COL9A3 (collagen type IX alpha 3 chain) - Rat Genome Database

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Gene: COL9A3 (collagen type IX alpha 3 chain) Pan paniscus
Analyze
Symbol: COL9A3
Name: collagen type IX alpha 3 chain
RGD ID: 11899928
Description: ENCODES a protein that exhibits extracellular matrix structural constituent conferring tensile strength (inferred); protein homodimerization activity (inferred); INVOLVED IN female gonad development (ortholog); male gonad development (ortholog); PARTICIPATES IN syndecan signaling pathway; ASSOCIATED WITH Autoinflammation, Immune Dysregulation, and Eosinophilia (ortholog); autosomal dominant nocturnal frontal lobe epilepsy (ortholog); benign familial infantile seizures 6 (ortholog); FOUND IN collagen type IX trimer (ortholog)
Type: protein-coding
RefSeq Status: MODEL
Previously known as: collagen alpha-3(IX) chain
RGD Orthologs
Human
Mouse
Rat
Chinchilla
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Mhudiblu_PPA_v0 - Bonobo Mhudiblu_PPA_v0 Assembly
Position:
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 (+)Ensemblpanpan1.1panPan2
JBrowse: View Region in Genome Browser (JBrowse)
Model


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
Additional References at PubMed
PMID:30032202  


Genomics

Comparative Map Data
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 (+)Ensemblpanpan1.1panPan2
COL9A3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh382062,816,213 - 62,841,159 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl2062,816,244 - 62,841,159 (+)EnsemblGRCh38hg38GRCh38
GRCh372061,448,402 - 61,472,511 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 362060,918,859 - 60,942,956 (+)NCBINCBI36Build 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 Ensembl
GRCm382180,598,102 - 180,622,192 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl2180,597,790 - 180,622,189 (+)EnsemblGRCm38mm10GRCm38
MGSCv372180,332,927 - 180,356,890 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv362180,527,652 - 180,551,593 (+)NCBIMGSCv36mm8
Celera2184,684,058 - 184,708,019 (+)NCBICelera
Cytogenetic Map2H4NCBI
cM Map2103.14NCBI
Col9a3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr83188,089,337 - 188,112,034 (+)NCBIGRCr8
mRatBN7.23167,711,776 - 167,734,468 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl3167,711,840 - 167,734,465 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx3172,092,068 - 172,114,688 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.03181,051,159 - 181,073,783 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.03177,712,766 - 177,735,392 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.03176,102,287 - 176,124,839 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl3176,102,351 - 176,124,306 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.03179,803,032 - 179,825,528 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.43169,704,893 - 169,712,492 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.13169,595,025 - 169,618,528 (+)NCBI
Celera3164,848,089 - 164,870,750 (-)NCBICelera
Cytogenetic Map3q43NCBI
Col9a3
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_0049555281,286,314 - 1,305,863 (-)NCBIChiLan1.0ChiLan1.0
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 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2445,837,732 - 45,853,448 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02447,526,060 - 47,541,889 (+)NCBIROS_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_1.0
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
SpeTri2.0NW_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 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
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_female_1.0HetGla 1.0hetGla2


Expression


Sequence

Nucleotide Sequences
RefSeq Transcripts XM_034947754 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide JARIFH020000021 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSPPAT00000039489   ⟹   ENSPPAP00000016791
Type: CODING
Position:
Bonobo AssemblyChrPosition (strand)Source
PanPan1.1 Ensembl2060,499,089 - 60,521,871 (+)Ensembl
RefSeq Acc Id: XM_034947754   ⟹   XP_034803645
Type: CODING
Position:
Bonobo AssemblyChrPosition (strand)Source
NHGRI_mPanPan1-v22168,604,201 - 68,629,406 (+)NCBI
NHGRI_mPanPan12068,597,320 - 68,622,526 (+)NCBI
Mhudiblu_PPA_v02059,203,959 - 59,229,221 (+)NCBI
Protein Sequences
Protein RefSeqs XP_034803645 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSPPAP00000016791.1
Reference Protein Sequences
RefSeq Acc Id: XP_034803645   ⟸   XM_034947754
RefSeq Acc Id: ENSPPAP00000016791   ⟸   ENSPPAT00000039489


Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSPPAG00000031491 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSPPAT00000039489.1 UniProtKB/TrEMBL
InterPro Collagen UniProtKB/TrEMBL
NCBI Gene COL9A3 ENTREZGENE
PANTHER COLLAGEN ALPHA UniProtKB/TrEMBL
  ZGC:113232 UniProtKB/TrEMBL
Pfam Collagen UniProtKB/TrEMBL
UniProt A0A2R9AHG9_PANPA UniProtKB/TrEMBL