Col9a3 (collagen type IX alpha 3 chain) - Rat Genome Database

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Gene: Col9a3 (collagen type IX alpha 3 chain) Rattus norvegicus
Analyze
Symbol: Col9a3
Name: collagen type IX alpha 3 chain
RGD ID: 1310255
Description: Predicted to enable protein homodimerization activity. Predicted to be an extracellular matrix structural constituent conferring tensile strength. Predicted to be involved in extracellular matrix organization; female gonad development; and male gonad development. Predicted to be part of collagen type IX trimer. Predicted to be active in basement membrane. Human ortholog(s) of this gene implicated in Stickler syndrome; multiple epiphyseal dysplasia 3; and osteochondrodysplasia. Orthologous to human COL9A3 (collagen type IX alpha 3 chain); PARTICIPATES IN syndecan signaling pathway; INTERACTS WITH 17alpha-ethynylestradiol; amitrole; bisphenol A.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: collagen alpha-3(IX) chain; collagen, type IX, alpha 3; LOC362285; procollagen, type IX, alpha 3
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr83188,089,337 - 188,112,034 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl3188,089,403 - 188,112,270 (+)EnsemblGRCr8
mRatBN7.23167,711,776 - 167,734,468 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl3167,711,840 - 167,734,465 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx3172,092,068 - 172,114,688 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.03181,051,159 - 181,073,783 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.03177,712,766 - 177,735,392 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Dahl_SR_JrHsd3186,698,223 - 186,720,843 (+)NCBIDahl_SR_JrHsd
Lyon_Normotensive3193,559,222 - 193,581,842 (+)NCBILyon_Normotensive
Lyon_Hypertensive3185,529,004 - 185,551,630 (+)NCBILyon_Hypertensive
F344_StmMcwi3166,469,829 - 166,492,449 (+)NCBIF344_StmMcwi
Rnor_6.03176,102,287 - 176,124,839 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl3176,102,351 - 176,124,306 (+)Ensemblrn6Rnor6.0
Rnor_5.03179,803,032 - 179,825,528 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.43169,704,893 - 169,712,492 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera3164,848,089 - 164,870,750 (-)NCBICelera
RGSC_v3.13169,595,025 - 169,618,528 (+)NCBI
Cytogenetic Map3q43NCBI
JBrowse:




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. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
4. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
5. COL9A3: A third locus for multiple epiphyseal dysplasia. Paassilta P, etal., Am J Hum Genet. 1999 Apr;64(4):1036-44.
6. GOA pipeline RGD automated data pipeline
7. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
8. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
9. Comprehensive gene review and curation RGD comprehensive gene curation
Additional References at PubMed
PMID:8660302   PMID:8889548   PMID:11145610   PMID:18448257   PMID:32964953  


Genomics

Comparative Map Data
Col9a3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr83188,089,337 - 188,112,034 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl3188,089,403 - 188,112,270 (+)EnsemblGRCr8
mRatBN7.23167,711,776 - 167,734,468 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl3167,711,840 - 167,734,465 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx3172,092,068 - 172,114,688 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.03181,051,159 - 181,073,783 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.03177,712,766 - 177,735,392 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Dahl_SR_JrHsd3186,698,223 - 186,720,843 (+)NCBIDahl_SR_JrHsd
Lyon_Normotensive3193,559,222 - 193,581,842 (+)NCBILyon_Normotensive
Lyon_Hypertensive3185,529,004 - 185,551,630 (+)NCBILyon_Hypertensive
F344_StmMcwi3166,469,829 - 166,492,449 (+)NCBIF344_StmMcwi
Rnor_6.03176,102,287 - 176,124,839 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl3176,102,351 - 176,124,306 (+)Ensemblrn6Rnor6.0
Rnor_5.03179,803,032 - 179,825,528 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.43169,704,893 - 169,712,492 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera3164,848,089 - 164,870,750 (-)NCBICelera
RGSC_v3.13169,595,025 - 169,618,528 (+)NCBI
Cytogenetic Map3q43NCBI
COL9A3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh382062,816,213 - 62,841,159 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl2062,816,244 - 62,841,163 (+)Ensemblhg38GRCh38
GRCh372061,448,402 - 61,472,511 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 362060,918,859 - 60,942,956 (+)NCBIBuild 36Build 36hg18NCBI36
Build 342060,918,831 - 60,942,955NCBI
Celera2058,124,036 - 58,148,542 (+)NCBICelera
Cytogenetic Map20q13.33NCBI
HuRef2058,166,446 - 58,190,556 (+)NCBIHuRef
CHM1_12061,349,484 - 61,373,428 (+)NCBICHM1_1
T2T-CHM13v2.02064,616,007 - 64,640,720 (+)NCBIT2T-CHM13v2.0
Col9a3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm392180,239,895 - 180,263,985 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl2180,239,583 - 180,263,982 (+)EnsemblGRCm39 EnsemblGRCm39
GRCm382180,598,102 - 180,622,192 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl2180,597,790 - 180,622,189 (+)Ensemblmm10GRCm38
MGSCv372180,332,927 - 180,356,890 (+)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv362180,527,652 - 180,551,593 (+)NCBIMGSCv36mm8
Celera2184,684,058 - 184,708,019 (+)NCBICelera
Cytogenetic Map2H4NCBI
cM Map2103.14NCBI
Col9a3
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555281,286,314 - 1,305,863 (-)Ensembl
ChiLan1.0NW_0049555281,286,314 - 1,305,863 (-)NCBIChiLan1.0ChiLan1.0
COL9A3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v22168,604,201 - 68,629,406 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan12068,597,320 - 68,622,526 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v02059,203,959 - 59,229,221 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.12060,496,269 - 60,522,232 (+)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2060,499,089 - 60,521,871 (+)EnsemblpanPan2panpan1.1
COL9A3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12446,653,400 - 46,669,183 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2446,662,376 - 46,667,884 (+)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha2445,837,732 - 45,853,448 (+)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.02447,526,060 - 47,541,889 (+)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2447,526,108 - 47,541,879 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12446,623,806 - 46,639,485 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02446,747,099 - 46,762,848 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02447,503,126 - 47,518,786 (+)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Col9a3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024408640194,865,544 - 194,887,279 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493651410,320,396 - 10,340,434 (+)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_00493651410,319,187 - 10,340,921 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
COL9A3
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1762,074,855 - 62,093,703 (+)EnsemblsusScr11Sscrofa11.1
Sscrofa11.11762,074,108 - 62,094,228 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
COL9A3
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.121,385,108 - 1,411,960 (-)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366605049,238,887 - 49,266,141 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Col9a3
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462474128,591,529 - 28,610,382 (+)NCBIHetGla 1.0HetGla 1.0hetGla2
Col9a3
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v15157,699,191 - 157,721,262 (+)NCBIRrattus_CSIRO_v1

miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:45
Count of miRNA genes:39
Interacting mature miRNAs:45
Transcripts:ENSRNOT00000013105
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 (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
9589106Insul23Insulin level QTL 2313.860.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)3152055202189428310Rat
1559282Emca5Estrogen-induced mammary cancer QTL 53.9mammary gland integrity trait (VT:0010552)percentage of study population developing mammary tumors during a period of time (CMO:0000948)3145335553189428310Rat
1578653Vnigr3Vascular neointimal growth QTL 33.1artery morphology trait (VT:0002191)artery neointimal hyperplastic lesion area (CMO:0001414)3151075912189428310Rat
1298068Bp167Blood pressure QTL 1670.004arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3161492708189428310Rat
1582256Insul9Insulin level QTL 94.40.0016blood insulin amount (VT:0001560)absolute change in serum insulin level (CMO:0002038)3155759447189428310Rat
1582248Insul7Insulin level QTL 73.90.0041blood insulin amount (VT:0001560)calculated serum insulin level (CMO:0000359)3155759447189428310Rat
1578666Vnigr1Vascular neointimal growth QTL 14.6artery morphology trait (VT:0002191)artery lumen area (CMO:0001409)3151075912189428310Rat
1300161Rf10Renal function QTL 103.57renal blood flow trait (VT:2000006)absolute change in renal vascular resistance (CMO:0001900)3181611379189428310Rat
8552791Vie2Viral induced encephalitis QTL 24.1brain integrity trait (VT:0010579)encephalitis incidence/prevalence measurement (CMO:0002361)3166376089189428310Rat
1578656Vnigr2Vascular neointimal growth QTL 24.2artery morphology trait (VT:0002191)lesioned artery residual lumen area (CMO:0001417)3151075912189428310Rat
631541Bp81Blood pressure QTL 814arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3144575244189428310Rat
1582213Insul6Insulin level QTL 63.70.0009blood insulin amount (VT:0001560)calculated serum insulin level (CMO:0000359)3155759447189428310Rat
1598854Memor10Memory QTL 102exploratory behavior trait (VT:0010471)average horizontal distance between subject and target during voluntary locomotion in an experimental apparatus (CMO:0002674)3166376089189428310Rat

Markers in Region
D3Mco45  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.23167,725,610 - 167,725,829 (+)MAPPERmRatBN7.2
Rnor_6.03176,116,100 - 176,116,318NCBIRnor6.0
Rnor_5.03179,816,789 - 179,817,007UniSTSRnor5.0
RGSC_v3.43169,702,831 - 169,703,623UniSTSRGSC3.4
RGSC_v3.43169,702,831 - 169,703,049UniSTSRGSC3.4
Celera3164,856,721 - 164,856,933UniSTS
Cytogenetic Map3q43UniSTS
PMC15572P1  
Rat AssemblyChrPosition (strand)SourceJBrowse
Celera3164,859,644 - 164,860,278UniSTS
Cytogenetic Map3q43UniSTS


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
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
16 12 66 162 86 85 54 84 54 6 325 183 11 141 64 92 31 17 17

Sequence


Ensembl Acc Id: ENSRNOT00000013105   ⟹   ENSRNOP00000013105
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl3188,089,403 - 188,112,270 (+)Ensembl
mRatBN7.2 Ensembl3167,711,840 - 167,734,465 (+)Ensembl
Rnor_6.0 Ensembl3176,102,351 - 176,124,306 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000153306   ⟹   ENSRNOP00000102380
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl3188,089,403 - 188,112,270 (+)Ensembl
RefSeq Acc Id: NM_001108611   ⟹   NP_001102081
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr83188,089,410 - 188,112,034 (+)NCBI
mRatBN7.23167,711,842 - 167,734,468 (+)NCBI
Dahl_SR_JrHsd3186,698,223 - 186,720,843 (+)NCBI
Lyon_Normotensive3193,559,222 - 193,581,842 (+)NCBI
Lyon_Hypertensive3185,529,004 - 185,551,630 (+)NCBI
F344_StmMcwi3166,469,829 - 166,492,449 (+)NCBI
RefSeq Acc Id: XM_063284234   ⟹   XP_063140304
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr83188,089,337 - 188,109,766 (+)NCBI
Protein Sequences
Protein RefSeqs NP_001102081 (Get FASTA)   NCBI Sequence Viewer  
  XP_063140304 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL88796 (Get FASTA)   NCBI Sequence Viewer  
  EDL88797 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000013105
  ENSRNOP00000013105.7
  ENSRNOP00000102380.1
Ensembl Acc Id: ENSRNOP00000013105   ⟸   ENSRNOT00000013105
RefSeq Acc Id: NP_001102081   ⟸   NM_001108611
- Peptide Label: precursor
- UniProtKB: D3ZX71 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063140304   ⟸   XM_063284234
- Peptide Label: isoform X1
Ensembl Acc Id: ENSRNOP00000102380   ⟸   ENSRNOT00000153306

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZX71-F1-model_v2 AlphaFold D3ZX71 1-680 view protein structure

Transcriptome

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

Promoters
RGD ID:13692748
Promoter ID:EPDNEW_R3264
Type:initiation region
Name:Col9a3_1
Description:collagen type IX alpha 3 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_6.03176,102,308 - 176,102,368EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1310255 AgrOrtholog
BioCyc Gene G2FUF-46326 BioCyc
Ensembl Genes ENSRNOG00000009531 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000013105 ENTREZGENE
  ENSRNOT00000013105.9 UniProtKB/TrEMBL
  ENSRNOT00000153306.1 UniProtKB/TrEMBL
InterPro Collagen UniProtKB/TrEMBL
  Collagen_superfamily UniProtKB/TrEMBL
NCBI Gene 362285 ENTREZGENE
PANTHER COLLAGEN ALPHA UniProtKB/TrEMBL
  COLLAGEN TRIPLE HELIX REPEAT UniProtKB/TrEMBL
Pfam Collagen UniProtKB/TrEMBL
PhenoGen Col9a3 PhenoGen
RatGTEx ENSRNOG00000009531 RatGTEx
UniProt A0ABK0L1V4_RAT UniProtKB/TrEMBL
  D3ZX71 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-07-27 Col9a3  collagen type IX alpha 3 chain  Col9a3  collagen, type IX, alpha 3  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2013-03-20 Col9a3  collagen, type IX, alpha 3  Col9a3  procollagen, type IX, alpha 3  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 Col9a3  procollagen, type IX, alpha 3   Col9a3_predicted  procollagen, type IX, alpha 3 (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Col9a3_predicted  procollagen, type IX, alpha 3 (predicted)      Symbol and Name status set to approved 70820 APPROVED