Col6a2 (collagen type VI alpha 2 chain) - Rat Genome Database

Send us a Message
Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Search RGD Grant Resources Citing RGD About Us Contact Us
Genes Variants Community Projects QTLs Strains Markers Genome Information Ontologies Cell Lines References Download Submit Data
OntoMate (Literature Search) JBrowse (Genome Browser) Synteny Browser (VCMap) Variant Visualizer Multi-Ontology Enrichment (MOET) Gene-Ortholog Location Finder (GOLF) InterViewer (Protein-Protein Interactions) PhenoMiner (Quatitative Phenotypes) Gene Annotator OLGA (Gene List Generator) AllianceMine GViewer (Genome Viewer)
Aging & Age-Related Disease Cancer & Neoplastic Disease Cardiovascular Disease Coronavirus Disease Developmental Disease Diabetes Hematologic Disease Immune & Inflammatory Disease Infectious Disease Liver Disease Neurological Disease Obesity & Metabolic Syndrome Renal Disease Respiratory Disease Sensory Organ Disease
Find Models   new Genetic Models Autism Models Rat PhenoMiner (Quantitative Phenotypes) Chinchilla PhenoMiner Expected Ranges (Quantitative Phenotype) PhenoMiner Term Comparison Hybrid Rat Diversity Panel Phenotypes Phenotypes in Other Animal Models Animal Husbandry Strain Medical Records Phylogenetics Strain Availability Calendar Rats 101 Submissions Photo Archive
Pathways
Rat Community Forum Directory of Rat Laboratories Video Tutorials News RGD Publications RGD Presentations Archive Nomenclature Guidelines Resource Links Laboratory Resources Employment Resources
Gene: Col6a2 (collagen type VI alpha 2 chain) Heterocephalus glaber
Analyze
Symbol: Col6a2
Name: collagen type VI alpha 2 chain
RGD ID: 18923628
Description: ENCODES a protein that exhibits collagen binding (ortholog); INVOLVED IN neuron apoptotic process (ortholog); phosphatidylinositol 3-kinase/protein kinase B signal transduction (ortholog); response to glucose (ortholog); PARTICIPATES IN syndecan signaling pathway; ASSOCIATED WITH autistic disorder (ortholog); Axenfeld-Rieger syndrome type 3 (ortholog); Bethlem myopathy (ortholog); FOUND IN extracellular region (ortholog); protein-containing complex (ortholog); sarcolemma (ortholog)
Type: protein-coding
RefSeq Status: MODEL
Previously known as: Collagen alpha-2(VI) chain; collagen alpha-2(VI) chain isoform 2C2
RGD Orthologs
Human
Mouse
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Alliance Genes
More Info more info ...
Latest Assembly: HetGla 1.0 - Naked Mole-Rat female 1.0 Assembly
Position:
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462474531,258,825 - 31,272,524 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462474531,246,458 - 31,272,403 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2
JBrowse: View Region in Genome Browser (JBrowse)
Model


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:21993625  


Genomics

Comparative Map Data
Col6a2
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462474531,258,825 - 31,272,524 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462474531,246,458 - 31,272,403 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2
COL6A2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh382146,098,112 - 46,132,848 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl2146,098,112 - 46,132,848 (+)EnsemblGRCh38hg38GRCh38
GRCh372147,518,026 - 47,552,762 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 362146,342,461 - 46,377,191 (+)NCBINCBI36Build 36hg18NCBI36
Build 342146,342,469 - 46,374,147NCBI
Celera2132,629,797 - 32,665,343 (+)NCBICelera
Cytogenetic Map21q22.3NCBI
HuRef2132,899,133 - 32,933,853 (+)NCBIHuRef
CHM1_12147,078,809 - 47,113,491 (+)NCBICHM1_1
T2T-CHM13v2.02144,476,193 - 44,510,935 (+)NCBIT2T-CHM13v2.0
Col6a2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391076,431,590 - 76,459,464 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1076,431,596 - 76,459,464 (-)EnsemblGRCm39 Ensembl
GRCm381076,595,756 - 76,623,630 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1076,595,762 - 76,623,630 (-)EnsemblGRCm38mm10GRCm38
MGSCv371076,058,501 - 76,086,149 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361076,039,478 - 76,067,030 (-)NCBIMGSCv36mm8
Celera1077,640,875 - 77,668,353 (-)NCBICelera
Cytogenetic Map10C1NCBI
cM Map1039.32NCBI
Col6a2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr82012,021,182 - 12,048,932 (+)NCBIGRCr8
mRatBN7.22012,021,676 - 12,049,425 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl2012,021,767 - 12,057,564 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx2012,718,053 - 12,745,716 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.02012,078,971 - 12,106,636 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.02012,550,765 - 12,578,421 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.02012,773,472 - 12,801,179 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2012,773,427 - 12,801,180 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02014,931,484 - 14,959,214 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42012,436,783 - 12,464,512 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.12012,445,140 - 12,461,566 (+)NCBI
Celera2013,520,111 - 13,547,903 (+)NCBICelera
Cytogenetic Map20p12NCBI
Col6a2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495540742,575,170 - 42,600,495 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495540742,575,677 - 42,600,967 (+)NCBIChiLan1.0ChiLan1.0
COL6A2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v22242,198,729 - 42,234,261 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan12137,070,722 - 37,105,973 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v02132,442,859 - 32,478,076 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.12145,696,865 - 45,731,192 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2145,710,491 - 45,730,895 (+)Ensemblpanpan1.1panPan2
COL6A2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.13139,433,174 - 39,448,051 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha3138,644,112 - 38,676,023 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.03139,056,885 - 39,089,141 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl3139,056,960 - 39,089,152 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.13138,918,380 - 38,950,842 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.03138,893,797 - 38,911,284 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.03139,397,110 - 39,429,683 (+)NCBIUU_Cfam_GSD_1.0
Col6a2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440497138,700,077 - 38,735,225 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936778394,953 - 430,113 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_004936778394,985 - 430,070 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
COL6A2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa10.213218,600,867 - 218,616,309 (+)NCBISscrofa10.2Sscrofa10.2susScr3
COL6A2
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1289,724,355 - 89,758,389 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl289,737,003 - 89,758,425 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366605418,038,715 - 18,072,843 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0


Expression


Sequence


Reference Sequences
RefSeq Acc Id: ENSHGLT00000012884   ⟹   ENSHGLP00000012747
Type: CODING
Position:
Naked Mole-Rat AssemblyChrPosition (strand)Source
HetGla_female_1.0 EnsemblNW_00462474531,258,825 - 31,272,524 (+)Ensembl
RefSeq Acc Id: ENSHGLT00000012885   ⟹   ENSHGLP00000012748
Type: CODING
Position:
Naked Mole-Rat AssemblyChrPosition (strand)Source
HetGla_female_1.0 EnsemblNW_00462474531,258,851 - 31,272,027 (+)Ensembl
RefSeq Acc Id: XM_004842535   ⟹   XP_004842592
Type: CODING
Position:
Naked Mole-Rat AssemblyChrPosition (strand)Source
HetGla 1.0NW_00462474531,246,458 - 31,272,403 (+)NCBI
RefSeq Acc Id: XM_004842536   ⟹   XP_004842593
Type: CODING
Position:
Naked Mole-Rat AssemblyChrPosition (strand)Source
HetGla 1.0NW_00462474531,246,461 - 31,272,403 (+)NCBI
RefSeq Acc Id: XM_004842537   ⟹   XP_004842594
Type: CODING
Position:
Naked Mole-Rat AssemblyChrPosition (strand)Source
HetGla 1.0NW_00462474531,246,458 - 31,271,159 (+)NCBI
Protein Sequences
Protein RefSeqs XP_004842592 (Get FASTA)   NCBI Sequence Viewer  
  XP_004842593 (Get FASTA)   NCBI Sequence Viewer  
  XP_004842594 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EHB17619 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSHGLP00000012747
GenBank Protein JAO02826 (Get FASTA)   NCBI Sequence Viewer  
Reference Protein Sequences
RefSeq Acc Id: XP_004842592   ⟸   XM_004842535
- Peptide Label: isoform X1
- UniProtKB: A0A0P6JLU0 (UniProtKB/TrEMBL),   G5C7V8 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_004842594   ⟸   XM_004842537
- Peptide Label: isoform X2
- UniProtKB: A0A0P6JLU0 (UniProtKB/TrEMBL),   G5C7V8 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_004842593   ⟸   XM_004842536
- Peptide Label: isoform X1
- UniProtKB: A0A0P6JLU0 (UniProtKB/TrEMBL),   G5C7V8 (UniProtKB/TrEMBL)
RefSeq Acc Id: ENSHGLP00000012748   ⟸   ENSHGLT00000012885
RefSeq Acc Id: ENSHGLP00000012747   ⟸   ENSHGLT00000012884


Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSHGLG00000009116 Ensembl, ENTREZGENE
Ensembl Transcript ENSHGLT00000012884 ENTREZGENE
Gene3D-CATH 3.40.50.410 UniProtKB/TrEMBL
  6-Phosphogluconate Dehydrogenase, domain 3 UniProtKB/TrEMBL
InterPro Collagen UniProtKB/TrEMBL
  VWF_A UniProtKB/TrEMBL
  vWFA_dom_sf UniProtKB/TrEMBL
NCBI Gene Col6a2 ENTREZGENE
PANTHER COLLAGEN ALPHA UniProtKB/TrEMBL
  VWFA DOMAIN-CONTAINING PROTEIN UniProtKB/TrEMBL
Pfam Collagen UniProtKB/TrEMBL
  VWA UniProtKB/TrEMBL
PRINTS VWFADOMAIN UniProtKB/TrEMBL
PROSITE VWFA UniProtKB/TrEMBL
SMART VWA UniProtKB/TrEMBL
Superfamily-SCOP SSF53300 UniProtKB/TrEMBL
UniProt A0A0P6JLU0 ENTREZGENE, UniProtKB/TrEMBL
  G5C7V8 ENTREZGENE, UniProtKB/TrEMBL