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

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Gene: Col4a1 (collagen type IV alpha 1 chain) Ictidomys tridecemlineatus
Analyze
Symbol: Col4a1
Name: collagen type IV alpha 1 chain
RGD ID: 12642368
Description: ENCODES a protein that exhibits extracellular matrix structural constituent (inferred); extracellular matrix structural constituent conferring tensile strength (inferred); platelet-derived growth factor binding (inferred); INVOLVED IN cellular response to amino acid stimulus (ortholog); collagen-activated tyrosine kinase receptor signaling pathway (ortholog); epithelial cell differentiation (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 (inferred); collagen trimer (inferred); collagen type IV trimer (inferred)
Type: protein-coding
RefSeq Status: MODEL
Previously known as: collagen alpha-1(IV) chain
RGD Orthologs
Human
Mouse
Rat
Chinchilla
Bonobo
Dog
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: SpeTri2.0 - Squirrel SpeTri2.0 Assembly
Position:
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404945193,408,026 - 193,536,112 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049364722,416,566 - 2,542,814 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049364722,416,043 - 2,543,561 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

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


Genomics

Comparative Map Data
Col4a1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404945193,408,026 - 193,536,112 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049364722,416,566 - 2,542,814 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049364722,416,043 - 2,543,561 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
COL4A1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh3813110,148,963 - 110,307,157 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl13110,148,963 - 110,307,202 (-)EnsemblGRCh38hg38GRCh38
GRCh3713110,801,310 - 110,959,504 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 3613109,599,311 - 109,757,497 (-)NCBINCBI36Build 36hg18NCBI36
Build 3413109,599,311 - 109,757,459NCBI
Celera1391,645,588 - 91,803,669 (-)NCBICelera
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 (-)NCBIT2T-CHM13v2.0
Col4a1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39811,248,423 - 11,362,889 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl811,248,423 - 11,362,826 (-)EnsemblGRCm39 Ensembl
GRCm38811,198,423 - 11,312,889 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl811,198,423 - 11,312,826 (-)EnsemblGRCm38mm10GRCm38
MGSCv37811,198,423 - 11,312,826 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36811,198,403 - 11,312,702 (-)NCBIMGSCv36mm8
Celera811,372,057 - 11,487,438 (-)NCBICelera
Cytogenetic Map8A1.1NCBI
cM Map85.53NCBI
Col4a1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81684,885,597 - 84,996,482 (+)NCBIGRCr8
mRatBN7.21678,183,533 - 78,294,412 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1678,183,533 - 78,294,412 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1683,463,953 - 83,574,826 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01686,916,625 - 87,027,510 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01682,157,396 - 82,268,610 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
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 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11683,031,106 - 83,143,679 (+)NCBI
Celera1675,981,231 - 76,092,476 (+)NCBICelera
Cytogenetic Map16q12.5NCBI
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
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v214111,642,358 - 111,800,305 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan113110,324,917 - 110,482,747 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01391,282,617 - 91,440,187 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.113110,407,009 - 110,562,529 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl13110,407,009 - 110,562,529 (-)Ensemblpanpan1.1panPan2
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 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02259,132,853 - 59,274,724 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2259,133,398 - 59,274,709 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12258,634,288 - 58,774,752 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02258,625,802 - 58,767,327 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02258,660,825 - 58,801,735 (-)NCBIUU_Cfam_GSD_1.0
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 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl388,412,168 - 88,564,057 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604645,126,545 - 45,280,009 (-)NCBIVero_WHO_p1.0Vero_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_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247932,325,104 - 2,426,814 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2


Expression


Sequence

Nucleotide Sequences
RefSeq Transcripts XM_005317129 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide JAESOR010000004 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSSTOT00000004305   ⟹   ENSSTOP00000003864
Type: CODING
Position:
Squirrel AssemblyChrPosition (strand)Source
SpeTri2.0 EnsemblNW_0049364722,416,566 - 2,542,814 (+)Ensembl
RefSeq Acc Id: XM_005317129   ⟹   XP_005317186
Type: CODING
Position:
Squirrel AssemblyChrPosition (strand)Source
HiC_Itri_2NW_024404945193,408,026 - 193,536,112 (-)NCBI
SpeTri2.0NW_0049364722,416,043 - 2,543,561 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs XP_005317186 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSSTOP00000003864.3
GenBank Protein KAG3293402 (Get FASTA)   NCBI Sequence Viewer  
Reference Protein Sequences
RefSeq Acc Id: XP_005317186   ⟸   XM_005317129
- Sequence:
RefSeq Acc Id: ENSSTOP00000003864   ⟸   ENSSTOT00000004305
Protein Domains
Collagen IV NC1


Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSSTOG00000004254 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSSTOT00000004305.3 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
PANTHER COLLAGEN UniProtKB/TrEMBL
  COLLAGEN ALPHA UniProtKB/TrEMBL
Pfam Collagen UniProtKB/TrEMBL
  PF01413 UniProtKB/TrEMBL
PROSITE NC1_IV UniProtKB/TrEMBL
SMART SM00111 UniProtKB/TrEMBL
Superfamily-SCOP SSF56436 UniProtKB/TrEMBL
UniProt I3M3Z8_ICTTR UniProtKB/TrEMBL