Col5a1 (collagen type V alpha 1 chain) - Rat Genome Database

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Gene: Col5a1 (collagen type V alpha 1 chain) Rattus norvegicus
Analyze
Symbol: Col5a1
Name: collagen type V alpha 1 chain
RGD ID: 70920
Description: Enables heparin binding activity. Predicted to be involved in several processes, including collagen biosynthetic process; collagen fibril organization; and wound healing, spreading of epidermal cells. Predicted to act upstream of or within several processes, including circulatory system development; skin development; and tendon development. Predicted to be located in basement membrane. Predicted to be part of collagen type V trimer. Predicted to be active in collagen-containing extracellular matrix and extracellular space. Human ortholog(s) of this gene implicated in Ehlers-Danlos syndrome and Ehlers-Danlos syndrome classic type 1. Orthologous to human COL5A1 (collagen type V alpha 1 chain); PARTICIPATES IN syndecan signaling pathway; cell-extracellular matrix signaling pathway; Entamoebiasis pathway; INTERACTS WITH 1-naphthyl isothiocyanate; 17alpha-ethynylestradiol; 17beta-estradiol.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: collagen alpha 1 (V); collagen alpha-1(V) chain; collagen, type V, alpha 1; procollagen, type V, alpha 1
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8331,606,475 - 31,755,097 (+)NCBIGRCr8
mRatBN7.2311,208,429 - 11,356,715 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl311,208,512 - 11,354,588 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx314,276,142 - 14,421,992 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0322,861,404 - 23,007,143 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0321,115,526 - 21,261,367 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.036,430,180 - 6,581,010 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl36,430,201 - 6,578,882 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0311,788,675 - 11,937,880 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.436,826,169 - 6,971,054 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.136,826,468 - 6,971,354 (+)NCBI
Celera36,002,130 - 6,146,263 (+)NCBICelera
Cytogenetic Map3p12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(1->4)-beta-D-glucan  (ISO)
1,2-dimethylhydrazine  (ISO)
1-naphthyl isothiocyanate  (EXP)
17alpha-ethynylestradiol  (EXP,ISO)
17beta-estradiol  (EXP,ISO)
17beta-estradiol 3-benzoate  (EXP)
2,2',4,4'-Tetrabromodiphenyl ether  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,3,7,8-Tetrachlorodibenzofuran  (ISO)
2,4,6-tribromophenol  (ISO)
2,4,6-trinitrobenzenesulfonic acid  (ISO)
2-methylcholine  (ISO)
3,3',5,5'-tetrabromobisphenol A  (ISO)
3-methylcholanthrene  (ISO)
4,4'-diaminodiphenylmethane  (EXP)
4,4'-sulfonyldiphenol  (ISO)
4-hydroxyphenyl retinamide  (ISO)
4-phenylbutyric acid  (ISO)
6-propyl-2-thiouracil  (EXP)
7,12-dimethyltetraphene  (EXP)
acetamide  (EXP)
aconitine  (EXP)
aflatoxin B1  (ISO)
Aflatoxin B2 alpha  (ISO)
alachlor  (EXP)
aldehydo-D-glucose  (ISO)
alendronic acid  (EXP)
all-trans-retinoic acid  (ISO)
alpha-Zearalanol  (EXP)
amphotericin B  (ISO)
aristolochic acid A  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenite(3-)  (ISO)
atrazine  (ISO)
Azoxymethane  (ISO)
benzo[a]pyrene  (ISO)
benzo[e]pyrene  (ISO)
beta-naphthoflavone  (ISO)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP,ISO)
bisphenol AF  (EXP,ISO)
Bisphenol B  (ISO)
bisphenol F  (ISO)
bleomycin A2  (EXP,ISO)
C60 fullerene  (EXP)
cadmium atom  (ISO)
cadmium dichloride  (ISO)
cantharidin  (ISO)
carbon nanotube  (ISO)
CGP 52608  (ISO)
chloroprene  (EXP,ISO)
chromium(6+)  (ISO)
ciglitazone  (EXP)
cisplatin  (ISO)
clobetasol  (ISO)
copper atom  (EXP,ISO)
copper(0)  (EXP,ISO)
crocidolite asbestos  (ISO)
CU-O LINKAGE  (ISO)
curcumin  (ISO)
cyclosporin A  (ISO)
cytarabine  (ISO)
D-glucose  (ISO)
decabromodiphenyl ether  (ISO)
deoxynivalenol  (ISO)
dexamethasone  (EXP,ISO)
dextran sulfate  (ISO)
dimethyl sulfoxide  (EXP)
diquat  (ISO)
disulfiram  (ISO)
diuron  (EXP)
dorsomorphin  (ISO)
doxorubicin  (ISO)
endosulfan  (EXP)
Enterolactone  (ISO)
entinostat  (ISO)
ethanol  (ISO)
flutamide  (EXP)
folic acid  (ISO)
fulvestrant  (ISO)
furan  (EXP)
genistein  (EXP)
gentamycin  (EXP)
glucose  (ISO)
isoprenaline  (ISO)
isotretinoin  (ISO)
methapyrilene  (ISO)
methyl methanesulfonate  (ISO)
methylmercury chloride  (ISO)
miconazole  (ISO)
mono(2-ethylhexyl) phthalate  (ISO)
N,N-diethyl-m-toluamide  (EXP)
N-nitrosodimethylamine  (EXP)
naphthalene  (ISO)
nickel sulfate  (ISO)
oxaliplatin  (EXP)
ozone  (EXP,ISO)
paracetamol  (EXP,ISO)
paraquat  (ISO)
pentane-2,3-dione  (EXP)
perfluorooctane-1-sulfonic acid  (ISO)
perfluorooctanoic acid  (EXP,ISO)
permethrin  (EXP)
PhIP  (EXP)
pirinixic acid  (ISO)
potassium chromate  (ISO)
potassium dichromate  (ISO)
propanal  (ISO)
raloxifene  (EXP)
resveratrol  (ISO)
rotenone  (EXP)
SB 431542  (ISO)
serpentine asbestos  (ISO)
silicon dioxide  (EXP)
simvastatin  (ISO)
sodium arsenite  (ISO)
succimer  (ISO)
sulforaphane  (ISO)
tamoxifen  (ISO)
tert-butyl hydroperoxide  (ISO)
testosterone  (EXP)
testosterone enanthate  (ISO)
tetrachloromethane  (EXP,ISO)
tetradecane  (EXP)
thapsigargin  (ISO)
titanium dioxide  (ISO)
topotecan  (EXP)
trichloroethene  (EXP)
trichostatin A  (ISO)
triclosan  (ISO)
triphenyl phosphate  (EXP)
troglitazone  (ISO)
tunicamycin  (ISO)
valproic acid  (ISO)
vanadium atom  (ISO)
vanadium(0)  (ISO)
vinclozolin  (EXP)
Y-27632  (ISO)
zoledronic acid  (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. COL5A1 exon 14 splice acceptor mutation causes a functional null allele, haploinsufficiency of alpha 1(V) and abnormal heterotypic interstitial fibrils in Ehlers-Danlos syndrome II. Bouma P, etal., J Biol Chem. 2001 Apr 20;276(16):13356-64. Epub 2001 Jan 19.
2. The gene encoding collagen alpha1(V)(COL5A1) is linked to mixed Ehlers-Danlos syndrome type I/II. Burrows NP, etal., J Invest Dermatol 1996 Jun;106(6):1273-6.
3. Schwann cells synthesize type V collagen that contains a novel alpha 4 chain. Molecular cloning, biochemical characterization, and high affinity heparin binding of alpha 4(V) collagen. Chernousov MA, etal., J Biol Chem 2000 Sep 8;275(36):28208-15.
4. 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.
5. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
6. Gene Data Set MGD Curation, June 12, 2002
7. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
8. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
9. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
10. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
11. PID Annotation Import Pipeline Pipeline to import Pathway Interaction Database annotations from NCI into RGD
12. GOA pipeline RGD automated data pipeline
13. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
14. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
15. Comprehensive gene review and curation RGD comprehensive gene curation
16. Order of intron removal influences multiple splice outcomes, including a two-exon skip, in a COL5A1 acceptor-site mutation that results in abnormal pro-alpha1(V) N-propeptides and Ehlers-Danlos syndrome type I. Takahara K, etal., Am J Hum Genet. 2002 Sep;71(3):451-65. Epub 2002 Jul 17.
17. COL5A1 haploinsufficiency is a common molecular mechanism underlying the classical form of EDS. Wenstrup RJ, etal., Am J Hum Genet. 2000 Jun;66(6):1766-76. Epub 2000 Apr 24.
Additional References at PubMed
PMID:2203476   PMID:8900172   PMID:9099729   PMID:9683580   PMID:9822201   PMID:12477932   PMID:14676276   PMID:14970208   PMID:15095409   PMID:15383546   PMID:16431952   PMID:16492673  
PMID:17029294   PMID:17683922   PMID:18305566   PMID:20551380   PMID:21467034   PMID:21713001   PMID:22206666   PMID:23154389   PMID:23376485   PMID:23658023   PMID:24006456   PMID:27068509  
PMID:27559042   PMID:35352799  


Genomics

Comparative Map Data
Col5a1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8331,606,475 - 31,755,097 (+)NCBIGRCr8
mRatBN7.2311,208,429 - 11,356,715 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl311,208,512 - 11,354,588 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx314,276,142 - 14,421,992 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0322,861,404 - 23,007,143 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0321,115,526 - 21,261,367 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.036,430,180 - 6,581,010 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl36,430,201 - 6,578,882 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0311,788,675 - 11,937,880 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.436,826,169 - 6,971,054 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.136,826,468 - 6,971,354 (+)NCBI
Celera36,002,130 - 6,146,263 (+)NCBICelera
Cytogenetic Map3p12NCBI
COL5A1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh389134,641,803 - 134,844,843 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl9134,641,803 - 134,844,843 (+)EnsemblGRCh38hg38GRCh38
GRCh379137,533,649 - 137,736,689 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 369136,673,473 - 136,876,510 (+)NCBINCBI36Build 36hg18NCBI36
Build 349134,759,596 - 134,960,684NCBI
Celera9108,048,806 - 108,251,522 (+)NCBICelera
Cytogenetic Map9q34.3NCBI
HuRef9106,996,262 - 107,200,594 (+)NCBIHuRef
CHM1_19137,682,127 - 137,886,117 (+)NCBICHM1_1
T2T-CHM13v2.09146,859,174 - 147,065,950 (+)NCBIT2T-CHM13v2.0
Col5a1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39227,776,393 - 27,929,522 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl227,776,437 - 27,929,526 (+)EnsemblGRCm39 Ensembl
GRCm38227,886,381 - 28,039,510 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl227,886,425 - 28,039,514 (+)EnsemblGRCm38mm10GRCm38
MGSCv37227,741,945 - 27,895,030 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36227,708,694 - 27,859,533 (+)NCBIMGSCv36mm8
Celera227,589,197 - 27,742,307 (+)NCBICelera
Cytogenetic Map2A3NCBI
cM Map219.38NCBI
Col5a1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555133,533,614 - 3,658,161 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049555133,533,612 - 3,660,605 (+)NCBIChiLan1.0ChiLan1.0
COL5A1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2114,523,306 - 4,731,588 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan194,525,346 - 4,733,918 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v09105,746,388 - 105,956,280 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.19134,391,081 - 134,543,769 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl9134,342,955 - 134,544,651 (+)Ensemblpanpan1.1panPan2
COL5A1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1950,706,852 - 50,856,691 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl950,770,277 - 50,854,728 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha949,989,837 - 50,140,047 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0951,583,512 - 51,733,920 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl951,583,513 - 51,732,204 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1950,343,968 - 50,494,164 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0950,687,121 - 50,838,052 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0950,765,252 - 50,915,697 (+)NCBIUU_Cfam_GSD_1.0
Col5a1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404947200,761,510 - 200,900,677 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049366692,476,818 - 2,580,891 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049366692,474,381 - 2,613,541 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
COL5A1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1273,971,971 - 274,085,111 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11273,934,219 - 274,083,264 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21308,064,240 - 308,174,334 (+)NCBISscrofa10.2Sscrofa10.2susScr3
COL5A1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1123,301,643 - 3,507,300 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl123,301,175 - 3,459,607 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_0236660581,612,962 - 1,827,783 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Col5a1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247602,593,961 - 2,713,772 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247602,593,923 - 2,713,772 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Col5a1
639 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:104
Count of miRNA genes:80
Interacting mature miRNAs:90
Transcripts:ENSRNOT00000012334
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 (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1558647Cm46Cardiac mass QTL 465.40.0000055heart mass (VT:0007028)heart wet weight (CMO:0000069)31077882330356773Rat
1358357Srcrtb1Stress Responsive Cort Basal QTL 16.360.002blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)3865816227494778Rat
6893355Bw101Body weight QTL 1010.40.38body mass (VT:0001259)body weight (CMO:0000012)31077870430357018Rat
4889966Bss95Bone structure and strength QTL 954.4tibia area (VT:1000281)tibia-fibula cross-sectional area (CMO:0001718)3136847613Rat
1558654Bw56Body weight QTL 564.50.0000171body mass (VT:0001259)body weight (CMO:0000012)31077870430357018Rat
10401810Kidm53Kidney mass QTL 53kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)3822719447233430Rat
1298526Arunc3Aerobic running capacity QTL 32.2exercise endurance trait (VT:0002332)maximum distance run on treadmill (CMO:0001406)3822719433703538Rat
8693641Alc30Alcohol consumption QTL 3020.739drinking behavior trait (VT:0001422)calculated ethanol drink intake rate (CMO:0001615)31043430624512004Rat
1558650Cm48Cardiac mass QTL 4840.0001heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)31077882330356773Rat
1358905Hrtrt17Heart rate QTL 175.90.000014heart pumping trait (VT:2000009)heart rate (CMO:0000002)31086191289878372Rat
70191BpQTLcluster4Blood pressure QTL cluster 43arterial blood pressure trait (VT:2000000)absolute change in systolic blood pressure (CMO:0000607)31077870450302886Rat
631545Bp85Blood pressure QTL 853.1arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3133278763Rat
631679Cm10Cardiac mass QTL 107.340.0001heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)3131158234Rat
2290452Scl56Serum cholesterol level QTL 562.26blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)3191609953Rat
1558657Cm43Cardiac mass QTL 436.63e-08heart mass (VT:0007028)heart wet weight (CMO:0000069)31077882330356773Rat
631568Bp92Blood pressure QTL 922.20.005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3139874793Rat
70203Gcr2Gastric cancer resistance QTL 22.6stomach morphology trait (VT:0000470)stomach tumor susceptibility score (CMO:0002043)3865816227494778Rat
6893363Bw105Body weight QTL 1052.60.0036body mass (VT:0001259)body weight (CMO:0000012)31077870430357018Rat
70202Alc19Alcohol consumption QTL 192.5drinking behavior trait (VT:0001422)ethanol intake volume to total fluid intake volume ratio (CMO:0001591)3127494778Rat
2312664Scl62Serum cholesterol level QTL 620.05blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)3138710544Rat
61468Bp15Blood pressure QTL 154.4blood pressure trait (VT:0000183)pulse pressure (CMO:0000292)3133278763Rat
631831Alc8Alcohol consumption QTL 82.7consumption behavior trait (VT:0002069)calculated ethanol drink intake rate (CMO:0001615)3133230976Rat

Markers in Region
RH128099  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2311,355,049 - 11,355,252 (+)MAPPERmRatBN7.2
Rnor_6.036,579,338 - 6,579,540NCBIRnor6.0
Rnor_5.0311,936,213 - 11,936,415UniSTSRnor5.0
RGSC_v3.436,971,516 - 6,971,718UniSTSRGSC3.4
Celera36,146,725 - 6,146,927UniSTS
RH 3.4 Map319.2UniSTS
Cytogenetic Map3p12UniSTS
RH139630  
Rat AssemblyChrPosition (strand)SourceJBrowse
GRCr8331,734,668 - 31,735,039 (+)Marker Load Pipeline
mRatBN7.2311,336,631 - 11,337,002 (+)MAPPERmRatBN7.2
Rnor_6.036,560,920 - 6,561,290NCBIRnor6.0
Rnor_5.0311,917,795 - 11,918,165UniSTSRnor5.0
RGSC_v3.436,953,098 - 6,953,468UniSTSRGSC3.4
Celera36,128,250 - 6,128,620UniSTS
Cytogenetic Map3p12UniSTS


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 11 49 113 91 90 59 25 59 6 218 97 93 45 60 31

Sequence


Ensembl Acc Id: ENSRNOT00000012334   ⟹   ENSRNOP00000012334
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl311,208,835 - 11,354,588 (+)Ensembl
Rnor_6.0 Ensembl36,430,589 - 6,578,882 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000086352   ⟹   ENSRNOP00000070132
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl311,208,512 - 11,347,485 (+)Ensembl
Rnor_6.0 Ensembl36,430,201 - 6,571,377 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000110258   ⟹   ENSRNOP00000084311
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl311,240,164 - 11,354,588 (+)Ensembl
RefSeq Acc Id: NM_134452   ⟹   NP_604447
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8331,606,880 - 31,752,625 (+)NCBI
mRatBN7.2311,208,837 - 11,354,588 (+)NCBI
Rnor_6.036,430,591 - 6,578,876 (+)NCBI
Rnor_5.0311,788,675 - 11,937,880 (+)NCBI
RGSC_v3.436,826,169 - 6,971,054 (+)RGD
Celera36,002,130 - 6,146,263 (+)RGD
Sequence:
RefSeq Acc Id: XM_006233873   ⟹   XP_006233935
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8331,606,475 - 31,755,097 (+)NCBI
mRatBN7.2311,208,429 - 11,356,715 (+)NCBI
Rnor_6.036,430,180 - 6,581,010 (+)NCBI
Rnor_5.0311,788,675 - 11,937,880 (+)NCBI
Sequence:
RefSeq Acc Id: XM_063284748   ⟹   XP_063140818
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8331,616,994 - 31,755,097 (+)NCBI
RefSeq Acc Id: NP_604447   ⟸   NM_134452
- Peptide Label: precursor
- UniProtKB: Q9JI03 (UniProtKB/Swiss-Prot),   A6JTM0 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006233935   ⟸   XM_006233873
- Peptide Label: isoform X1
- Sequence:
Ensembl Acc Id: ENSRNOP00000012334   ⟸   ENSRNOT00000012334
Ensembl Acc Id: ENSRNOP00000070132   ⟸   ENSRNOT00000086352
Ensembl Acc Id: ENSRNOP00000084311   ⟸   ENSRNOT00000110258
RefSeq Acc Id: XP_063140818   ⟸   XM_063284748
- Peptide Label: isoform X2
- UniProtKB: A0A8I6GA68 (UniProtKB/TrEMBL)
Protein Domains
Fibrillar collagen NC1   Laminin G-like

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q9JI03-F1-model_v2 AlphaFold Q9JI03 1-1840 view protein structure

Transcriptome

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

Promoters
RGD ID:13691952
Promoter ID:EPDNEW_R2453
Type:initiation region
Name:Col5a1_1
Description:collagen type V 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_6.036,430,230 - 6,430,290EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:70920 AgrOrtholog
BioCyc Gene G2FUF-50287 BioCyc
Ensembl Genes ENSRNOG00000008749 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000012334.8 UniProtKB/TrEMBL
  ENSRNOT00000086352.2 UniProtKB/TrEMBL
  ENSRNOT00000110258.1 UniProtKB/TrEMBL
Gene3D-CATH 2.60.120.1000 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  2.60.120.200 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro Collagen UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Collagen_superfamily UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ConA-like_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Fib_collagen_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Laminin_G UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TSPN-like_N UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:85490 UniProtKB/Swiss-Prot
NCBI Gene 85490 ENTREZGENE
PANTHER COLLAGEN ALPHA UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  COLLAGEN ALPHA-4(IV) CHAIN-LIKE UniProtKB/Swiss-Prot
  COLLAGEN TRIPLE HELIX REPEAT UniProtKB/TrEMBL
  COLLAGEN TYPE III, PUTATIVE-RELATED UniProtKB/TrEMBL
Pfam COLFI UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Collagen UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Laminin_G_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Col5a1 PhenoGen
PROSITE NC1_FIB UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
RatGTEx ENSRNOG00000008749 RatGTEx
SMART COLFI UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  LamG UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TSPN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF49899 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A0G2JX47_RAT UniProtKB/TrEMBL
  A0A8I6GA68 ENTREZGENE, UniProtKB/TrEMBL
  A6JTM0 ENTREZGENE, UniProtKB/TrEMBL
  CO5A1_RAT UniProtKB/Swiss-Prot
  G3V763 ENTREZGENE, UniProtKB/TrEMBL
  Q9JI03 ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-07-27 Col5a1  collagen type V alpha 1 chain  Col5a1  collagen, type V, alpha 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-25 Col5a1  collagen, type V, alpha 1  Col5a1  procollagen, type V, alpha 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-30 Col5a1  procollagen, type V, alpha 1    collagen, type V, alpha 1  Name updated 1299863 APPROVED
2002-07-09 Col5a1  collagen, type V, alpha 1      Symbol and Name updated to reflect Human and Mouse nomenclature 70877 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_function binds heparin with high affinity 70693