Col1a2 (collagen type I alpha 2 chain) - Rat Genome Database

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Gene: Col1a2 (collagen type I alpha 2 chain) Rattus norvegicus
Analyze
Symbol: Col1a2
Name: collagen type I alpha 2 chain
RGD ID: 621351
Description: Predicted to enable several functions, including identical protein binding activity; platelet-derived growth factor binding activity; and protease binding activity. Predicted to be an extracellular matrix structural constituent conferring tensile strength. Involved in several processes, including cellular response to retinoic acid; cellular response to thyroid hormone stimulus; and response to norepinephrine. Predicted to be located in extracellular region. Predicted to be part of collagen type I trimer. Predicted to be active in collagen-containing extracellular matrix and extracellular space. Biomarker of hypothyroidism; muscular atrophy; pulmonary fibrosis; and ureteral obstruction. Human ortholog(s) of this gene implicated in Ehlers-Danlos syndrome (multiple); heart valve disease; intracranial aneurysm; osteogenesis imperfecta (multiple); and osteoporosis. Orthologous to human COL1A2 (collagen type I alpha 2 chain); PARTICIPATES IN endothelin signaling pathway; interleukin-4 signaling pathway; syndecan signaling pathway; INTERACTS WITH (S)-nicotine; 1-naphthyl isothiocyanate; 17alpha-ethynylestradiol.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: alpha-2 type I collagen; collagen alpha-2(I) chain; collagen, type I, alpha 2; NEWGENE_621351; procollagen, type I, alpha 2
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
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_5.0431,405,253 - 31,440,180 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Rnor_5.0429,442,828 - 29,478,616 (+)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
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(1->4)-beta-D-glucan  (ISO)
(R)-camphor  (ISO)
(S)-nicotine  (EXP,ISO)
1,2-dimethylhydrazine  (ISO)
1-naphthyl isothiocyanate  (EXP)
1-octadec-9-enoylglycero-3-phosphate  (ISO)
17alpha-ethynylestradiol  (EXP,ISO)
17beta-estradiol  (ISO)
1H-[1,2,4]oxadiazolo[4,3-a]quinoxalin-1-one  (ISO)
2,2',4,4'-Tetrabromodiphenyl ether  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,3,7,8-Tetrachlorodibenzofuran  (EXP)
2,4,6-trinitrobenzenesulfonic acid  (ISO)
2,4-dibromophenyl 2,4,5-tribromophenyl ether  (ISO)
2-butoxyethanol  (ISO)
2-nitrotoluene  (EXP)
3,4-methylenedioxymethamphetamine  (EXP)
3-methyladenine  (ISO)
4,4'-diaminodiphenylmethane  (EXP)
4,4'-sulfonyldiphenol  (ISO)
4-hydroxyphenyl retinamide  (ISO)
4-tert-Octylphenol  (EXP)
5'-S-methyl-5'-thioadenosine  (ISO)
5-aza-2'-deoxycytidine  (ISO)
5-fluorouracil  (ISO)
6-propyl-2-thiouracil  (EXP)
7,12-dimethyltetraphene  (EXP)
9-cis-retinoic acid  (EXP)
acetaldehyde  (ISO)
acrylamide  (ISO)
actinomycin D  (EXP)
adenine  (ISO)
aflatoxin B1  (ISO)
aldehydo-D-glucose  (ISO)
aldosterone  (ISO)
all-trans-retinoic acid  (EXP,ISO)
alpha-Zearalanol  (EXP)
aluminium oxide  (ISO)
AM-251  (ISO)
amlodipine  (EXP)
amphetamine  (EXP)
amphibole asbestos  (EXP,ISO)
andrographolide  (EXP,ISO)
apocynin  (EXP)
Archazolid B  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenite(3-)  (ISO)
arsenous acid  (ISO)
Atractylodin  (ISO)
baicalein  (EXP)
baicalin  (EXP)
belinostat  (ISO)
benzo[a]pyrene  (EXP,ISO)
benzo[b]fluoranthene  (ISO)
bisphenol A  (EXP,ISO)
Bisphenol B  (ISO)
bisphenol F  (ISO)
bleomycin A2  (EXP,ISO)
boric acid  (ISO)
boron nitride  (ISO)
bosentan  (ISO)
bromochloroacetic acid  (EXP)
buspirone  (EXP)
cadmium atom  (ISO)
cadmium dichloride  (EXP,ISO)
calcitriol  (ISO)
calcium atom  (ISO)
calcium(0)  (ISO)
Calphostin C  (ISO)
camphor  (ISO)
candesartan  (ISO)
cannabidiol  (ISO)
carbon nanotube  (ISO)
CGP 52608  (ISO)
chenodeoxycholic acid  (ISO)
chlordecone  (ISO)
choline  (ISO)
chrysene  (ISO)
cisplatin  (ISO)
clofibric acid  (EXP)
cobalt dichloride  (EXP)
copper atom  (EXP,ISO)
copper(0)  (EXP,ISO)
copper(II) sulfate  (ISO)
crocidolite asbestos  (ISO)
Cuprizon  (EXP)
curcumin  (ISO)
cyclosporin A  (ISO)
cytarabine  (ISO)
cytochalasin D  (ISO)
D-glucose  (ISO)
dexamethasone  (ISO)
dextran sulfate  (ISO)
diarsenic trioxide  (ISO)
diazinon  (EXP)
dibromoacetic acid  (EXP)
Didecyldimethylammonium  (ISO)
diethylstilbestrol  (EXP,ISO)
dimethyl sulfoxide  (ISO)
dimethylarsinic acid  (EXP)
Diosbulbin B  (ISO)
dioxygen  (EXP,ISO)
diquat  (ISO)
disulfiram  (ISO)
diuron  (EXP)
divanadium pentaoxide  (ISO)
dorsomorphin  (ISO)
doxorubicin  (ISO)
emodin  (EXP)
endosulfan  (EXP)
entinostat  (ISO)
erastin  (ISO)
ethanol  (EXP,ISO)
Ethoxyacetic acid  (ISO)
ferulic acid  (ISO)
flavonoids  (EXP)
flusilazole  (ISO)
folic acid  (EXP,ISO)
formaldehyde  (ISO)
furan  (EXP)
gamma-aminobutyric acid  (EXP)
gamma-Oryzanol (TN)  (EXP)
genistein  (EXP)
gentamycin  (EXP)
glucose  (ISO)
gold atom  (ISO)
gold(0)  (ISO)
hexaconazole  (ISO)
hydroxyurea  (ISO)
icariside II  (EXP)
Icaritin  (EXP)
inulin  (ISO)
ivermectin  (ISO)
L-arginine  (EXP)
L-ascorbic acid  (EXP,ISO)
L-ascorbic acid 2-phosphate  (ISO)
L-methionine  (ISO)
lipopolysaccharide  (ISO)
lipoxin A4  (ISO)
lithium chloride  (ISO)
LY-2157299  (ISO)
LY294002  (ISO)
magnesium atom  (ISO)
malathion  (ISO)
malonaldehyde  (EXP)
maraviroc  (ISO)
mercury dibromide  (ISO)
methapyrilene  (EXP)
methotrexate  (ISO)
methylmercury chloride  (ISO)
methylparaben  (ISO)
mifepristone  (EXP)
Muraglitazar  (EXP)
N-acetyl-1,4-benzoquinone imine  (ISO)
N-acetyl-L-cysteine  (ISO)
N-ethyl-N-nitrosourea  (ISO)
N-methyl-N'-nitro-N-nitrosoguanidine  (ISO)
N-nitrosodiethylamine  (EXP)
N-nitrosodimethylamine  (EXP)
naphthalene  (ISO)
nefazodone  (EXP)
nickel atom  (ISO)
nickel dichloride  (ISO)
nickel subsulfide  (EXP)
nicotinamide  (ISO)
nicotine  (EXP,ISO)
nimesulide  (EXP)
nitric oxide  (EXP)
nitroprusside  (ISO)
okadaic acid  (ISO)
oxaliplatin  (EXP)
ozone  (EXP,ISO)
p-chloromercuribenzoic acid  (ISO)
p-tert-Amylphenol  (EXP)
Pachymic acid  (EXP)
paclitaxel  (ISO)
panobinostat  (ISO)
paracetamol  (EXP,ISO)
paraquat  (ISO)
pentane-2,3-dione  (EXP)
perfluorohexanesulfonic acid  (ISO)
perfluorooctane-1-sulfonic acid  (ISO)
perfluorooctanoic acid  (EXP)
perindopril  (EXP)
Phenelzine  (ISO)
phenobarbital  (ISO)
phenylmercury acetate  (ISO)
phenytoin  (ISO)
PhIP  (EXP)
phorbol 13-acetate 12-myristate  (ISO)
potassium dichromate  (ISO)
progesterone  (ISO)
pyrrolidine dithiocarbamate  (ISO)
quartz  (ISO)
quercetin  (EXP)
raloxifene  (ISO)
resveratrol  (EXP,ISO)
rotenone  (EXP)
S-(1,2-dichlorovinyl)-L-cysteine  (ISO)
S-adenosyl-L-homocysteine  (ISO)
S-adenosyl-L-methioninate  (EXP,ISO)
S-adenosyl-L-methionine  (EXP,ISO)
S-butyl-DL-homocysteine (S,R)-sulfoximine  (ISO)
salvianolic acid B  (EXP)
SB 203580  (EXP)
SB 431542  (ISO)
Se-methyl-L-selenocysteine  (ISO)
Se-methylselenocysteine  (ISO)
serpentine asbestos  (ISO)
silicon dioxide  (ISO)
sirolimus  (EXP,ISO)
sodium arsenate  (ISO)
sodium arsenite  (ISO)
sodium atom  (ISO)
sodium dichromate  (EXP)
sodium hydroxide  (EXP)
sotorasib  (ISO)
sulindac  (ISO)
sunitinib  (ISO)
T-2 toxin  (ISO)
tacrolimus hydrate  (ISO)
teprenone  (ISO)
tert-butyl hydroperoxide  (ISO)
testosterone enanthate  (ISO)
tetrachloromethane  (EXP,ISO)
tetraphene  (ISO)
tetrathiomolybdate(2-)  (ISO)
thalidomide  (EXP)
thioacetamide  (EXP,ISO)
titanium dioxide  (ISO)
toluene  (EXP)
topotecan  (EXP,ISO)
trametinib  (ISO)
tributylstannane  (EXP)
trichloroethene  (ISO)
trichostatin A  (ISO)
triclosan  (ISO)
triphenyl phosphate  (EXP)
troglitazone  (EXP,ISO)
valproic acid  (ISO)
vancomycin  (ISO)
vincristine  (ISO)
vitamin E  (ISO)
vorinostat  (ISO)
wortmannin  (ISO)
Y-27632  (ISO)
zinc atom  (ISO)
zinc(0)  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. Aldehydes potentiate alpha(2)(I) collagen gene activity by JNK in hepatic stellate cells. Anania FA, etal., Free Radic Biol Med. 2001 Apr 15;30(8):846-57.
2. Changes in expression of the albumin, fibronectin and type I procollagen genes in CCl4-induced liver fibrosis: effect of pyridoxol L,2-pyrrolidon-5 carboxylate. Arosio B, etal., Pharmacol Toxicol. 1993 Dec;73(6):301-4.
3. Effect of norepinephrine on myocardial collagen gene expression and response of cardiac fibroblasts after norepinephrine treatment. Bhambi B and Eghbali M, Am J Pathol. 1991 Nov;139(5):1131-42.
4. Defective pro alpha 2(I) collagen synthesis in a recessive mutation in mice: a model of human osteogenesis imperfecta. Chipman SD, etal., Proc Natl Acad Sci U S A. 1993 Mar 1;90(5):1701-5.
5. 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.
6. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
7. TGF-beta1 and TNF-alpha are involved in the transcription of type I collagen alpha2 gene in soleus muscle atrophied by mechanical unloading. Hirose T, etal., J Appl Physiol. 2008 Jan;104(1):170-7. Epub 2007 Oct 4.
8. Upregulation of collagen type I gene expression in the ventricular myocardium of thyroidectomized male and female rats. Klein LE, etal., J Mol Cell Cardiol. 1996 Jan;28(1):33-42.
9. Mutational spectrum of type I collagen genes in Korean patients with osteogenesis imperfecta. Lee KS, etal., Hum Mutat. 2006 Jun;27(6):599.
10. Integrative urinary peptidomics in renal transplantation identifies biomarkers for acute rejection. Ling XB, etal., J Am Soc Nephrol. 2010 Apr;21(4):646-53. doi: 10.1681/ASN.2009080876. Epub 2010 Feb 11.
11. Total absence of the alpha2(I) chain of collagen type I causes a rare form of Ehlers-Danlos syndrome with hypermobility and propensity to cardiac valvular problems. Malfait F, etal., J Med Genet. 2006 Jul;43(7):e36.
12. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
13. Mouse Genome Database (MGD) Mouse Genome Database (MGD)
14. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
15. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
16. Online Mendelian Inheritance in Man, OMIM (TM). Online Mendelian Inheritance in Man, OMIM (TM).
17. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
18. PID Annotation Import Pipeline Pipeline to import Pathway Interaction Database annotations from NCI into RGD
19. GOA pipeline RGD automated data pipeline
20. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
21. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
22. Comprehensive gene review and curation RGD comprehensive gene curation
23. Rare autosomal recessive cardiac valvular form of Ehlers-Danlos syndrome results from mutations in the COL1A2 gene that activate the nonsense-mediated RNA decay pathway. Schwarze U, etal., Am J Hum Genet. 2004 May;74(5):917-30. Epub 2004 Apr 9.
24. Involvement of renal corpuscle microRNA expression on epithelial-to-mesenchymal transition in maternal low protein diet in adult programmed rats. Sene Lde B, etal., PLoS One. 2013 Aug 19;8(8):e71310. doi: 10.1371/journal.pone.0071310. eCollection 2013.
25. The RFX family interacts at the collagen (COL1A2) start site and represses transcription. Sengupta PK, etal., J Biol Chem 2002 Jul 12;277(28):24926-37.
26. Clinical variability of osteogenesis imperfecta linked to COL1A2 and associated with a structural defect in the type I collagen molecule. Superti-Furga A, etal., J Med Genet 1989 Jun;26(6):358-62.
27. Differential regulation of TGF-beta signal in hepatic stellate cells between acute and chronic rat liver injury. Tahashi Y, etal., Hepatology. 2002 Jan;35(1):49-61.
28. A sensitive short-term evaluation of antifibrotic effects using newly established type I collagen reporter transgenic rats. Terashima H, etal., Am J Physiol Renal Physiol. 2010 Oct;299(4):F792-801. Epub 2010 Jul 21.
29. Regulation of alpha 2(I) collagen expression in stellate cells by retinoic acid and retinoid X receptors through interactions with their cofactors. Wang L, etal., Arch Biochem Biophys. 2004 Aug 1;428(1):92-8.
30. Mutation characteristics in type I collagen genes in Chinese patients with osteogenesis imperfecta. Yang Z, etal., Genet Mol Res. 2011 Feb 8;10(1):177-85. doi: 10.4238/vol10-1gmr984.
31. Decreased collagen gene expression and absence of fibrosis in thyroid hormone-induced myocardial hypertrophy. Response of cardiac fibroblasts to thyroid hormone in vitro. Yao J and Eghbali M, Circ Res. 1992 Oct;71(4):831-9.
32. Collagen type I alpha2 (COL1A2) is the susceptible gene for intracranial aneurysms. Yoneyama T, etal., Stroke. 2004 Feb;35(2):443-8. Epub 2004 Jan 22.
33. In situ hybridization analysis of rat lung alpha 1(I) and alpha 2(I) collagen gene expression in pulmonary fibrosis induced by endotracheal bleomycin injection. Zhang K, etal., Lab Invest. 1994 Feb;70(2):192-202.
34. Integrated Analysis of Multiple Microarray Studies to Identify Core Gene-Expression Signatures Involved in Tubulointerstitial Injury in Diabetic Nephropathy. Zhou H, etal., Biomed Res Int. 2022 May 10;2022:9554658. doi: 10.1155/2022/9554658. eCollection 2022.
Additional References at PubMed
PMID:1590760   PMID:4435743   PMID:4636752   PMID:4763308   PMID:5337886   PMID:5443712   PMID:5544653   PMID:5785232   PMID:6395893   PMID:7825727   PMID:8686743   PMID:8841196  
PMID:8900172   PMID:9213002   PMID:10608859   PMID:12477932   PMID:12704794   PMID:12968017   PMID:14559231   PMID:17211858   PMID:17217948   PMID:17334644   PMID:17662583   PMID:17955022  
PMID:18375391   PMID:19156436   PMID:19362560   PMID:19755419   PMID:19932771   PMID:20053668   PMID:20548288   PMID:20551380   PMID:21362503   PMID:22049076   PMID:22910579   PMID:23399546  
PMID:23658023   PMID:24006456   PMID:24782617   PMID:25655816   PMID:25931508   PMID:27068509   PMID:27559042   PMID:30053369   PMID:36324232  


Genomics

Comparative Map Data
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_5.0431,405,253 - 31,440,180 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Rnor_5.0429,442,828 - 29,478,616 (+)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
(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
(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
(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
(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

Variants

.
Variants in Col1a2
83 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:48
Count of miRNA genes:30
Interacting mature miRNAs:41
Transcripts:ENSRNOT00000016423
Prediction methods: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
2302371Stl22Serum triglyceride level QTL 225.15blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)4521829457114705Rat
2303585Bw86Body weight QTL 864body mass (VT:0001259)body weight (CMO:0000012)41467806559678065Rat
8552906Pigfal3Plasma insulin-like growth factor 1 level QTL 3blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)41008408955084089Rat
1357341Gluco5Glucose level QTL 56.4adipocyte free fatty acid secretion trait (VT:0010465)absolute change in adipocyte free fatty acid secretion per unit volume (CMO:0001446)4133250345Rat
10755501Bp390Blood pressure QTL 3902.5arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)426775591168368347Rat
1357343Gluco4Glucose level QTL 40.00002adipocyte glucose uptake trait (VT:0004185)adipocyte maximal glucose uptake to basal glucose uptake ratio (CMO:0000874)4133250345Rat
6478766Anxrr47Anxiety related response QTL 470.09637locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)41008408955084089Rat
70222Eae2Experimental allergic encephalomyelitis QTL 24.3nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)42133334339505420Rat
631642Stl2Serum triglyceride level QTL 23.3blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)4521917856647776Rat
6478769Anxrr48Anxiety related response QTL 480.02514locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)41008408955084089Rat
631261Tcas3Tongue tumor susceptibility QTL 36.88tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)41081417091360527Rat
634323Hc2Hypercalciuria QTL 22.15urine calcium amount (VT:0002985)urine calcium excretion rate (CMO:0000763)421079645210796Rat
2313401Anxrr27Anxiety related response QTL 27aggression-related behavior trait (VT:0015014)tameness/aggressiveness composite score (CMO:0002136)41793350862933508Rat
631209Bw2Body weight QTL24.2retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)4994088544463908Rat
8552803Bw144Body weight QTL 14416body mass (VT:0001259)change in body weight to body weight ratio (CMO:0002216)42271068534430484Rat
6909128Pancm4Pancreatic morphology QTL 411.35pancreas mass (VT:0010144)pancreas wet weight (CMO:0000626)42690728575585128Rat
8694374Bw155Body weight QTL 1553.390.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)41008408955084089Rat
2303168Bp330Blood pressure QTL 3304.250.017arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)45214602146446691Rat
61412Pia2Pristane induced arthritis QTL 23.9joint integrity trait (VT:0010548)post-insult time to onset of experimental arthritis (CMO:0001450)42133334362278020Rat
6478724Anxrr35Anxiety related response QTL 350.00449defecation behavior trait (VT:0010462)defecation measurement (CMO:0000997)41008408955084089Rat
8655906Rf60Renal function QTL 603.8blood creatinine amount (VT:0005328)creatinine clearance (CMO:0000765)42949419581006281Rat
61415Eae11Experimental allergic encephalomyelitis QTL 112.9nervous system integrity trait (VT:0010566)post-insult time to onset of experimental autoimmune encephalomyelitis (CMO:0001422)4139505420Rat
619616Bp79Blood pressure QTL 790.0292arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)4521460278882945Rat
7387227Uae40Urinary albumin excretion QTL 402.90.0052urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)41794699962946999Rat
6909122Insul22Insulin level QTL 224.63blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)42690728575585128Rat
738021Hcar13Hepatocarcinoma resistance QTL 134.3liver integrity trait (VT:0010547)liver nonremodeling tumorous lesion volume to total liver volume ratio (CMO:0001464)4132584199Rat
1358203Stl19Serum triglyceride level QTL 192.80.002blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)4521829465958103Rat
9590304Scort17Serum corticosterone level QTL 174.960.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)41008408955084089Rat
12798520Anxrr55Anxiety related response QTL 554.450.01locomotor behavior trait (VT:0001392)number of rearing movements with lid-pushing in an experimental apparatus (CMO:0002715)432583980114627242Rat
11530004Niddm71Non-insulin dependent diabetes mellitus QTL 710.001blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)43258419952754138Rat
2316958Gluco58Glucose level QTL 5810blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)411320076180699135Rat
1354665Stl10Serum triglyceride level QTL 103.57blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)42133334344463908Rat
1300141Bp178Blood pressure QTL 178arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)41002490139524530Rat

Markers in Region
D4Rat151  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2432,583,980 - 32,584,199 (+)MAPPERmRatBN7.2
Rnor_6.0431,554,266 - 31,554,484NCBIRnor6.0
Rnor_6.0429,549,895 - 29,550,113NCBIRnor6.0
Rnor_5.0429,463,219 - 29,463,437UniSTSRnor5.0
Rnor_5.0431,425,294 - 31,425,512UniSTSRnor5.0
RGSC_v3.4429,413,686 - 29,413,904UniSTSRGSC3.4
RGSC_v3.4429,413,655 - 29,414,068RGDRGSC3.4
RGSC_v3.1429,452,129 - 29,452,347RGD
Celera427,967,860 - 27,968,078UniSTS
RH 3.4 Map4449.82RGD
RH 3.4 Map4449.82UniSTS
RH 2.0 Map4215.3RGD
SHRSP x BN Map417.0799RGD
Cytogenetic Map4q13UniSTS
RH132451  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2432,598,608 - 32,598,800 (+)MAPPERmRatBN7.2
Rnor_6.0431,568,893 - 31,569,084NCBIRnor6.0
Rnor_6.0429,564,522 - 29,564,713NCBIRnor6.0
Rnor_5.0431,439,921 - 31,440,112UniSTSRnor5.0
Rnor_5.0429,477,846 - 29,478,037UniSTSRnor5.0
RGSC_v3.4429,428,313 - 29,428,504UniSTSRGSC3.4
Celera427,982,399 - 27,982,590UniSTS
RH 3.4 Map4435.74UniSTS
Cytogenetic Map4q13UniSTS
RH133324  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2432,599,105 - 32,599,295 (+)MAPPERmRatBN7.2
Rnor_6.0431,569,390 - 31,569,579NCBIRnor6.0
Rnor_6.0429,565,019 - 29,565,208NCBIRnor6.0
Rnor_5.0431,440,418 - 31,440,607UniSTSRnor5.0
Rnor_5.0429,478,343 - 29,478,532UniSTSRnor5.0
RGSC_v3.4429,428,810 - 29,428,999UniSTSRGSC3.4
Celera427,982,896 - 27,983,085UniSTS
RH 3.4 Map4435.74UniSTS
Cytogenetic Map4q13UniSTS
AI179432  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2432,584,697 - 32,584,884 (+)MAPPERmRatBN7.2
Rnor_6.0431,554,983 - 31,555,169NCBIRnor6.0
Rnor_6.0429,550,612 - 29,550,798NCBIRnor6.0
Rnor_5.0429,463,936 - 29,464,122UniSTSRnor5.0
Rnor_5.0431,426,011 - 31,426,197UniSTSRnor5.0
RGSC_v3.4429,414,403 - 29,414,589UniSTSRGSC3.4
Celera427,968,577 - 27,968,763UniSTS
Cytogenetic Map4q13UniSTS
AA819207  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2432,597,337 - 32,598,521 (+)MAPPERmRatBN7.2
Rnor_6.0431,567,622 - 31,568,805NCBIRnor6.0
Rnor_6.0429,563,251 - 29,564,434NCBIRnor6.0
Rnor_5.0431,438,650 - 31,439,833UniSTSRnor5.0
Rnor_5.0429,476,575 - 29,477,758UniSTSRnor5.0
RGSC_v3.4429,427,042 - 29,428,225UniSTSRGSC3.4
Celera427,981,128 - 27,982,311UniSTS
RH 3.4 Map4219.24UniSTS
Cytogenetic Map4q13UniSTS
Col1a2  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2432,597,213 - 32,598,399 (+)MAPPERmRatBN7.2
Rnor_6.0431,567,498 - 31,568,683NCBIRnor6.0
Rnor_6.0429,563,127 - 29,564,312NCBIRnor6.0
Rnor_5.0429,476,451 - 29,477,636UniSTSRnor5.0
Rnor_5.0431,438,526 - 31,439,711UniSTSRnor5.0
RGSC_v3.4429,426,918 - 29,428,103UniSTSRGSC3.4
Celera427,981,004 - 27,982,189UniSTS
Cytogenetic Map4q13UniSTS
GDB:177260  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_5.07139,647,866 - 139,648,445NCBIRnor5.0
Rnor_5.0429,475,523 - 29,476,477NCBIRnor5.0
Rnor_5.0431,437,598 - 31,438,552NCBIRnor5.0
RGSC_v3.4429,425,991 - 29,426,944UniSTSRGSC3.4
RGSC_v3.47136,680,091 - 136,680,669UniSTSRGSC3.4
Celera427,980,077 - 27,981,030UniSTS
Celera7125,590,621 - 125,591,199UniSTS
Cytogenetic Map4q13UniSTS
Cytogenetic Map7q36UniSTS
GDB:180350  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2432,589,485 - 32,590,378 (+)MAPPERmRatBN7.2
Rnor_6.0431,559,770 - 31,560,662NCBIRnor6.0
Rnor_6.0429,555,399 - 29,556,291NCBIRnor6.0
Rnor_5.0429,468,723 - 29,469,615UniSTSRnor5.0
Rnor_5.0431,430,798 - 31,431,690UniSTSRnor5.0
RGSC_v3.4429,419,190 - 29,420,082UniSTSRGSC3.4
Celera427,973,363 - 27,974,255UniSTS
Cytogenetic Map4q13UniSTS
Col1a2  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2432,563,837 - 32,564,004 (+)MAPPERmRatBN7.2
Rnor_6.0431,534,125 - 31,534,291NCBIRnor6.0
Rnor_6.0429,529,754 - 29,529,920NCBIRnor6.0
Rnor_5.0429,443,078 - 29,443,244UniSTSRnor5.0
Rnor_5.0431,405,153 - 31,405,319UniSTSRnor5.0
RGSC_v3.4429,393,545 - 29,393,711UniSTSRGSC3.4
Celera427,947,792 - 27,947,958UniSTS
Cytogenetic Map4q13UniSTS


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
nervous system
renal system
reproductive system
respiratory system
9 9 45 82 67 69 45 15 45 6 176 79 66 37 56 24

Sequence


Ensembl Acc Id: ENSRNOT00000016423   ⟹   ENSRNOP00000016423
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl432,563,381 - 32,598,867 (+)Ensembl
Rnor_6.0 Ensembl431,534,225 - 31,569,151 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000087619   ⟹   ENSRNOP00000073398
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl432,563,381 - 32,598,867 (+)Ensembl
Rnor_6.0 Ensembl429,535,852 - 29,564,768 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000089292   ⟹   ENSRNOP00000075459
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl431,534,225 - 31,568,806 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000089564   ⟹   ENSRNOP00000069327
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl429,529,854 - 29,564,435 (+)Ensembl
RefSeq Acc Id: NM_053356   ⟹   NP_445808
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8433,518,557 - 33,553,484 (+)NCBI
mRatBN7.2432,563,938 - 32,598,868 (+)NCBI
Rnor_6.0431,534,225 - 31,569,152 (+)NCBI
Rnor_5.0431,405,253 - 31,440,180 (+)NCBI
RGSC_v3.4429,393,645 - 29,428,572 (+)RGD
Celera427,947,892 - 27,982,658 (+)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_445808 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAA40835 (Get FASTA)   NCBI Sequence Viewer  
  AAA40836 (Get FASTA)   NCBI Sequence Viewer  
  AAD41775 (Get FASTA)   NCBI Sequence Viewer  
  CAA46960 (Get FASTA)   NCBI Sequence Viewer  
  EDL84402 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000016423.7
  ENSRNOP00000073398.2
GenBank Protein P02466 (Get FASTA)   NCBI Sequence Viewer  
RefSeq Acc Id: NP_445808   ⟸   NM_053356
- Peptide Label: precursor
- UniProtKB: A0A0G2KAN1 (UniProtKB/TrEMBL),   F1LS40 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000075459   ⟸   ENSRNOT00000089292
Ensembl Acc Id: ENSRNOP00000016423   ⟸   ENSRNOT00000016423
Ensembl Acc Id: ENSRNOP00000073398   ⟸   ENSRNOT00000087619
Ensembl Acc Id: ENSRNOP00000069327   ⟸   ENSRNOT00000089564
Protein Domains
Fibrillar collagen NC1

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-P02466-F1-model_v2 AlphaFold P02466 1-1372 view protein structure

Transcriptome

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


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:621351 AgrOrtholog
BioCyc Gene G2FUF-45721 BioCyc
Ensembl Genes ENSRNOG00000011292 Ensembl, UniProtKB/TrEMBL
  ENSRNOG00000052925 Ensembl
Ensembl Transcript ENSRNOT00000016423.7 UniProtKB/TrEMBL
  ENSRNOT00000087619.2 UniProtKB/TrEMBL
Gene3D-CATH 2.60.120.1000 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro Collagen UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Collagen_superfamily UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Fib_collagen_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:84352 UniProtKB/Swiss-Prot
NCBI Gene 84352 ENTREZGENE
PANTHER COLLAGEN ALPHA UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ENDOSTATIN DOMAIN-CONTAINING PROTEIN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  FIBRILLAR COLLAGEN NC1 DOMAIN-CONTAINING PROTEIN UniProtKB/TrEMBL
Pfam COLFI UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Collagen UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PharmGKB COL1A2 RGD
PhenoGen Col1a2 PhenoGen
PROSITE NC1_FIB UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
RatGTEx ENSRNOG00000011292 RatGTEx
  ENSRNOG00000052925 RatGTEx
SMART COLFI UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A0G2K5E8_RAT UniProtKB/TrEMBL
  A0A0G2KAN1 ENTREZGENE
  A6K2C0_RAT UniProtKB/TrEMBL
  CO1A2_RAT UniProtKB/Swiss-Prot
  F1LS40 ENTREZGENE, UniProtKB/TrEMBL
  P02466 ENTREZGENE
UniProt Secondary A0A0G2KAN1 UniProtKB/TrEMBL
  Q9R1E8 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2021-03-09 Col1a2  collagen type I alpha 2 chain  NEWGENE_621351  collagen, type I, alpha 2  Data merged from RGD:9452897 737654 PROVISIONAL
2016-06-01 Col1a2  collagen type I alpha 2 chain  Col1a2  collagen, type I, alpha 2  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2014-08-25 NEWGENE_621351  collagen, type I, alpha 2      Symbol and Name status set to provisional 70820 PROVISIONAL
2008-03-10 Col1a2  collagen, type I, alpha 2  Col1a2  procollagen, type I, alpha 2  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2004-12-14 Col1a2  procollagen, type I, alpha 2      Symbol and Name status set to approved 1299863 APPROVED
2002-08-07 Col1a2  procollagen, type I, alpha 2      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_regulation gene transcription was repressed by RFX1 625584
gene_transcript contains a binding site for the DNA methylation-responsive binding protein, regulatory factor for X-box 1 (RFX1) 625584