COL1A2 (collagen type I 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 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
Advanced Search (OLGA)
Gene: COL1A2 (collagen type I alpha 2 chain) Pan paniscus
Analyze
Symbol: COL1A2
Name: collagen type I alpha 2 chain
RGD ID: 11677625
Description: ENCODES a protein that exhibits extracellular matrix structural constituent (inferred); extracellular matrix structural constituent conferring tensile strength (inferred); identical protein binding (inferred); INVOLVED IN bone mineralization (ortholog); cellular response to aldehyde (ortholog); cellular response to amino acid stimulus (ortholog); PARTICIPATES IN endothelin signaling pathway; interleukin-4 signaling pathway; syndecan signaling pathway; ASSOCIATED WITH Acute Liver Failure (ortholog); ARTERIAL DISSECTION (ortholog); Bruck Syndrome 1 (ortholog); FOUND IN collagen trimer (inferred); collagen type I trimer (inferred); collagen-containing extracellular matrix (inferred)
Type: protein-coding
RefSeq Status: MODEL
Previously known as: collagen alpha-2(I) chain
RGD Orthologs
Human
Mouse
Rat
Chinchilla
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: Mhudiblu_PPA_v0 - Bonobo Mhudiblu_PPA_v0 Assembly
Position:
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v26112,232,392 - 112,268,547 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan17160,497,349 - 160,533,186 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0786,344,657 - 86,381,282 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1799,935,185 - 99,971,810 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl799,935,185 - 99,971,803 (+)Ensemblpanpan1.1panPan2
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:30032202  


Genomics

Comparative Map Data
COL1A2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v26112,232,392 - 112,268,547 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan17160,497,349 - 160,533,186 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0786,344,657 - 86,381,282 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1799,935,185 - 99,971,810 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl799,935,185 - 99,971,803 (+)Ensemblpanpan1.1panPan2
COL1A2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38794,394,895 - 94,431,227 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl794,394,895 - 94,431,227 (+)EnsemblGRCh38hg38GRCh38
GRCh37794,024,207 - 94,060,539 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36793,861,809 - 93,898,480 (+)NCBINCBI36Build 36hg18NCBI36
Build 34793,668,523 - 93,705,195NCBI
Celera788,722,142 - 88,758,790 (+)NCBICelera
Cytogenetic Map7q21.3NCBI
HuRef788,631,579 - 88,668,235 (+)NCBIHuRef
CHM1_1793,953,972 - 93,990,650 (+)NCBICHM1_1
T2T-CHM13v2.0795,630,848 - 95,667,187 (+)NCBIT2T-CHM13v2.0
CRA_TCAGchr7v2793,353,052 - 93,389,700 (+)NCBI
Col1a2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3964,505,618 - 4,541,543 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl64,504,814 - 4,541,544 (+)EnsemblGRCm39 Ensembl
GRCm3864,505,618 - 4,541,543 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl64,504,814 - 4,541,544 (+)EnsemblGRCm38mm10GRCm38
MGSCv3764,455,697 - 4,491,543 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv3664,455,761 - 4,490,730 (+)NCBIMGSCv36mm8
Celera64,648,226 - 4,684,066 (+)NCBICelera
Cytogenetic Map6A1NCBI
cM Map61.81NCBI
Col1a2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8433,518,557 - 33,553,484 (+)NCBIGRCr8
mRatBN7.2432,563,938 - 32,598,868 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl432,563,381 - 32,598,867 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx437,550,562 - 37,585,439 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0433,476,688 - 33,511,565 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0431,846,998 - 31,881,902 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0431,534,225 - 31,569,152 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl431,534,225 - 31,569,151 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0429,442,828 - 29,478,616 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Rnor_5.0431,405,253 - 31,440,180 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4429,393,645 - 29,428,572 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1429,431,383 - 29,467,014 (+)NCBI
Celera427,947,892 - 27,982,658 (+)NCBICelera
Cytogenetic Map4q21NCBI
Col1a2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495543211,128,112 - 11,163,302 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495543211,127,961 - 11,164,145 (+)NCBIChiLan1.0ChiLan1.0
COL1A2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11419,883,731 - 19,919,527 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1419,883,868 - 19,919,527 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1419,443,112 - 19,478,898 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01419,699,099 - 19,734,901 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1419,699,098 - 19,734,902 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11419,850,793 - 19,886,662 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01419,585,955 - 19,621,759 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01419,843,097 - 19,878,889 (+)NCBIUU_Cfam_GSD_1.0
Col1a2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440511833,176,893 - 33,212,967 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365855,651,180 - 5,685,923 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365855,650,322 - 5,686,393 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
COL1A2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl974,173,931 - 74,210,397 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1974,174,484 - 74,210,407 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2981,357,192 - 81,393,118 (+)NCBISscrofa10.2Sscrofa10.2susScr3
COL1A2
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12154,602,780 - 54,639,832 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2154,602,398 - 54,632,780 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604249,682,896 - 49,719,954 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Col1a2
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248131,174,224 - 1,209,616 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248131,174,071 - 1,209,929 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2


Expression

RNA-SEQ Expression


Sequence

Nucleotide Sequences
RefSeq Transcripts XM_063606253 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide JARIFH020000006 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Ensembl Acc Id: ENSPPAT00000062203   ⟹   ENSPPAP00000039293
Type: CODING
Position:
Bonobo AssemblyChrPosition (strand)Source
PanPan1.1 Ensembl799,935,185 - 99,971,803 (+)Ensembl
RefSeq Acc Id: XM_063606253   ⟹   XP_063462323
Type: CODING
Position:
Bonobo AssemblyChrPosition (strand)Source
NHGRI_mPanPan1-v26112,232,392 - 112,268,547 (+)NCBI
Protein Sequences
Protein RefSeqs XP_063462323 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSPPAP00000039293.1
Ensembl Acc Id: ENSPPAP00000039293   ⟸   ENSPPAT00000062203
RefSeq Acc Id: XP_063462323   ⟸   XM_063606253
Protein Domains
Fibrillar collagen NC1


Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSPPAG00000042352 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSPPAT00000062203.1 UniProtKB/TrEMBL
Gene3D-CATH 2.60.120.1000 UniProtKB/TrEMBL
InterPro Collagen UniProtKB/TrEMBL
  Collagen_superfamily UniProtKB/TrEMBL
  Fib_collagen_C UniProtKB/TrEMBL
NCBI Gene COL1A2 ENTREZGENE
PANTHER COLLAGEN ALPHA UniProtKB/TrEMBL
  ENDOSTATIN DOMAIN-CONTAINING PROTEIN UniProtKB/TrEMBL
Pfam COLFI UniProtKB/TrEMBL
  Collagen UniProtKB/TrEMBL
PROSITE NC1_FIB UniProtKB/TrEMBL
SMART COLFI UniProtKB/TrEMBL
UniProt A0A2R9CE70_PANPA UniProtKB/TrEMBL