OR4D9 (olfactory receptor family 4 subfamily D member 9) - Rat Genome Database

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Gene: OR4D9 (olfactory receptor family 4 subfamily D member 9) Homo sapiens
Analyze
Symbol: OR4D9
Name: olfactory receptor family 4 subfamily D member 9
RGD ID: 1606644
HGNC Page HGNC:15178
Description: Predicted to enable olfactory receptor activity. Predicted to be involved in G protein-coupled receptor signaling pathway and detection of chemical stimulus involved in sensory perception of smell. Predicted to be located in plasma membrane.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: olfactory receptor 4D9; olfactory receptor OR11-253; olfactory receptor, family 4, subfamily D, member 9 pseudogene; OR11-253
RGD Orthologs
Mouse
Rat
Bonobo
Dog
Pig
Green Monkey
Alliance Orthologs
More Info more info ...
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381159,511,539 - 59,520,703 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1159,511,368 - 59,520,703 (+)EnsemblGRCh38hg38GRCh38
GRCh371159,279,012 - 59,288,176 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361159,038,962 - 59,039,906 (+)NCBINCBI36Build 36hg18NCBI36
Celera1156,645,048 - 56,645,992 (+)NCBICelera
Cytogenetic Map11q12.1NCBI
HuRef1155,630,217 - 55,631,161 (+)NCBIHuRef
CHM1_11159,148,162 - 59,149,106 (+)NCBICHM1_1
T2T-CHM13v2.01159,462,418 - 59,471,582 (+)NCBIT2T-CHM13v2.0
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
Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
membrane  (IEA)
plasma membrane  (IBA,IEA)

Molecular Function

Phenotype Annotations     Click to see Annotation Detail View

Human Phenotype
References

References - curated
# Reference Title Reference Citation
1. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:14983052   PMID:16554811   PMID:21873635  


Genomics

Comparative Map Data
OR4D9
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381159,511,539 - 59,520,703 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1159,511,368 - 59,520,703 (+)EnsemblGRCh38hg38GRCh38
GRCh371159,279,012 - 59,288,176 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361159,038,962 - 59,039,906 (+)NCBINCBI36Build 36hg18NCBI36
Celera1156,645,048 - 56,645,992 (+)NCBICelera
Cytogenetic Map11q12.1NCBI
HuRef1155,630,217 - 55,631,161 (+)NCBIHuRef
CHM1_11159,148,162 - 59,149,106 (+)NCBICHM1_1
T2T-CHM13v2.01159,462,418 - 59,471,582 (+)NCBIT2T-CHM13v2.0
Or4d10
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391912,051,059 - 12,051,994 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1912,050,598 - 12,055,095 (-)EnsemblGRCm39 Ensembl
GRCm381912,073,695 - 12,074,630 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1912,073,234 - 12,077,731 (-)EnsemblGRCm38mm10GRCm38
MGSCv371912,148,185 - 12,149,120 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361912,140,740 - 12,141,675 (-)NCBIMGSCv36mm8
Celera1912,771,072 - 12,772,007 (-)NCBICelera
Cytogenetic Map19ANCBI
cM Map198.59NCBI
Or4d10
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81218,422,033 - 218,422,968 (-)NCBIGRCr8
mRatBN7.21208,997,300 - 208,998,235 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1208,996,643 - 209,001,372 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1217,371,960 - 217,372,895 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01224,348,157 - 224,349,092 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01217,126,396 - 217,127,331 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01228,504,037 - 228,541,080 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1228,504,145 - 228,505,080 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01235,568,408 - 235,569,343 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41214,920,362 - 214,921,297 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11215,078,791 - 215,079,727 (-)NCBI
Celera1206,463,455 - 206,464,390 (-)NCBICelera
Cytogenetic Map1q43NCBI
LOC100973708
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2960,643,705 - 60,652,969 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11161,686,836 - 61,696,086 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01154,741,306 - 54,742,254 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11158,192,150 - 58,193,094 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1158,192,150 - 58,193,094 (+)Ensemblpanpan1.1panPan2
OR4D9
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11837,225,144 - 37,226,200 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1837,224,676 - 37,226,079 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1836,874,544 - 36,875,479 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01837,865,404 - 37,866,339 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1837,864,936 - 37,866,339 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11837,455,185 - 37,456,120 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01837,031,292 - 37,032,227 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01837,660,906 - 37,661,841 (-)NCBIUU_Cfam_GSD_1.0
LOC110258207
(Sus scrofa - pig)		 No map positions available.
LOC103234916
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1114,087,060 - 14,122,985 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl114,087,468 - 14,088,409 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_023666038111,414,895 - 111,415,868 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0

Variants

.
Variants in OR4D9
12 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
Single allele deletion Intellectual disability [RCV001293382] Chr11:118359328..118372573 [GRCh37]
Chr11:11p15.3-q23.3		 pathogenic
GRCh37/hg19 11p15.5-q25(chr11:230616-134938470) copy number gain See cases [RCV000511729] Chr11:230616..134938470 [GRCh37]
Chr11:11p15.5-q25		 pathogenic
GRCh37/hg19 11p15.5-q25(chr11:230616-134938470)x3 copy number gain See cases [RCV000510881] Chr11:230616..134938470 [GRCh37]
Chr11:11p15.5-q25		 pathogenic
GRCh37/hg19 11q12.1-12.3(chr11:58935215-62177656)x3 copy number gain not provided [RCV000683362] Chr11:58935215..62177656 [GRCh37]
Chr11:11q12.1-12.3		 likely pathogenic
GRCh37/hg19 11p15.5-q25(chr11:198510-134934063)x3 copy number gain not provided [RCV000737348] Chr11:198510..134934063 [GRCh37]
Chr11:11p15.5-q25		 pathogenic
GRCh37/hg19 11p15.5-q25(chr11:70864-134938470)x3 copy number gain not provided [RCV000749874] Chr11:70864..134938470 [GRCh37]
Chr11:11p15.5-q25		 pathogenic
NM_001004711.2(OR4D9):c.106A>G (p.Met36Val) single nucleotide variant not specified [RCV004314627] Chr11:59515018 [GRCh38]
Chr11:59282491 [GRCh37]
Chr11:11q12.1		 uncertain significance
NM_001004711.2(OR4D9):c.322G>T (p.Gly108Trp) single nucleotide variant not specified [RCV004321402] Chr11:59515234 [GRCh38]
Chr11:59282707 [GRCh37]
Chr11:11q12.1		 uncertain significance
NC_000011.9:g.(?_58916346)_(64972349_?)dup duplication Leukocyte adhesion deficiency 3 [RCV003113394]|not provided [RCV003113393] Chr11:58916346..64972349 [GRCh37]
Chr11:11q12.1-13.1		 uncertain significance|no classifications from unflagged records
GRCh37/hg19 11p13-q25(chr11:32799481-134938470)x3 copy number gain MISSED ABORTION [RCV002282973] Chr11:32799481..134938470 [GRCh37]
Chr11:11p13-q25		 pathogenic
GRCh37/hg19 11p11.2-q12.2(chr11:51581311-54891247)x3 copy number gain See cases [RCV002286338] Chr11:51581311..54891247 [GRCh37]
Chr11:11p11.2-q12.2		 pathogenic
NM_001004711.2(OR4D9):c.163C>A (p.Leu55Ile) single nucleotide variant not specified [RCV004294864] Chr11:59515075 [GRCh38]
Chr11:59282548 [GRCh37]
Chr11:11q12.1		 uncertain significance
NM_001004711.2(OR4D9):c.175A>G (p.Met59Val) single nucleotide variant not specified [RCV004141267] Chr11:59515087 [GRCh38]
Chr11:59282560 [GRCh37]
Chr11:11q12.1		 uncertain significance
NM_001004711.2(OR4D9):c.388C>G (p.Leu130Val) single nucleotide variant not specified [RCV004154836] Chr11:59515300 [GRCh38]
Chr11:59282773 [GRCh37]
Chr11:11q12.1		 uncertain significance
NM_001004711.2(OR4D9):c.371T>C (p.Ile124Thr) single nucleotide variant not specified [RCV004123205] Chr11:59515283 [GRCh38]
Chr11:59282756 [GRCh37]
Chr11:11q12.1		 uncertain significance
NM_001004711.2(OR4D9):c.775G>A (p.Ala259Thr) single nucleotide variant not specified [RCV004177036] Chr11:59515687 [GRCh38]
Chr11:59283160 [GRCh37]
Chr11:11q12.1		 uncertain significance
NM_001004711.2(OR4D9):c.334G>T (p.Val112Phe) single nucleotide variant not specified [RCV004170673] Chr11:59515246 [GRCh38]
Chr11:59282719 [GRCh37]
Chr11:11q12.1		 uncertain significance
NM_001004711.2(OR4D9):c.266C>A (p.Thr89Lys) single nucleotide variant not specified [RCV004239513] Chr11:59515178 [GRCh38]
Chr11:59282651 [GRCh37]
Chr11:11q12.1		 uncertain significance
NM_001004711.2(OR4D9):c.436G>A (p.Val146Met) single nucleotide variant not specified [RCV004193564] Chr11:59515348 [GRCh38]
Chr11:59282821 [GRCh37]
Chr11:11q12.1		 uncertain significance
NM_001004711.2(OR4D9):c.400A>G (p.Thr134Ala) single nucleotide variant not specified [RCV004353785] Chr11:59515312 [GRCh38]
Chr11:59282785 [GRCh37]
Chr11:11q12.1		 uncertain significance
NM_001004711.2(OR4D9):c.761G>C (p.Cys254Ser) single nucleotide variant not provided [RCV003390062] Chr11:59515673 [GRCh38]
Chr11:59283146 [GRCh37]
Chr11:11q12.1		 likely benign
GRCh37/hg19 11q12.1-13.3(chr11:56895955-69295402)x3 copy number gain not specified [RCV003986944] Chr11:56895955..69295402 [GRCh37]
Chr11:11q12.1-13.3		 likely pathogenic
GRCh37/hg19 11p11.12-q13.1(chr11:50398499-63924462)x3 copy number gain not specified [RCV003986918] Chr11:50398499..63924462 [GRCh37]
Chr11:11p11.12-q13.1		 likely pathogenic
NM_001004711.2(OR4D9):c.326G>T (p.Gly109Val) single nucleotide variant not specified [RCV004496875] Chr11:59515238 [GRCh38]
Chr11:59282711 [GRCh37]
Chr11:11q12.1		 uncertain significance
NM_001004711.2(OR4D9):c.531C>G (p.Phe177Leu) single nucleotide variant not specified [RCV004496876] Chr11:59515443 [GRCh38]
Chr11:59282916 [GRCh37]
Chr11:11q12.1		 uncertain significance
NM_001004711.2(OR4D9):c.602C>T (p.Ser201Leu) single nucleotide variant not specified [RCV004496878] Chr11:59515514 [GRCh38]
Chr11:59282987 [GRCh37]
Chr11:11q12.1		 uncertain significance
NM_001004711.2(OR4D9):c.59C>T (p.Ser20Phe) single nucleotide variant not specified [RCV004496877] Chr11:59514971 [GRCh38]
Chr11:59282444 [GRCh37]
Chr11:11q12.1		 uncertain significance
NM_001004711.2(OR4D9):c.794T>C (p.Leu265Pro) single nucleotide variant not specified [RCV004496879] Chr11:59515706 [GRCh38]
Chr11:59283179 [GRCh37]
Chr11:11q12.1		 uncertain significance
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:74
Count of miRNA genes:72
Interacting mature miRNAs:74
Transcripts:ENST00000329328
Prediction methods:Miranda, Rnahybrid
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.

Markers in Region
OR4D9__6033  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh371159,282,638 - 59,283,460UniSTSGRCh37
Build 361159,039,214 - 59,040,036RGDNCBI36
Celera1156,645,300 - 56,646,122RGD
HuRef1155,630,469 - 55,631,291UniSTS


Expression

RNA-SEQ Expression

adipose tissue
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
sensory system
28 82 63 43 132 37 58 10 85 7 100 211 191 63 26 87 44 3

Sequence


Ensembl Acc Id: ENST00000329328   ⟹   ENSP00000328563
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1159,514,913 - 59,515,857 (+)Ensembl
Ensembl Acc Id: ENST00000641278   ⟹   ENSP00000493042
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1159,511,368 - 59,520,703 (+)Ensembl
Ensembl Acc Id: ENST00000641962   ⟹   ENSP00000493010
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1159,511,539 - 59,520,703 (+)Ensembl
RefSeq Acc Id: NM_001004711   ⟹   NP_001004711
RefSeq Status: VALIDATED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381159,511,539 - 59,520,703 (+)NCBI
GRCh371159,282,386 - 59,283,330 (+)RGD
Build 361159,038,962 - 59,039,906 (+)NCBI Archive
Celera1156,645,048 - 56,645,992 (+)RGD
HuRef1155,630,217 - 55,631,161 (+)RGD
CHM1_11159,148,162 - 59,149,106 (+)NCBI
T2T-CHM13v2.01159,462,418 - 59,471,582 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001004711 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein ALI87467 (Get FASTA)   NCBI Sequence Viewer  
  BAC06079 (Get FASTA)   NCBI Sequence Viewer  
  DAA04707 (Get FASTA)   NCBI Sequence Viewer  
  EAW73848 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSP00000493010
  ENSP00000493010.1
  ENSP00000493042.1
GenBank Protein Q8NGE8 (Get FASTA)   NCBI Sequence Viewer  
RefSeq Acc Id: NP_001004711   ⟸   NM_001004711
- UniProtKB: Q8NGE8 (UniProtKB/Swiss-Prot),   Q6IFF3 (UniProtKB/Swiss-Prot),   A0A126GVP8 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSP00000493042   ⟸   ENST00000641278
Ensembl Acc Id: ENSP00000493010   ⟸   ENST00000641962
Ensembl Acc Id: ENSP00000328563   ⟸   ENST00000329328
Protein Domains
G-protein coupled receptors family 1 profile

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q8NGE8-F1-model_v2 AlphaFold Q8NGE8 1-314 view protein structure


Additional Information

Database Acc Id Source(s)
AGR Gene HGNC:15178 AgrOrtholog
COSMIC OR4D9 COSMIC
Ensembl Genes ENSG00000172742 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENST00000641278.1 UniProtKB/Swiss-Prot
  ENST00000641962 ENTREZGENE
  ENST00000641962.1 UniProtKB/Swiss-Prot
Gene3D-CATH Rhodopsin 7-helix transmembrane proteins UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
GTEx ENSG00000172742 GTEx
HGNC ID HGNC:15178 ENTREZGENE
Human Proteome Map OR4D9 Human Proteome Map
InterPro GPCR_Rhodpsn UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  GPCR_Rhodpsn_7TM UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Olfact_rcpt UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Olfactory_Receptors UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report hsa:390199 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
NCBI Gene OR4D9 ENTREZGENE
PANTHER OLFACTORY RECEPTOR UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  OLFACTORY RECEPTOR 4D9 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam 7tm_4 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PharmGKB PA32276 PharmGKB
PRINTS GPCRRHODOPSN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  OLFACTORYR UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE G_PROTEIN_RECEP_F1_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  G_PROTEIN_RECEP_F1_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP Family A G protein-coupled receptor-like UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A126GVP8 ENTREZGENE, UniProtKB/TrEMBL
  OR4D9_HUMAN UniProtKB/Swiss-Prot
  Q6IFF3 ENTREZGENE
  Q8NGE8 ENTREZGENE
UniProt Secondary Q6IFF3 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2015-12-15 OR4D9  olfactory receptor family 4 subfamily D member 9  OR4D9  olfactory receptor, family 4, subfamily D, member 9  Symbol and/or name change 5135510 APPROVED