Col5a3 (collagen, type V, alpha 3) - Rat Genome Database

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Gene: Col5a3 (collagen, type V, alpha 3) Mus musculus
Analyze
Symbol: Col5a3
Name: collagen, type V, alpha 3
RGD ID: 731805
MGI Page MGI
Description: Exhibits heparin binding activity. Involved in cell-matrix adhesion. Localizes to collagen type V trimer. Is expressed in several structures, including bone; embryo mesenchyme; extraembryonic component; placenta; and tongue. Orthologous to human COL5A3 (collagen type V alpha 3 chain); PARTICIPATES IN cell-extracellular matrix signaling pathway; Entamoebiasis pathway; INTERACTS WITH 1,2-dichloroethane; 1,2-dimethylhydrazine; 2,3,7,8-tetrachlorodibenzodioxine.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: collagen alpha-3(V) chain; Pro-alpha3(V); procollagen, type V, alpha 3
RGD Orthologs
Human
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: GRCm38 - Mouse Genome Assembly GRCm38
Position:
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39920,681,353 - 20,726,363 (-)NCBIGRCm39mm39
GRCm39 Ensembl920,681,346 - 20,726,363 (-)Ensembl
GRCm38920,770,050 - 20,815,117 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl920,770,050 - 20,815,067 (-)EnsemblGRCm38mm10GRCm38
MGSCv37920,574,494 - 20,619,478 (-)NCBIGRCm37mm9NCBIm37
MGSCv36920,520,452 - 20,565,436 (-)NCBImm8
Celera918,038,765 - 18,083,744 (-)NCBICelera
Cytogenetic Map9A3NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
1,2-dichloroethane  (EXP)
1,2-dimethylhydrazine  (EXP)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2-butoxyethanol  (EXP)
4,4'-sulfonyldiphenol  (ISO)
4-\{[(5,5,8,8-tetramethyl-5,6,7,8-tetrahydronaphthalen-2-yl)carbonyl]amino\}benzoic acid  (ISO)
4-hydroxyphenyl retinamide  (EXP)
6-propyl-2-thiouracil  (ISO)
7,12-dimethyltetraphene  (ISO)
acetamide  (ISO)
aflatoxin B2  (ISO)
all-trans-retinoic acid  (EXP)
antirheumatic drug  (ISO)
arsenite(3-)  (EXP)
benzo[a]pyrene  (EXP,ISO)
benzo[b]fluoranthene  (EXP)
Benzo[ghi]perylene  (EXP)
bisphenol A  (EXP,ISO)
bisphenol F  (EXP)
carbon nanotube  (EXP)
carmustine  (ISO)
chrysene  (EXP)
cisplatin  (ISO)
dexamethasone  (ISO)
dibenz[a,h]anthracene  (EXP)
diethylstilbestrol  (ISO)
diuron  (ISO)
dorsomorphin  (ISO)
doxorubicin  (ISO)
endosulfan  (ISO)
entinostat  (ISO)
fenvalerate  (ISO)
furan  (EXP,ISO)
methotrexate  (ISO)
methyl methanesulfonate  (ISO)
mifepristone  (ISO)
N-methyl-N-nitrosourea  (ISO)
naphthalene  (EXP)
nitric oxide  (EXP)
panobinostat  (ISO)
paracetamol  (EXP)
pentane-2,3-dione  (ISO)
perfluorooctanoic acid  (ISO)
phenobarbital  (EXP)
pirinixic acid  (EXP)
potassium dichromate  (EXP)
S-butyl-DL-homocysteine (S,R)-sulfoximine  (EXP)
SB 431542  (ISO)
silver atom  (EXP)
silver(0)  (EXP)
Soman  (ISO)
testosterone  (ISO)
tetrachloroethene  (EXP)
tetrachloromethane  (EXP)
tetraphene  (EXP)
tioguanine  (ISO)
titanium dioxide  (EXP)
trichostatin A  (ISO)
triclosan  (ISO)
trimellitic anhydride  (EXP)
tungsten  (EXP)
undecane  (ISO)
valproic acid  (EXP,ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Pathway Annotations     Click to see Annotation Detail View
References

Additional References at PubMed
PMID:10722718   PMID:10922068   PMID:12477932   PMID:12819125   PMID:15136578   PMID:15345741   PMID:15872058   PMID:15908193   PMID:16537572   PMID:18287559   PMID:19906978   PMID:20059976  
PMID:20206127   PMID:20424664   PMID:21267068   PMID:21293061   PMID:21873635   PMID:21888903   PMID:22159717   PMID:22214369   PMID:28071719   PMID:28102194   PMID:30840660  


Genomics

Comparative Map Data
Col5a3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39920,681,353 - 20,726,363 (-)NCBIGRCm39mm39
GRCm39 Ensembl920,681,346 - 20,726,363 (-)Ensembl
GRCm38920,770,050 - 20,815,117 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl920,770,050 - 20,815,067 (-)EnsemblGRCm38mm10GRCm38
MGSCv37920,574,494 - 20,619,478 (-)NCBIGRCm37mm9NCBIm37
MGSCv36920,520,452 - 20,565,436 (-)NCBImm8
Celera918,038,765 - 18,083,744 (-)NCBICelera
Cytogenetic Map9A3NCBI
COL5A3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl199,959,561 - 10,010,504 (-)EnsemblGRCh38hg38GRCh38
GRCh38199,959,561 - 10,010,532 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh371910,070,237 - 10,121,180 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36199,931,237 - 9,982,147 (-)NCBINCBI36hg18NCBI36
Build 34199,931,236 - 9,982,147NCBI
Celera199,965,704 - 10,016,619 (-)NCBI
Cytogenetic Map19p13.2NCBI
HuRef199,650,383 - 9,701,624 (-)NCBIHuRef
CHM1_11910,069,976 - 10,120,955 (-)NCBICHM1_1
Col5a3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2819,304,564 - 19,349,809 (-)NCBI
Rnor_6.0 Ensembl821,786,324 - 21,831,668 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0821,786,324 - 21,831,751 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0821,842,413 - 21,887,757 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4819,789,061 - 19,834,241 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1819,789,060 - 19,834,241 (-)NCBI
Celera820,699,885 - 20,745,065 (-)NCBICelera
Cytogenetic Map8q13NCBI
Col5a3
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_0049554951,347,171 - 1,386,683 (-)NCBIChiLan1.0ChiLan1.0
COL5A3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11910,173,669 - 10,219,487 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1910,174,519 - 10,218,974 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0199,512,028 - 9,563,306 (-)NCBIMhudiblu_PPA_v0panPan3
COL5A3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12051,037,604 - 51,075,220 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2051,037,621 - 51,074,993 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2050,904,135 - 50,941,637 (+)NCBI
ROS_Cfam_1.02051,559,592 - 51,597,067 (+)NCBI
UMICH_Zoey_3.12050,767,386 - 50,804,867 (+)NCBI
UNSW_CanFamBas_1.02051,194,321 - 51,231,828 (+)NCBI
UU_Cfam_GSD_1.02051,435,361 - 51,472,809 (+)NCBI
Col5a3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405118209,916,821 - 209,952,872 (+)NCBI
SpeTri2.0NW_004936659401,834 - 437,896 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
COL5A3
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl268,827,562 - 68,869,884 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1268,828,197 - 68,869,914 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2269,156,853 - 69,193,735 (-)NCBISscrofa10.2Sscrofa10.2susScr3
COL5A3
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.169,033,298 - 9,092,061 (-)NCBI
ChlSab1.1 Ensembl69,033,287 - 9,091,826 (-)Ensembl
Col5a3
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248282,216,179 - 2,254,868 (-)NCBI

Position Markers
Col5a3  
Mouse AssemblyChrPosition (strand)SourceJBrowse
MGSCv37920,580,004 - 20,580,289UniSTSGRCm37
Celera918,044,275 - 18,044,560UniSTS
Cytogenetic Map9A3UniSTS
cM Map9 UniSTS
Col5a3  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm38920,775,560 - 20,775,845UniSTSGRCm38
MGSCv37920,580,004 - 20,580,289UniSTSGRCm37
Celera918,044,275 - 18,044,560UniSTS
Cytogenetic Map9A3UniSTS
cM Map9 UniSTS


QTLs in Region (GRCm38)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
4142326Tgq19_mtriglyceride QTL 19 (mouse)Not determined121060750Mouse
1300899Chol6_mcholesterol 6 (mouse)Not determined9129902908Mouse
13434920Dcollq1_mdifferential colonization level QTL 1 (mouse)9130430544Mouse
35673312Ari7_mantibody response to influenza 7, day 45, IgG3 (mouse)9780000022300000Mouse
1300849Sles4_msystemic lupus erythmatosus suppressor 4 (mouse)Not determined9910756137395074Mouse
13504833Bglu19_mblood glucose level 19 (mouse)9999947243999472Mouse
1300532Tbs2_mtuberculosis severity 2 (mouse)Not determined91245867446458818Mouse
10043917Obq37_mobesity QTL 37 (mouse)Not determined91347987947479879Mouse
1357637Si5lq2_mserum IGFBP-5 level QTL 2 (mouse)Not determined91550045549500594Mouse
4141447Cfmq2_mcystic fibrosis modifier QTL 2 (mouse)Not determined91550045549500594Mouse
4141591Cq4_mcholesterol QTL 4 (mouse)Not determined91550045549500594Mouse
1301421Lgth4_mbody length 4 (mouse)Not determined91550045549500594Mouse
11354951Pdcc3_mplasmacytoid dentritic cell compartment 3 (mouse)91583833149838331Mouse
12790993Adq1_maortic diameter QTL 1 (mouse)91583833149838331Mouse
12790997Adq2_maortic diameter QTL 2 (mouse)91583833149838331Mouse
12880415V125Dq7_mvitamin D active form serum level QTL 7 (mouse)91610000050100000Mouse
12880416V125Dq8_mvitamin D active form serum level QTL 8 (mouse)91610000050100000Mouse
13504834Hdlq109_mHDL QTL 109 (mouse)91679834550798345Mouse
1357465Vtbt6_mvertebral trabecular bone trait 6 (mouse)Not determined91706754451067647Mouse
1300643Pvcan2_mprotection against vaginal candidiasis 2 (mouse)Not determined92003211054032229Mouse
1301439Morph2_mmorphine antinociception 2 (mouse)Not determined92024206654242196Mouse
1301045Sluc10_msusceptibility to lung cancer 10 (mouse)Not determined92039490154395074Mouse
1301883Skull12_mskull morphology 12 (mouse)Not determined92039490154395074Mouse
4142352Lmr17_mleishmaniasis resistance 17 (mouse)Not determined92039490154395074Mouse
10043950Pbft5_mpercent body fat 5 (mouse)Not determined92039490154395074Mouse

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:604
Count of miRNA genes:354
Interacting mature miRNAs:402
Transcripts:ENSMUST00000004201, ENSMUST00000145974
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.


Expression


Sequence


Reference Sequences
RefSeq Acc Id: ENSMUST00000004201   ⟹   ENSMUSP00000004201
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38.p6 Ensembl920,770,050 - 20,815,067 (-)Ensembl
RefSeq Acc Id: ENSMUST00000145974
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38.p6 Ensembl920,782,794 - 20,815,067 (-)Ensembl
RefSeq Acc Id: NM_001317388   ⟹   NP_001304317
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39920,681,353 - 20,726,363 (-)NCBI
GRCm38920,770,057 - 20,815,067 (-)NCBI
Sequence:
RefSeq Acc Id: NM_016919   ⟹   NP_058615
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39920,681,353 - 20,726,363 (-)NCBI
GRCm38920,770,057 - 20,815,067 (-)NCBI
MGSCv37920,574,494 - 20,619,478 (-)RGD
Celera918,038,765 - 18,083,744 (-)RGD
cM Map9 ENTREZGENE
Sequence:
Reference Sequences
RefSeq Acc Id: NP_058615   ⟸   NM_016919
- Peptide Label: isoform 1 precursor
- UniProtKB: Q9JLI2 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: NP_001304317   ⟸   NM_001317388
- Peptide Label: isoform 2 precursor
- UniProtKB: Q9JLI2 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSMUSP00000004201   ⟸   ENSMUST00000004201
Promoters
RGD ID:6844347
Promoter ID:MM_KWN:56526
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:3T3L1_Day1,   3T3L1_Day3,   MEF_B4,   MEF_B6
Transcripts:OTTMUST00000053292,   OTTMUST00000053293
Position:
Mouse AssemblyChrPosition (strand)Source
MGSCv36920,619,186 - 20,619,686 (-)MPROMDB
RGD ID:8668890
Promoter ID:EPDNEW_M12476
Type:initiation region
Name:Col5a3_1
Description:Mus musculus collagen, type V, alpha 3 , transcript variant 1,mRNA.
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38920,815,055 - 20,815,115EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene MGI:1858212 AgrOrtholog
Ensembl Genes ENSMUSG00000004098 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSMUSP00000004201 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSMUST00000004201 ENTREZGENE, UniProtKB/TrEMBL
InterPro Collagen UniProtKB/TrEMBL
  ConA-like_subgrp UniProtKB/TrEMBL
  Fib_collagen_C UniProtKB/TrEMBL
  Laminin_G UniProtKB/TrEMBL
KEGG Report mmu:53867 UniProtKB/TrEMBL
MGD MGI:1858212 ENTREZGENE
NCBI Gene 53867 ENTREZGENE
Pfam COLFI UniProtKB/TrEMBL
  Collagen UniProtKB/TrEMBL
  Laminin_G_2 UniProtKB/TrEMBL
PhenoGen Col5a3 PhenoGen
PROSITE LAM_G_DOMAIN UniProtKB/TrEMBL
  NC1_FIB UniProtKB/TrEMBL
SMART COLFI UniProtKB/TrEMBL
  TSPN UniProtKB/TrEMBL
Superfamily-SCOP ConA_like_lec_gl UniProtKB/TrEMBL
UniProt A1A4B3_MOUSE UniProtKB/TrEMBL
  Q920S4_MOUSE UniProtKB/TrEMBL
  Q9JLI2 ENTREZGENE, UniProtKB/TrEMBL