Col4a1 (collagen type IV alpha 1 chain) - Rat Genome Database

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Gene: Col4a1 (collagen type IV alpha 1 chain) Chinchilla lanigera
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Symbol: Col4a1
Name: collagen type IV alpha 1 chain
RGD ID: 8910733
Description: ENCODES a protein that exhibits extracellular matrix structural constituent (ortholog); extracellular matrix structural constituent conferring tensile strength (ortholog); platelet-derived growth factor binding (ortholog); INVOLVED IN basement membrane organization (ortholog); blood vessel morphogenesis (ortholog); brain development (ortholog); PARTICIPATES IN syndecan signaling pathway; ASSOCIATED WITH Agenesis of Corpus Callosum (ortholog); Anal Atresia, Hypospadias, and Penoscrotal Inversion (ortholog); anterior segment dysgenesis (ortholog); FOUND IN basement membrane (ortholog); collagen type IV trimer (ortholog)
Type: protein-coding
RefSeq Status: MODEL
Previously known as: collagen alpha-1(IV) chain; collagen, type IV, alpha 1
RGD Orthologs
Human
Mouse
Rat
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: ChiLan1.0 - Chinchilla ChiLan1.0 Assembly
Position:
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554042,260,029 - 2,326,074 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554042,196,193 - 2,327,324 (+)NCBIChiLan1.0ChiLan1.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. Transitive Annotation Pipeline Automated assignment of GO, PW and RDO ISS annotations to Chinchilla, Squirrel, Bonobo and/or Dog genes from Human gene annotations
2. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline

Genomics

Comparative Map Data
Col4a1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554042,260,029 - 2,326,074 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554042,196,193 - 2,327,324 (+)NCBIChiLan1.0ChiLan1.0
COL4A1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh3813110,148,963 - 110,307,157 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl13110,148,963 - 110,307,157 (-)EnsemblGRCh38hg38GRCh38
GRCh3713110,801,310 - 110,959,504 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 3613109,599,311 - 109,757,497 (-)NCBINCBI36hg18NCBI36
Build 3413109,599,311 - 109,757,459NCBI
Celera1391,645,588 - 91,803,669 (-)NCBI
Cytogenetic Map13q34NCBI
HuRef1391,400,456 - 91,558,957 (-)NCBIHuRef
CHM1_113110,770,028 - 110,927,927 (-)NCBICHM1_1
T2T-CHM13v2.013109,377,773 - 109,536,621 (-)NCBI
Col4a1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39811,248,423 - 11,362,889 (-)NCBIGRCm39mm39
GRCm39 Ensembl811,248,423 - 11,362,826 (-)Ensembl
GRCm38811,198,423 - 11,312,889 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl811,198,423 - 11,312,826 (-)EnsemblGRCm38mm10GRCm38
MGSCv37811,198,423 - 11,312,826 (-)NCBIGRCm37mm9NCBIm37
MGSCv36811,198,403 - 11,312,702 (-)NCBImm8
Celera811,372,057 - 11,487,438 (-)NCBICelera
Cytogenetic Map8A1.1NCBI
cM Map85.53NCBI
Col4a1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21678,183,533 - 78,294,412 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl1678,183,533 - 78,294,412 (+)Ensembl
Rnor_6.01683,522,162 - 83,632,153 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1683,522,162 - 83,632,153 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01682,987,857 - 83,097,435 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41683,045,183 - 83,157,835 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11683,031,106 - 83,143,679 (+)NCBI
Celera1675,981,231 - 76,092,476 (+)NCBICelera
Cytogenetic Map16q12.5NCBI
COL4A1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.113110,407,009 - 110,562,529 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl13110,407,009 - 110,562,529 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01391,282,617 - 91,440,187 (-)NCBIMhudiblu_PPA_v0panPan3
COL4A1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12258,511,210 - 58,651,949 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2258,512,212 - 58,588,666 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2258,264,155 - 58,360,735 (-)NCBI
ROS_Cfam_1.02259,132,853 - 59,274,724 (-)NCBI
ROS_Cfam_1.0 Ensembl2259,133,398 - 59,274,709 (-)Ensembl
UMICH_Zoey_3.12258,634,288 - 58,774,752 (-)NCBI
UNSW_CanFamBas_1.02258,625,802 - 58,767,327 (-)NCBI
UU_Cfam_GSD_1.02258,660,825 - 58,801,735 (-)NCBI
Col4a1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404945193,408,026 - 193,536,112 (-)NCBI
SpeTri2.0NW_0049364722,416,043 - 2,543,561 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
COL4A1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1176,858,356 - 76,997,322 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11176,858,332 - 76,997,409 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21184,372,388 - 84,460,293 (-)NCBISscrofa10.2Sscrofa10.2susScr3
COL4A1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1388,410,800 - 88,564,191 (-)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl388,412,168 - 88,564,057 (-)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366604645,126,545 - 45,280,009 (-)NCBIVero_WHO_p1.0
Col4a1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247932,325,128 - 2,426,817 (+)EnsemblHetGla_female_1.0hetGla2
HetGla 1.0NW_0046247932,325,104 - 2,426,814 (+)NCBIHetGla_female_1.0hetGla2


Expression


Sequence


Reference Sequences
RefSeq Acc Id: ENSCLAT00000004669   ⟹   ENSCLAP00000004583
RefSeq Status:
Type: CODING
Position:
Chinchilla AssemblyChrPosition (strand)Source
ChiLan1.0 EnsemblNW_0049554042,260,029 - 2,326,074 (+)Ensembl
RefSeq Acc Id: XM_013516808   ⟹   XP_013372262
RefSeq Status:
Type: CODING
Position:
Chinchilla AssemblyChrPosition (strand)Source
ChiLan1.0NW_0049554042,196,193 - 2,327,324 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs XP_013372262 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: XP_013372262   ⟸   XM_013516808
- Sequence:
RefSeq Acc Id: ENSCLAP00000004583   ⟸   ENSCLAT00000004669
Protein Domains
Collagen IV NC1


Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSCLAG00000003263 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSCLAP00000004583 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSCLAT00000004669 ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH 2.170.240.10 UniProtKB/TrEMBL
InterPro Collagen UniProtKB/TrEMBL
  Collagen_IV_NC UniProtKB/TrEMBL
  Collagen_IV_NC_sf UniProtKB/TrEMBL
  CTDL_fold UniProtKB/TrEMBL
NCBI Gene Col4a1 ENTREZGENE
Pfam Collagen UniProtKB/TrEMBL
  PF01413 UniProtKB/TrEMBL
PROSITE NC1_IV UniProtKB/TrEMBL
SMART SM00111 UniProtKB/TrEMBL
Superfamily-SCOP SSF56436 UniProtKB/TrEMBL
UniProt A0A8C2YK54_CHILA UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-08-03 Col4a1  collagen type IV alpha 1 chain    collagen, type IV, alpha 1  Symbol and/or name change 5135510 APPROVED