OR1D4 (olfactory receptor family 1 subfamily D member 4) - Rat Genome Database

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Gene: OR1D4 (olfactory receptor family 1 subfamily D member 4) Homo sapiens
Analyze
Symbol: OR1D4
Name: olfactory receptor family 1 subfamily D member 4
RGD ID: 1346947
HGNC Page HGNC:8185
Description: Predicted to enable olfactory receptor activity. Predicted to be involved in signal transduction. Predicted to be located in membrane. Predicted to be active in plasma membrane.
Type: protein-coding (Ensembl: transcribed_unprocessed_pseudogene)
RefSeq Status: VALIDATED
Previously known as: MGC125396; MGC199013; olfactory receptor 17-30; olfactory receptor 1D4; olfactory receptor family 1 subfamily D member 4 (gene/pseudogene); olfactory receptor OR17-1; olfactory receptor pseudogene; olfactory receptor, family 1, subfamily D, member 4 pseudogene; OR17-30
RGD Orthologs
Bonobo
Alliance Genes
More Info more info ...
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
NCBI Annotation Information: Annotation category: suggests misassembly; Note: Genetic polymorphisms result in both protein coding and non-coding alleles of this gene.
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38173,240,676 - 3,241,614 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl173,240,676 - 3,241,614 (+)EnsemblGRCh38hg38GRCh38
GRCh37173,143,970 - 3,144,908 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36173,090,566 - 3,091,758 (+)NCBINCBI36Build 36hg18NCBI36
Build 34172,912,712 - 2,913,651NCBI
Celera172,984,518 - 2,985,107 (-)NCBICelera
Cytogenetic Map17p13.3NCBI
HuRef173,036,202 - 3,036,791 (+)NCBIHuRef
CHM1_1173,152,859 - 3,153,448 (+)NCBICHM1_1
T2T-CHM13v2.0173,128,907 - 3,129,845 (+)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


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,TAS)

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. GOAs Human GO annotations GOA_HUMAN data from the GO Consortium
2. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:8004088   PMID:10673334   PMID:12213199   PMID:12477932   PMID:14983052   PMID:21873635   PMID:33961781  


Genomics

Comparative Map Data
OR1D4
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38173,240,676 - 3,241,614 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl173,240,676 - 3,241,614 (+)EnsemblGRCh38hg38GRCh38
GRCh37173,143,970 - 3,144,908 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36173,090,566 - 3,091,758 (+)NCBINCBI36Build 36hg18NCBI36
Build 34172,912,712 - 2,913,651NCBI
Celera172,984,518 - 2,985,107 (-)NCBICelera
Cytogenetic Map17p13.3NCBI
HuRef173,036,202 - 3,036,791 (+)NCBIHuRef
CHM1_1173,152,859 - 3,153,448 (+)NCBICHM1_1
T2T-CHM13v2.0173,128,907 - 3,129,845 (+)NCBIT2T-CHM13v2.0
LOC100974833
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21910,830,672 - 10,831,625 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11712,797,031 - 12,797,984 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0173,240,088 - 3,241,191 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1173,271,210 - 3,272,162 (+)NCBIpanpan1.1PanPan1.1panPan2

Variants

.
Variants in OR1D4
1 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 17p13.3-13.2(chr17:2357067-4328426)x3 copy number gain See cases [RCV000052456] Chr17:2357067..4328426 [GRCh38]
Chr17:2260361..4231721 [GRCh37]
Chr17:2207111..4178470 [NCBI36]
Chr17:17p13.3-13.2
pathogenic
GRCh38/hg38 17p13.3-13.2(chr17:193307-5652222)x1 copy number loss See cases [RCV000053384] Chr17:193307..5652222 [GRCh38]
Chr17:45835..5555542 [GRCh37]
Chr17:43098..5496266 [NCBI36]
Chr17:17p13.3-13.2
pathogenic
GRCh38/hg38 17p13.3-13.2(chr17:198748-3436345)x1 copy number loss Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000053386]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000053386]|See cases [RCV000053386] Chr17:198748..3436345 [GRCh38]
Chr17:50690..3339639 [GRCh37]
Chr17:48539..3286389 [NCBI36]
Chr17:17p13.3-13.2
pathogenic
GRCh38/hg38 17p13.3-13.2(chr17:2527510-3467165)x1 copy number loss See cases [RCV000053405] Chr17:2527510..3467165 [GRCh38]
Chr17:2430804..3370459 [GRCh37]
Chr17:2377554..3317209 [NCBI36]
Chr17:17p13.3-13.2
pathogenic
GRCh38/hg38 17p13.3-13.2(chr17:3036729-3684667)x3 copy number gain See cases [RCV000053972] Chr17:3036729..3684667 [GRCh38]
Chr17:2940023..3587961 [GRCh37]
Chr17:2886773..3534710 [NCBI36]
Chr17:17p13.3-13.2
uncertain significance
GRCh38/hg38 17p13.3-13.2(chr17:3208843-3839780)x3 copy number gain Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000053973]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000053973]|See cases [RCV000053973] Chr17:3208843..3839780 [GRCh38]
Chr17:3112137..3743074 [GRCh37]
Chr17:3058887..3689823 [NCBI36]
Chr17:17p13.3-13.2
uncertain significance
GRCh38/hg38 17p13.3-13.2(chr17:2062380-5258340)x1 copy number loss See cases [RCV000133721] Chr17:2062380..5258340 [GRCh38]
Chr17:1965674..5161635 [GRCh37]
Chr17:1912424..5102359 [NCBI36]
Chr17:17p13.3-13.2
pathogenic
GRCh38/hg38 17p13.3-13.2(chr17:3155468-3543868)x1 copy number loss See cases [RCV000133921] Chr17:3155468..3543868 [GRCh38]
Chr17:3058762..3447162 [GRCh37]
Chr17:3005512..3393912 [NCBI36]
Chr17:17p13.3-13.2
benign
GRCh38/hg38 17p13.3-13.1(chr17:162088-6959050)x1 copy number loss See cases [RCV000134135] Chr17:162088..6959050 [GRCh38]
Chr17:45835..6862369 [GRCh37]
Chr17:11879..6803093 [NCBI36]
Chr17:17p13.3-13.1
pathogenic
GRCh38/hg38 17p13.3-13.1(chr17:198748-7491129)x3 copy number gain See cases [RCV000134970] Chr17:198748..7491129 [GRCh38]
Chr17:50690..7394448 [GRCh37]
Chr17:48539..7335172 [NCBI36]
Chr17:17p13.3-13.1
pathogenic
GRCh38/hg38 17p13.3-13.2(chr17:226472-3655099)x1 copy number loss See cases [RCV000135857] Chr17:226472..3655099 [GRCh38]
Chr17:396627..3558393 [GRCh37]
Chr17:76263..3505142 [NCBI36]
Chr17:17p13.3-13.2
pathogenic
GRCh38/hg38 17p13.3-13.2(chr17:1348488-3513273)x3 copy number gain See cases [RCV000137603] Chr17:1348488..3513273 [GRCh38]
Chr17:1251782..3416567 [GRCh37]
Chr17:1198532..3363317 [NCBI36]
Chr17:17p13.3-13.2
likely pathogenic
GRCh38/hg38 17p13.3-13.1(chr17:162016-7697012)x1 copy number loss See cases [RCV000138214] Chr17:162016..7697012 [GRCh38]
Chr17:45835..7600330 [GRCh37]
Chr17:11807..7541055 [NCBI36]
Chr17:17p13.3-13.1
pathogenic
GRCh38/hg38 17p13.3-12(chr17:162016-12343901)x3 copy number gain See cases [RCV000138531] Chr17:162016..12343901 [GRCh38]
Chr17:45835..12247218 [GRCh37]
Chr17:11807..12187943 [NCBI36]
Chr17:17p13.3-12
pathogenic
GRCh38/hg38 17p13.3-13.2(chr17:2062429-4141883)x3 copy number gain See cases [RCV000139738] Chr17:2062429..4141883 [GRCh38]
Chr17:1965723..4045177 [GRCh37]
Chr17:1912473..3991926 [NCBI36]
Chr17:17p13.3-13.2
pathogenic
GRCh38/hg38 17p13.3-13.2(chr17:237248-4735533)x1 copy number loss See cases [RCV000141559] Chr17:237248..4735533 [GRCh38]
Chr17:396627..4638828 [GRCh37]
Chr17:87039..4585577 [NCBI36]
Chr17:17p13.3-13.2
pathogenic
GRCh38/hg38 17p13.3-13.2(chr17:150732-5935377)x1 copy number loss See cases [RCV000141658] Chr17:150732..5935377 [GRCh38]
Chr17:525..5838697 [GRCh37]
Chr17:525..5779421 [NCBI36]
Chr17:17p13.3-13.2
pathogenic
GRCh38/hg38 17p13.3-13.2(chr17:3168370-3862518)x3 copy number gain See cases [RCV000142062] Chr17:3168370..3862518 [GRCh38]
Chr17:3071664..3765812 [GRCh37]
Chr17:3018414..3712561 [NCBI36]
Chr17:17p13.3-13.2
uncertain significance
GRCh38/hg38 17p13.3-12(chr17:150732-14764202)x3 copy number gain See cases [RCV000142236] Chr17:150732..14764202 [GRCh38]
Chr17:525..14667519 [GRCh37]
Chr17:525..14608244 [NCBI36]
Chr17:17p13.3-12
pathogenic
GRCh38/hg38 17p13.3(chr17:150732-3242868)x1 copy number loss See cases [RCV000142323] Chr17:150732..3242868 [GRCh38]
Chr17:525..3146162 [GRCh37]
Chr17:525..3092912 [NCBI36]
Chr17:17p13.3
pathogenic
GRCh38/hg38 17p13.3-13.2(chr17:198748-4265640)x1 copy number loss See cases [RCV000142440] Chr17:198748..4265640 [GRCh38]
Chr17:50690..4168935 [GRCh37]
Chr17:48539..4115684 [NCBI36]
Chr17:17p13.3-13.2
pathogenic
GRCh38/hg38 17p13.3-13.2(chr17:3187406-3880628)x3 copy number gain See cases [RCV000142793] Chr17:3187406..3880628 [GRCh38]
Chr17:3090700..3783922 [GRCh37]
Chr17:3037450..3730671 [NCBI36]
Chr17:17p13.3-13.2
uncertain significance
GRCh38/hg38 17p13.3-13.2(chr17:2922729-3436438)x3 copy number gain See cases [RCV000142895] Chr17:2922729..3436438 [GRCh38]
Chr17:2826023..3339732 [GRCh37]
Chr17:2772773..3286482 [NCBI36]
Chr17:17p13.3-13.2
pathogenic
GRCh38/hg38 17p13.3-13.2(chr17:3168370-3852982)x3 copy number gain See cases [RCV000143610] Chr17:3168370..3852982 [GRCh38]
Chr17:3071664..3756276 [GRCh37]
Chr17:3018414..3703025 [NCBI36]
Chr17:17p13.3-13.2
likely benign|uncertain significance
GRCh38/hg38 17p13.3-13.2(chr17:3102273-3667053)x3 copy number gain See cases [RCV000137331] Chr17:3102273..3667053 [GRCh38]
Chr17:3005567..3570347 [GRCh37]
Chr17:2952317..3517096 [NCBI36]
Chr17:17p13.3-13.2
likely pathogenic|uncertain significance
GRCh38/hg38 17p13.3-12(chr17:165730-11404096)x3 copy number gain Chromosome 17p13.3 duplication syndrome [RCV003327726] Chr17:165730..11404096 [GRCh38]
Chr17:17p13.3-12
pathogenic
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:286
Count of miRNA genes:258
Interacting mature miRNAs:264
Transcripts:ENST00000525719, ENST00000531680
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
OR1D5__5969  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37173,144,258 - 3,145,004UniSTSGRCh37
GRCh37172,965,867 - 2,966,613UniSTSGRCh37
Build 36172,912,617 - 2,913,363RGDNCBI36
Celera172,984,073 - 2,984,819RGD
HuRef173,036,490 - 3,037,236UniSTS
HuRef172,858,112 - 2,858,858UniSTS
UniSTS:484278  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37173,143,970 - 3,144,559UniSTSGRCh37
GRCh37172,966,312 - 2,966,901UniSTSGRCh37
Celera172,984,518 - 2,985,107UniSTS
HuRef173,036,202 - 3,036,791UniSTS
HuRef172,858,557 - 2,859,146UniSTS


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system sensory system adipose tissue appendage
High
Medium
Low 1 1 1
Below cutoff 56 129 41 11 116 8 116 54 152 8 127 68 3 33 83

Sequence


RefSeq Acc Id: ENST00000525719
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl173,240,676 - 3,241,614 (+)Ensembl
RefSeq Acc Id: ENST00000531680
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl173,235,703 - 3,241,265 (+)Ensembl
RefSeq Acc Id: NM_003552   ⟹   NP_003543
RefSeq Status: VALIDATED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
T2T-CHM13v2.0173,128,907 - 3,129,845 (+)NCBI
RefSeq Acc Id: NR_145519
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38173,240,676 - 3,241,614 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_003543 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAA18345 (Get FASTA)   NCBI Sequence Viewer  
  AAF37312 (Get FASTA)   NCBI Sequence Viewer  
  AAK95019 (Get FASTA)   NCBI Sequence Viewer  
  DAA04638 (Get FASTA)   NCBI Sequence Viewer  
  P47884 (Get FASTA)   NCBI Sequence Viewer  
RefSeq Acc Id: NP_003543   ⟸   NM_003552
- UniProtKB: A0A126GWT7 (UniProtKB/TrEMBL)
- Sequence:
Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-P47884-F1-model_v2 AlphaFold P47884 1-311 view protein structure


Additional Information

Database Acc Id Source(s)
AGR Gene HGNC:8185 AgrOrtholog
COSMIC OR1D4 COSMIC
Ensembl Genes ENSG00000255095 Ensembl, ENTREZGENE
Ensembl Transcript ENST00000525719 ENTREZGENE
Gene3D-CATH Rhodopsin 7-helix transmembrane proteins UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
GTEx ENSG00000255095 GTEx
HGNC ID HGNC:8185 ENTREZGENE
Human Proteome Map OR1D4 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
NCBI Gene 653166 ENTREZGENE
PANTHER OLFACTORY RECEPTOR UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  OLFACTORY RECEPTOR 1D4-RELATED UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam 7tm_4 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PharmGKB PA32059 PharmGKB
PRINTS GPCRRHODOPSN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  OLFACTORYR UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE G_PROTEIN_RECEP_F1_1 UniProtKB/Swiss-Prot
  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 A0A126GWT7 ENTREZGENE, UniProtKB/TrEMBL
  OR1D4_HUMAN UniProtKB/Swiss-Prot, ENTREZGENE
UniProt Secondary Q96RA5 UniProtKB/Swiss-Prot
  Q9UM75 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2020-05-11 OR1D4  olfactory receptor family 1 subfamily D member 4  OR1D4  olfactory receptor family 1 subfamily D member 4 (gene/pseudogene)  Symbol and/or name change 19259463 PROVISIONAL
2015-12-15 OR1D4  olfactory receptor family 1 subfamily D member 4 (gene/pseudogene)  OR1D4  olfactory receptor, family 1, subfamily D, member 4 (gene/pseudogene)  Symbol and/or name change 5135510 APPROVED
2011-07-27 OR1D4  olfactory receptor, family 1, subfamily D, member 4 (gene/pseudogene)  OR1D4  olfactory receptor, family 1, subfamily D, member 4  Symbol and/or name change 5135510 APPROVED