source
Vero_WHO_p1.0NW_023666041157,089,010 - 157,114,181 (+)NCBI
Protein Sequences
Protein RefSeqs XP_007982323 (Get FASTA)   NCBI Sequence Viewer  
  XP_037859908 (Get FASTA)   NCBI Sequence Viewer  
  XP_037859909 (Get FASTA)   NCBI Sequence Viewer  
  XP_037859910 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSCSAP00000011629.1
RefSeq Acc Id: XP_007982323   ⟸   XM_007984132
- Peptide Label: isoform X2
- UniProtKB: A0A0D9RSP0 (UniProtKB/TrEMBL)
RefSeq Acc Id: ENSCSAP00000011629   ⟸   ENSCSAT00000013637
RefSeq Acc Id: XP_037859909   ⟸   XM_038003981
- Peptide Label: isoform X3
- UniProtKB: A0A0D9RSP0 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_037859910   ⟸   XM_038003982
- Peptide Label: isoform X4
RefSeq Acc Id: XP_037859908   ⟸   XM_038003980
- Peptide Label: isoform X1
- UniProtKB: A0A0D9RSP0 (UniProtKB/TrEMBL)


Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSCSAG00000015684 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSCSAT00000013637.1 UniProtKB/TrEMBL
Gene3D-CATH 2.60.40.10 UniProtKB/TrEMBL
  3.40.50.410 UniProtKB/TrEMBL
  4.10.410.10 UniProtKB/TrEMBL
  6-Phosphogluconate Dehydrogenase, domain 3 UniProtKB/TrEMBL
InterPro Collagen UniProtKB/TrEMBL
  FN3_dom UniProtKB/TrEMBL
  FN3_sf UniProtKB/TrEMBL
  Ig-like_fold UniProtKB/TrEMBL
  Kunitz_BPTI UniProtKB/TrEMBL
  Kunitz_BPTI_sf UniProtKB/TrEMBL
  Prtase_inh_Kunz-CS UniProtKB/TrEMBL
  VWF_A UniProtKB/TrEMBL
  vWFA_dom_sf UniProtKB/TrEMBL
NCBI Gene COL7A1 ENTREZGENE
PANTHER COLLAGEN ALPHA UniProtKB/TrEMBL
  EMI DOMAIN-CONTAINING PROTEIN 1 ISOFORM X1 UniProtKB/TrEMBL
Pfam Collagen UniProtKB/TrEMBL
  fn3 UniProtKB/TrEMBL
  Kunitz_BPTI UniProtKB/TrEMBL
  VWA UniProtKB/TrEMBL
PRINTS BASICPTASE UniProtKB/TrEMBL
  VWFADOMAIN UniProtKB/TrEMBL
PROSITE BPTI_KUNITZ_1 UniProtKB/TrEMBL
  BPTI_KUNITZ_2 UniProtKB/TrEMBL
  FN3 UniProtKB/TrEMBL
  VWFA UniProtKB/TrEMBL
SMART FN3 UniProtKB/TrEMBL
  VWA UniProtKB/TrEMBL
Superfamily-SCOP SSF49265 UniProtKB/TrEMBL
  SSF53300 UniProtKB/TrEMBL
  SSF57362 UniProtKB/TrEMBL
UniProt A0A0D9RSP0 ENTREZGENE, UniProtKB/TrEMBL