Col12a1 (collagen type XII alpha 1 chain) - Rat Genome Database

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Gene: Col12a1 (collagen type XII alpha 1 chain) Ictidomys tridecemlineatus
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Symbol: Col12a1
Name: collagen type XII alpha 1 chain
RGD ID: 12684218
Description: INVOLVED IN endodermal cell differentiation (ortholog); PARTICIPATES IN syndecan signaling pathway; ASSOCIATED WITH Bethlem myopathy (ortholog); Bethlem Myopathy 2 (ortholog); Charcot-Marie-Tooth disease type 2 (ortholog); FOUND IN collagen type XII trimer (ortholog)
Type: protein-coding
RefSeq Status: MODEL
Also known as: collagen alpha-1(XII) chain
RGD Orthologs
Human
Mouse
Rat
Chinchilla
Bonobo
Dog
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: SpeTri2.0 - Squirrel SpeTri2.0 Assembly
Position:
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494672,151,620 - 72,263,479 (-)NCBI
SpeTri2.0NW_004936788533,811 - 645,821 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
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

Genomics

Comparative Map Data
Col12a1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494672,151,620 - 72,263,479 (-)NCBI
SpeTri2.0NW_004936788533,811 - 645,821 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
COL12A1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl675,084,326 - 75,206,053 (-)EnsemblGRCh38hg38GRCh38
GRCh38.p13 Ensembl675,084,326 - 75,206,267 (-)EnsemblGRCh38hg38GRCh38
GRCh38675,084,326 - 75,206,262 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37675,794,042 - 75,915,769 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36675,850,762 - 75,972,343 (-)NCBINCBI36hg18NCBI36
Build 34675,850,762 - 75,972,290NCBI
Celera676,187,813 - 76,309,373 (-)NCBI
Cytogenetic Map6q13-q14.1NCBI
HuRef672,993,071 - 73,114,767 (-)NCBIHuRef
CHM1_1675,960,467 - 76,082,046 (-)NCBICHM1_1
Col12a1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39979,506,269 - 79,628,423 (-)NCBIGRCm39mm39
GRCm39 Ensembl979,506,273 - 79,626,113 (-)Ensembl
GRCm38979,598,987 - 79,721,141 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl979,598,991 - 79,718,831 (-)EnsemblGRCm38mm10GRCm38
MGSCv37979,446,798 - 79,566,485 (-)NCBIGRCm37mm9NCBIm37
MGSCv36979,387,443 - 79,504,149 (-)NCBImm8
Celera976,744,488 - 76,862,823 (-)NCBICelera
Cytogenetic Map9E1NCBI
cM Map943.82NCBI
Col12a1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2880,547,592 - 80,665,665 (-)NCBI
Rnor_6.0 Ensembl887,040,799 - 87,158,368 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0887,042,820 - 87,150,701 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0886,584,555 - 86,701,809 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4884,641,358 - 84,756,923 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1884,660,818 - 84,677,966 (-)NCBI
Celera880,273,757 - 80,389,987 (-)NCBICelera
RH 3.4 Map10859.0RGD
Cytogenetic Map8q31NCBI
Col12a1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554888,131,846 - 8,240,777 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554888,128,816 - 8,240,714 (+)NCBIChiLan1.0ChiLan1.0
COL12A1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1676,219,319 - 76,340,496 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl676,219,319 - 76,340,496 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0672,927,897 - 73,049,168 (-)NCBIMhudiblu_PPA_v0panPan3
COL12A1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11236,720,686 - 36,838,321 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1236,646,408 - 36,838,622 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1236,591,487 - 36,714,157 (-)NCBI
ROS_Cfam_1.01237,264,259 - 37,387,691 (-)NCBI
UMICH_Zoey_3.11236,828,942 - 36,945,160 (-)NCBI
UNSW_CanFamBas_1.01236,819,169 - 36,935,951 (-)NCBI
UU_Cfam_GSD_1.01236,947,167 - 37,063,520 (-)NCBI
COL12A1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl190,744,429 - 90,875,118 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1190,744,409 - 90,875,127 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21101,693,208 - 101,890,887 (+)NCBISscrofa10.2Sscrofa10.2susScr3
COL12A1
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11783,473 - 205,366 (+)NCBI
ChlSab1.1 Ensembl1786,992 - 204,504 (+)Ensembl
Col12a1
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248192,085,654 - 2,200,843 (-)NCBI


Expression


Sequence


Reference Sequences
RefSeq Acc Id: XM_005340334   ⟹   XP_005340391
RefSeq Status:
Type: CODING
Position:
Squirrel AssemblyChrPosition (strand)Source
HiC_Itri_2NW_02440494672,152,473 - 72,263,479 (-)NCBI
SpeTri2.0NW_004936788533,811 - 645,821 (-)NCBI
Sequence:
RefSeq Acc Id: XM_021720224   ⟹   XP_021575899
RefSeq Status:
Type: CODING
Position:
Squirrel AssemblyChrPosition (strand)Source
HiC_Itri_2NW_02440494672,151,620 - 72,263,479 (-)NCBI
SpeTri2.0NW_004936788533,811 - 645,821 (-)NCBI
Sequence:
RefSeq Acc Id: XM_021720225   ⟹   XP_021575900
RefSeq Status:
Type: CODING
Position:
Squirrel AssemblyChrPosition (strand)Source
HiC_Itri_2NW_02440494672,151,622 - 72,259,900 (-)NCBI
SpeTri2.0NW_004936788533,813 - 645,821 (-)NCBI
Sequence:
RefSeq Acc Id: XM_021720226   ⟹   XP_021575901
RefSeq Status:
Type: CODING
Position:
Squirrel AssemblyChrPosition (strand)Source
HiC_Itri_2NW_02440494672,151,620 - 72,263,388 (-)NCBI
SpeTri2.0NW_004936788533,811 - 645,821 (-)NCBI
Sequence:
RefSeq Acc Id: XM_040282966   ⟹   XP_040138900
RefSeq Status:
Type: CODING
Position:
Squirrel AssemblyChrPosition (strand)Source
HiC_Itri_2NW_02440494672,151,620 - 72,259,900 (-)NCBI
Reference Sequences
RefSeq Acc Id: XP_005340391   ⟸   XM_005340334
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_021575901   ⟸   XM_021720226
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: XP_021575899   ⟸   XM_021720224
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_021575900   ⟸   XM_021720225
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_040138900   ⟸   XM_040282966
- Peptide Label: isoform X1
Protein Domains
Fibronectin type-III   VWFA


Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSSTOG00000002481 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSSTOP00000002261 ENTREZGENE, UniProtKB/TrEMBL
  ENSSTOP00000018132 UniProtKB/TrEMBL
Ensembl Transcript ENSSTOT00000002528 UniProtKB/TrEMBL
  ENSSTOT00000028101 UniProtKB/TrEMBL
Gene3D-CATH 2.60.40.10 UniProtKB/TrEMBL
  3.40.50.410 UniProtKB/TrEMBL
InterPro Collagen UniProtKB/TrEMBL
  ConA-like_dom_sf UniProtKB/TrEMBL
  FN3_dom UniProtKB/TrEMBL
  FN3_sf UniProtKB/TrEMBL
  Ig-like_fold UniProtKB/TrEMBL
  Laminin_G UniProtKB/TrEMBL
  VWF_A UniProtKB/TrEMBL
  vWFA_dom_sf UniProtKB/TrEMBL
NCBI Gene Col12a1 ENTREZGENE
Pfam Collagen UniProtKB/TrEMBL
  fn3 UniProtKB/TrEMBL
  VWA UniProtKB/TrEMBL
PROSITE FN3 UniProtKB/TrEMBL
  VWFA UniProtKB/TrEMBL
SMART FN3 UniProtKB/TrEMBL
  TSPN UniProtKB/TrEMBL
  VWA UniProtKB/TrEMBL
Superfamily-SCOP SSF49265 UniProtKB/TrEMBL
  SSF49899 UniProtKB/TrEMBL
  SSF53300 UniProtKB/TrEMBL
UniProt I3M0L4_ICTTR UniProtKB/TrEMBL
  I3N186_ICTTR UniProtKB/TrEMBL