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

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Gene: Col12a1 (collagen type XII alpha 1 chain) Rattus norvegicus
Analyze
Symbol: Col12a1
Name: collagen type XII alpha 1 chain
RGD ID: 2374
Description: Predicted to be an extracellular matrix structural constituent. Predicted to be involved in endodermal cell differentiation. Part of collagen type XII trimer. Human ortholog(s) of this gene implicated in Bethlem myopathy and Ullrich congenital muscular dystrophy. Orthologous to human COL12A1 (collagen type XII alpha 1 chain); PARTICIPATES IN syndecan signaling pathway; INTERACTS WITH 1-naphthyl isothiocyanate; 2,3,7,8-tetrachlorodibenzodioxine; 4,4'-diaminodiphenylmethane.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: collagen alpha-1(XII) chain; collagen, type XII, alpha 1; Procollagen type XII alpha 1; procollagen, type XII, alpha 1
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8889,427,834 - 89,545,886 (-)NCBIGRCr8
mRatBN7.2880,547,592 - 80,665,665 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl880,547,593 - 80,665,686 (-)EnsemblmRatBN7.2 Ensembl
Rnor_6.0887,042,820 - 87,150,701 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl887,040,799 - 87,158,368 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0886,584,555 - 86,701,809 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4884,641,358 - 84,756,923 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1884,660,818 - 84,677,966 (-)NCBI
Celera880,273,757 - 80,389,987 (-)NCBICelera
RH 3.4 Map10859.0RGD
Cytogenetic Map8q31NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
1,2-dichloroethane  (ISO)
1,2-dimethylhydrazine  (ISO)
1-naphthyl isothiocyanate  (EXP)
17alpha-ethynylestradiol  (ISO)
17beta-estradiol  (ISO)
17beta-hydroxy-5alpha-androstan-3-one  (ISO)
2,2',4,4',5,5'-hexachlorobiphenyl  (ISO)
2,2',4,4'-Tetrabromodiphenyl ether  (ISO)
2,2',5,5'-tetrachlorobiphenyl  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
4,4'-diaminodiphenylmethane  (EXP)
4,4'-sulfonyldiphenol  (ISO)
4-hydroxyphenyl retinamide  (ISO)
5-fluorouracil  (ISO)
6-propyl-2-thiouracil  (EXP)
9-cis-retinoic acid  (EXP)
acrolein  (ISO)
aflatoxin B1  (ISO)
all-trans-retinoic acid  (ISO)
alpha-pinene  (ISO)
amitrole  (EXP)
ammonium chloride  (EXP)
amphetamine  (EXP)
arsenite(3-)  (ISO)
arsenous acid  (ISO)
atrazine  (EXP)
bazedoxifene  (ISO)
benzo[a]pyrene  (ISO)
Benzo[ghi]perylene  (ISO)
bexarotene  (EXP)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP,ISO)
Bisphenol B  (ISO)
bisphenol F  (ISO)
cadmium atom  (ISO)
carbamazepine  (ISO)
carbon nanotube  (ISO)
CGP 52608  (ISO)
chlordecone  (ISO)
cisplatin  (ISO)
clobetasol  (ISO)
clothianidin  (ISO)
cobalt dichloride  (EXP,ISO)
copper atom  (ISO)
copper(0)  (ISO)
copper(II) sulfate  (ISO)
crocidolite asbestos  (ISO)
Cuprizon  (EXP)
cyclosporin A  (ISO)
decabromodiphenyl ether  (EXP)
dexamethasone  (ISO)
diarsenic trioxide  (ISO)
dibutyl phthalate  (EXP)
dioxygen  (EXP)
disulfiram  (ISO)
diuron  (EXP)
dopamine  (EXP)
dorsomorphin  (ISO)
doxorubicin  (ISO)
epoxiconazole  (ISO)
ethanol  (ISO)
fenamidone  (ISO)
fenoldopam  (EXP)
flavonoids  (EXP)
geldanamycin  (ISO)
genistein  (ISO)
indometacin  (ISO)
ivermectin  (ISO)
lipopolysaccharide  (ISO)
manganese atom  (ISO)
manganese(0)  (ISO)
manganese(II) chloride  (ISO)
mercury dibromide  (ISO)
methimazole  (EXP)
methylmercury chloride  (ISO)
mifepristone  (EXP)
mono(2-ethylhexyl) phthalate  (ISO)
N,N-diethyl-m-toluamide  (EXP)
N-methyl-4-phenylpyridinium  (EXP)
N-nitrosodimethylamine  (EXP)
nickel atom  (ISO)
nickel sulfate  (ISO)
oxaliplatin  (EXP,ISO)
ozone  (ISO)
paracetamol  (ISO)
paraquat  (ISO)
PCB138  (ISO)
pentane-2,3-dione  (EXP)
permethrin  (EXP)
Phenelzine  (ISO)
phenobarbital  (ISO)
phenylmercury acetate  (ISO)
PhIP  (EXP)
pirinixic acid  (ISO)
potassium chromate  (ISO)
progesterone  (ISO)
resveratrol  (ISO)
rotenone  (EXP)
SB 431542  (ISO)
silver atom  (ISO)
silver(0)  (ISO)
simvastatin  (ISO)
sodium arsenate  (ISO)
sodium arsenite  (ISO)
Soman  (EXP)
sunitinib  (ISO)
Tesaglitazar  (EXP)
titanium dioxide  (ISO)
topotecan  (EXP)
trimellitic anhydride  (ISO)
Triptolide  (ISO)
triptonide  (ISO)
valproic acid  (ISO)
vinclozolin  (EXP)

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

References - curated
# Reference Title Reference Citation
1. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
3. Structural variation of type XII collagen at its carboxyl-terminal NC1 domain generated by tissue-specific alternative splicing. Kania AM, etal., J Biol Chem 1999 Jul 30;274(31):22053-9.
4. High-density rat radiation hybrid maps containing over 24,000 SSLPs, genes, and ESTs provide a direct link to the rat genome sequence. Kwitek AE, etal., Genome Res. 2004 Apr;14(4):750-7
5. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
6. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
7. PID Annotation Import Pipeline Pipeline to import Pathway Interaction Database annotations from NCI into RGD
8. GOA pipeline RGD automated data pipeline
9. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
10. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:20551380   PMID:21362503   PMID:23154389   PMID:23376485   PMID:23658023   PMID:23979707   PMID:24006456   PMID:24769233   PMID:27068509   PMID:34233716  


Genomics

Comparative Map Data
Col12a1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8889,427,834 - 89,545,886 (-)NCBIGRCr8
mRatBN7.2880,547,592 - 80,665,665 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl880,547,593 - 80,665,686 (-)EnsemblmRatBN7.2 Ensembl
Rnor_6.0887,042,820 - 87,150,701 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl887,040,799 - 87,158,368 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0886,584,555 - 86,701,809 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4884,641,358 - 84,756,923 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1884,660,818 - 84,677,966 (-)NCBI
Celera880,273,757 - 80,389,987 (-)NCBICelera
RH 3.4 Map10859.0RGD
Cytogenetic Map8q31NCBI
COL12A1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38675,084,326 - 75,206,053 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl675,084,326 - 75,206,267 (-)EnsemblGRCh38hg38GRCh38
GRCh37675,794,042 - 75,915,769 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36675,850,762 - 75,972,343 (-)NCBINCBI36Build 36hg18NCBI36
Build 34675,850,762 - 75,972,290NCBI
Celera676,187,813 - 76,309,373 (-)NCBICelera
Cytogenetic Map6q13-q14.1NCBI
HuRef672,993,071 - 73,114,767 (-)NCBIHuRef
CHM1_1675,960,467 - 76,082,046 (-)NCBICHM1_1
T2T-CHM13v2.0676,261,502 - 76,383,203 (-)NCBIT2T-CHM13v2.0
Col12a1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39979,506,269 - 79,628,423 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl979,506,273 - 79,626,113 (-)EnsemblGRCm39 Ensembl
GRCm38979,598,987 - 79,721,141 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl979,598,991 - 79,718,831 (-)EnsemblGRCm38mm10GRCm38
MGSCv37979,446,798 - 79,566,485 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36979,387,443 - 79,504,149 (-)NCBIMGSCv36mm8
Celera976,744,488 - 76,862,823 (-)NCBICelera
Cytogenetic Map9E1NCBI
cM Map943.82NCBI
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
NHGRI_mPanPan1-v2595,131,719 - 95,284,459 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1693,009,460 - 93,162,227 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0672,927,897 - 73,049,168 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1676,219,319 - 76,340,496 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl676,219,319 - 76,340,496 (-)Ensemblpanpan1.1panPan2
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 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01237,264,259 - 37,387,691 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1237,266,365 - 37,537,523 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11236,828,942 - 36,945,160 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01236,819,169 - 36,935,951 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01236,947,167 - 37,063,520 (-)NCBIUU_Cfam_GSD_1.0
Col12a1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494672,151,620 - 72,263,479 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936788533,802 - 645,907 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_004936788533,811 - 645,821 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
COL12A1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl190,744,612 - 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 - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11783,473 - 205,366 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1786,992 - 204,504 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_0236660585,895,568 - 6,019,042 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Col12a1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248192,086,512 - 2,197,951 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248192,085,654 - 2,200,843 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Col12a1
530 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:189
Count of miRNA genes:131
Interacting mature miRNAs:157
Transcripts:ENSRNOT00000043691, ENSRNOT00000051159
Prediction methods:Microtar, Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1581557Eae16Experimental allergic encephalomyelitis QTL 163.8nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)88462195110921472Rat
631650Stl6Serum triglyceride level QTL 640.0019blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)810378157112202585Rat
631271Lecl1Lens clarity QTL 10.001lens clarity trait (VT:0001304)age of onset/diagnosis of cataract (CMO:0001584)81898416884531599Rat
731182Uae24Urinary albumin excretion QTL 246.4urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)81933115293965294Rat
1358892Kidm26Kidney mass QTL 263.69kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)82720571599103503Rat
1358896Bp262Blood pressure QTL 2622.89arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)82720571599103503Rat
1358907Cm40Cardiac mass QTL 401.89heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)82720571599103503Rat
8662823Vetf5Vascular elastic tissue fragility QTL 51.9artery integrity trait (VT:0010639)patent ductus arteriosus score (CMO:0002566)82824291299525068Rat
1549908Neudeg1Neurodegradation QTL 15.50nervous system integrity trait (VT:0010566)logarithm of the ratio of the lesioned side motor neuron count to contralateral side motor neuron count (CMO:0001986)83018886794457446Rat
2313046Bss78Bone structure and strength QTL 783.50.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)83084815482460899Rat
2313057Bss76Bone structure and strength QTL 7630.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)83084815482460899Rat
2313067Bss77Bone structure and strength QTL 773.10.0001tibia size trait (VT:0100001)tibia midshaft endosteal cross-sectional area (CMO:0001716)83084815482460899Rat
2313088Bss75Bone structure and strength QTL 753.10.0001body length (VT:0001256)body length, nose to rump (CMO:0000079)83084815482460899Rat
1578755Pur5Proteinuria QTL 53.30.0001urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)830848154101699754Rat
1578765Klgr1Kidney lesion grade QTL 13.30.0001kidney morphology trait (VT:0002135)organ lesion measurement (CMO:0000677)830848154101699754Rat
1578769Uae31Urinary albumin excretion QTL 313.30.001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)830848154101699754Rat
2316950Scl66Serum cholesterol level QTL 664.1blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)830848259105647037Rat
61358Bp39Blood pressure QTL 392arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)83555193880551938Rat
61464Niddm11Non-insulin dependent diabetes mellitus QTL 113.10.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)83558203280582032Rat
1331838Niddm61Non-insulin dependent diabetes mellitus QTL 613.530.0004blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)83646953599083736Rat
737824Hcar10Hepatocarcinoma resistance QTL 102.9liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)84071306682925667Rat
1358906Bp253Blood pressure QTL 25340.0004arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)84071306693965294Rat
1554321Bmd3Bone mineral density QTL 37.90.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)840952565123900184Rat
1298079Activ2Activity QTL 29.50.000001voluntary movement trait (VT:0003491)rearing measurement (CMO:0001515)84186687686866876Rat
70161Bp62Blood pressure QTL 622.90.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)84269268490165460Rat
12879882Am8Aortic mass QTL 80.001aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)84329616998968765Rat
12879878Bw183Body weight QTL 1830.001body mass (VT:0001259)body weight (CMO:0000012)84329616998968765Rat
12879879Cm99Cardiac mass QTL 990.001heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)84329616998968765Rat
12879880Cm100Cardiac mass QTL 1000.001heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)84329616998968765Rat
12879881Cm101Cardiac mass QTL 1010.001heart right ventricle mass (VT:0007033)heart right ventricle weight to body weight ratio (CMO:0000914)84329616998968765Rat
12879883Kidm65Kidney mass QTL 650.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)84329616998968765Rat
70197BpQTLcluster8Blood pressure QTL cluster 83.482arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)846531639119088626Rat
70197BpQTLcluster8Blood pressure QTL cluster 83.482arterial blood pressure trait (VT:2000000)pulse pressure (CMO:0000292)846531639119088626Rat
70197BpQTLcluster8Blood pressure QTL cluster 83.482arterial blood pressure trait (VT:2000000)absolute change in systolic blood pressure (CMO:0000607)846531639119088626Rat
70197BpQTLcluster8Blood pressure QTL cluster 83.482arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)846531639119088626Rat
1331837Bw23Body weight QTL 234.190.00007body mass (VT:0001259)body weight (CMO:0000012)84653172299083736Rat
2303570Gluco48Glucose level QTL 482blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)84980583194805831Rat
2313086Bss60Bone structure and strength QTL 604.10.0001tibia length (VT:0004357)tibia length (CMO:0000450)85009524982460899Rat
4889938Bss89Bone structure and strength QTL 893.8tibia size trait (VT:0100001)tibia cortical bone volume (CMO:0001725)85009524982460899Rat
5684973Bss100Bone structure and strength QTL 1004.7tibia area (VT:1000281)tibia area measurement (CMO:0001382)85009524982460899Rat
1358912Bw51Body weight QTL 512.95body mass (VT:0001259)body weight (CMO:0000012)851351728107062046Rat
10402857Bp380Blood pressure QTL 3800.95arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)85396876598968765Rat
2301402Bp316Blood pressure QTL 3160.005arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)85396876598968765Rat
2293697Bmd39Bone mineral density QTL 39femur strength trait (VT:0010010)femur total energy absorbed before break (CMO:0001677)85404374498968765Rat
1582243Bw66Body weight QTL 663.40.0048body mass (VT:0001259)body weight (CMO:0000012)85423764485365202Rat
1582254Kidm31Kidney mass QTL 313kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)85423764485365202Rat
631664Hcar3Hepatocarcinoma resistance QTL 32.90.0005liver integrity trait (VT:0010547)volume of individual liver tumorous lesion (CMO:0001078)85423764499103503Rat
1300177Cm2Cardiac mass QTL 23.65heart mass (VT:0007028)heart weight (CMO:0000017)854259986100382532Rat
2303171Bp331Blood pressure QTL 3315.570.005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)861290298119084929Rat
631653Bp125Blood pressure QTL 1253.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)866142385111142385Rat
631210Bw3Body weight QTL35.9mesenteric fat pad mass (VT:0010427)mesenteric fat pad weight to body weight ratio (CMO:0000654)869349194112783834Rat
1300171Bp184Blood pressure QTL 1843.66arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)870513503118219066Rat
8694446Bw170Body weight QTL 17012.070.001retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)871888757116888757Rat
9590292Uminl3Urine mineral level QTL 33.620.001urine mineral amount (VT:0015086)urine electrolyte level (CMO:0000593)871888757116888757Rat
8694200Abfw4Abdominal fat weight QTL 49.070.001visceral adipose mass (VT:0010063)abdominal fat pad weight to body weight ratio (CMO:0000095)871888757116888757Rat
8694392Bw161Body weight QTL 1618.060.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)871888757116888757Rat
1549909Stresp11Stress response QTL 116.830.0019stress-related behavior trait (VT:0010451)number of approaches toward negative stimulus before onset of defensive burying response (CMO:0001960)873473045118473045Rat
10450865Bw175Body weight QTL 1754.1total fat pad mass (VT:0015008)adipose tissue molecular composition measurement (CMO:0000484)87531177784531599Rat
634332Pia18Pristane induced arthritis QTL 184joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)87531193882925521Rat
2300181Bmd55Bone mineral density QTL 555.70.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)876468691121468691Rat

Markers in Region
RH132431  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2880,547,860 - 80,548,044 (+)MAPPERmRatBN7.2
Rnor_6.0887,041,065 - 87,041,248NCBIRnor6.0
Rnor_5.0886,584,824 - 86,585,007UniSTSRnor5.0
RGSC_v3.4884,641,627 - 84,641,810UniSTSRGSC3.4
RH 3.4 Map8919.5UniSTS
Cytogenetic Map8q31UniSTS
RH94627  
Rat AssemblyChrPosition (strand)SourceJBrowse
RH 3.4 Map10859.0UniSTS
Cytogenetic Map8q31UniSTS
RH143456  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2880,661,934 - 80,662,325 (+)MAPPERmRatBN7.2
Rnor_6.0887,154,646 - 87,155,036NCBIRnor6.0
Rnor_5.0886,698,080 - 86,698,470UniSTSRnor5.0
RGSC_v3.4884,756,563 - 84,756,953UniSTSRGSC3.4
Celera880,386,248 - 80,386,638UniSTS
RH 3.4 Map8924.7UniSTS
Cytogenetic Map8q31UniSTS
BE115111  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2880,627,395 - 80,627,545 (+)MAPPERmRatBN7.2
Rnor_6.0887,120,109 - 87,120,258NCBIRnor6.0
Rnor_5.0886,663,393 - 86,663,542UniSTSRnor5.0
RGSC_v3.4884,722,025 - 84,722,174UniSTSRGSC3.4
Celera880,351,825 - 80,351,974UniSTS
RH 3.4 Map8923.0UniSTS
Cytogenetic Map8q31UniSTS


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 1 6 10 12 6 7 13 35 30 11 6
Low 2 34 45 39 7 39 2 4 61 11 2
Below cutoff 3 2 2 2

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000077071   ⟹   ENSRNOP00000075422
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl880,547,593 - 80,665,686 (-)Ensembl
Rnor_6.0 Ensembl887,040,799 - 87,158,368 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000095926   ⟹   ENSRNOP00000096476
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl880,547,593 - 80,655,041 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000108595   ⟹   ENSRNOP00000080952
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl880,549,705 - 80,658,409 (-)Ensembl
RefSeq Acc Id: NM_013142   ⟹   NP_037274
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8889,427,834 - 89,545,711 (-)NCBI
mRatBN7.2880,547,592 - 80,665,477 (-)NCBI
RefSeq Acc Id: XM_039082533   ⟹   XP_038938461
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8889,427,834 - 89,545,886 (-)NCBI
mRatBN7.2880,547,592 - 80,665,665 (-)NCBI
RefSeq Acc Id: XM_039082534   ⟹   XP_038938462
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8889,427,834 - 89,545,867 (-)NCBI
mRatBN7.2880,547,596 - 80,665,648 (-)NCBI
RefSeq Acc Id: XM_063264976   ⟹   XP_063121046
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8889,427,834 - 89,545,867 (-)NCBI
Reference Protein Sequences
RefSeq Acc Id: ENSRNOP00000075422   ⟸   ENSRNOT00000077071
RefSeq Acc Id: XP_038938461   ⟸   XM_039082533
- Peptide Label: isoform X1
- UniProtKB: A0A0G2KAJ7 (UniProtKB/TrEMBL),   A0A8I5ZRE6 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038938462   ⟸   XM_039082534
- Peptide Label: isoform X2
- UniProtKB: A6I1L5 (UniProtKB/TrEMBL)
RefSeq Acc Id: ENSRNOP00000080952   ⟸   ENSRNOT00000108595
RefSeq Acc Id: ENSRNOP00000096476   ⟸   ENSRNOT00000095926
RefSeq Acc Id: NP_037274   ⟸   NM_013142
- Peptide Label: precursor
RefSeq Acc Id: XP_063121046   ⟸   XM_063264976
- Peptide Label: isoform X3
Protein Domains
Fibronectin type-III   VWFA

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-P70560-F1-model_v2 AlphaFold P70560 1-317 view protein structure

Transcriptome

eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen

Promoters
RGD ID:13696149
Promoter ID:EPDNEW_R6672
Type:multiple initiation site
Name:Col12a1_1
Description:collagen type XII alpha 1 chain
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0887,158,188 - 87,158,248EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:2374 AgrOrtholog
BioCyc Gene G2FUF-29743 BioCyc
Ensembl Genes ENSRNOG00000058470 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000077071.2 UniProtKB/TrEMBL
  ENSRNOT00000095926.1 UniProtKB/TrEMBL
  ENSRNOT00000108595 ENTREZGENE
  ENSRNOT00000108595.1 UniProtKB/TrEMBL
Gene3D-CATH 2.60.120.200 UniProtKB/TrEMBL
  2.60.40.10 UniProtKB/TrEMBL
  3.40.50.410 UniProtKB/TrEMBL
InterPro Collagen UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ConA-like_subgrp UniProtKB/TrEMBL
  FN3_sf UniProtKB/TrEMBL
  FN_III UniProtKB/TrEMBL
  Ig-like_fold UniProtKB/TrEMBL
  TSPN-like_N UniProtKB/TrEMBL
  VWF_A UniProtKB/TrEMBL
  vWFA_dom_sf UniProtKB/TrEMBL
NCBI Gene 25683 ENTREZGENE
PANTHER COLLAGEN ALPHA UniProtKB/Swiss-Prot
  COLLAGEN ALPHA UniProtKB/TrEMBL
  PH DOMAIN-CONTAINING PROTEIN UniProtKB/TrEMBL
  ZGC:113232 UniProtKB/Swiss-Prot
Pfam Collagen UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  fn3 UniProtKB/TrEMBL
  VWA UniProtKB/TrEMBL
PhenoGen Col12a1 PhenoGen
PRINTS VWFADOMAIN UniProtKB/TrEMBL
PROSITE FN3 UniProtKB/TrEMBL
  VWFA UniProtKB/TrEMBL
RatGTEx ENSRNOG00000058470 RatGTEx
SMART FN3 UniProtKB/TrEMBL
  TSPN UniProtKB/TrEMBL
  VWA UniProtKB/TrEMBL
Superfamily-SCOP ConA_like_lec_gl UniProtKB/TrEMBL
  FN_III-like UniProtKB/TrEMBL
  SSF53300 UniProtKB/TrEMBL
UniProt A0A0G2KAJ7 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I5ZRE6 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I6B493_RAT UniProtKB/TrEMBL
  A6I1L5 ENTREZGENE, UniProtKB/TrEMBL
  A6I1L6_RAT UniProtKB/TrEMBL
  A6I1L8_RAT UniProtKB/TrEMBL
  COCA1_RAT UniProtKB/Swiss-Prot, ENTREZGENE
UniProt Secondary P70559 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-06-01 Col12a1  collagen type XII alpha 1 chain  Col12a1  collagen, type XII, alpha 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-25 Col12a1  collagen, type XII, alpha 1  Col12a1  procollagen, type XII, alpha 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2002-11-06 Col12a1  procollagen, type XII, alpha 1    Procollagen type XII alpha 1  Name updated 625702 APPROVED
2002-06-10 Col12a1  Procollagen type XII alpha 1      Symbol and Name status set to approved 70586 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_transcript contains two alternative exons 1 and 2 that produce long and short NC1 domain isoforms 727275