Obp2a (odorant binding protein 2A) - Rat Genome Database

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Gene: Obp2a (odorant binding protein 2A) Rattus norvegicus
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Symbol: Obp2a
Name: odorant binding protein 2A
RGD ID: 1588212
Description: Predicted to enable odorant binding activity. Predicted to act upstream of or within several processes, including insulin receptor signaling pathway; negative regulation of gluconeogenesis; and regulation of lipid metabolic process. Predicted to be active in extracellular space. Orthologous to human OBP2A (odorant binding protein 2A) and OBP2B (odorant binding protein 2B); INTERACTS WITH 17beta-estradiol; 17beta-estradiol 3-benzoate; bisphenol A.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: Lcn13; lipocalin 13; LOC680754; Obp2b; odorant binding protein 2B; similar to lipocalin 13
RGD Orthologs
Human
Mouse
Alliance Orthologs
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8328,904,024 - 28,907,391 (+)NCBIGRCr8
mRatBN7.238,505,963 - 8,509,269 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl38,505,990 - 8,509,269 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx311,611,636 - 11,614,942 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0320,197,870 - 20,201,176 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0318,387,712 - 18,391,018 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.032,908,684 - 2,913,362 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl32,910,083 - 2,913,362 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.032,891,496 - 2,894,775 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.433,858,161 - 3,861,440 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera33,330,587 - 3,333,866 (+)NCBICelera
Cytogenetic Map3p13NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

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. GOA pipeline RGD automated data pipeline
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:36762499  


Genomics

Comparative Map Data
Obp2a
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8328,904,024 - 28,907,391 (+)NCBIGRCr8
mRatBN7.238,505,963 - 8,509,269 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl38,505,990 - 8,509,269 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx311,611,636 - 11,614,942 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0320,197,870 - 20,201,176 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0318,387,712 - 18,391,018 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.032,908,684 - 2,913,362 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl32,910,083 - 2,913,362 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.032,891,496 - 2,894,775 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.433,858,161 - 3,861,440 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera33,330,587 - 3,333,866 (+)NCBICelera
Cytogenetic Map3p13NCBI
OBP2A
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh389135,546,126 - 135,549,969 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl9135,546,126 - 135,549,969 (+)EnsemblGRCh38hg38GRCh38
GRCh379138,437,972 - 138,441,815 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 369137,577,806 - 137,581,636 (+)NCBINCBI36Build 36hg18NCBI36
Build 349135,663,929 - 135,667,747NCBI
Celera9108,955,036 - 108,958,682 (+)NCBICelera
Cytogenetic Map9q34.3NCBI
HuRef9107,899,754 - 107,903,624 (+)NCBIHuRef
CHM1_19138,586,564 - 138,590,394 (+)NCBICHM1_1
T2T-CHM13v2.09147,774,075 - 147,777,763 (+)NCBIT2T-CHM13v2.0
Obp2a
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39225,587,589 - 25,593,338 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl225,590,055 - 25,593,338 (+)EnsemblGRCm39 Ensembl
GRCm38225,697,577 - 25,703,326 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl225,700,043 - 25,703,326 (+)EnsemblGRCm38mm10GRCm38
MGSCv37225,555,594 - 25,558,846 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36225,522,083 - 25,525,335 (+)NCBIMGSCv36mm8
Celera225,428,230 - 25,431,482 (+)NCBICelera
Cytogenetic Map2A3NCBI
cM Map217.8NCBI

Variants

.
Variants in Obp2a
16 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:47
Count of miRNA genes:47
Interacting mature miRNAs:47
Transcripts:ENSRNOT00000064745
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.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
4889966Bss95Bone structure and strength QTL 954.4tibia area (VT:1000281)tibia-fibula cross-sectional area (CMO:0001718)3136847613Rat
2292615Ept17Estrogen-induced pituitary tumorigenesis QTL 176.7pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)3653764510778823Rat
10401810Kidm53Kidney mass QTL 53kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)3822719447233430Rat
1298526Arunc3Aerobic running capacity QTL 32.2exercise endurance trait (VT:0002332)maximum distance run on treadmill (CMO:0001406)3822719433703538Rat
631545Bp85Blood pressure QTL 853.1arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3133278763Rat
631679Cm10Cardiac mass QTL 107.340.0001heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)3131158234Rat
2290452Scl56Serum cholesterol level QTL 562.26blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)3191609953Rat
631568Bp92Blood pressure QTL 922.20.005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3139874793Rat
70202Alc19Alcohol consumption QTL 192.5drinking behavior trait (VT:0001422)ethanol intake volume to total fluid intake volume ratio (CMO:0001591)3127494778Rat
2312664Scl62Serum cholesterol level QTL 620.05blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)3138710544Rat
61468Bp15Blood pressure QTL 154.4blood pressure trait (VT:0000183)pulse pressure (CMO:0000292)3133278763Rat
1358185Ept6Estrogen-induced pituitary tumorigenesis QTL 66.7pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)3653764510778823Rat
631831Alc8Alcohol consumption QTL 82.7consumption behavior trait (VT:0002069)calculated ethanol drink intake rate (CMO:0001615)3133230976Rat


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
circulatory system
ectoderm
endocrine system
endoderm
hemolymphoid system
integumental system
mesenchyme
mesoderm
nervous system
renal system
reproductive system
respiratory system
9 1 14 10 13 2 6 15 4 7 2 39 13

Sequence


Ensembl Acc Id: ENSRNOT00000064745   ⟹   ENSRNOP00000062414
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl38,505,990 - 8,509,269 (+)Ensembl
Rnor_6.0 Ensembl32,910,083 - 2,913,362 (+)Ensembl
RefSeq Acc Id: NM_001128139   ⟹   NP_001121611
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8328,904,083 - 28,907,389 (+)NCBI
mRatBN7.238,505,963 - 8,509,269 (+)NCBI
Rnor_6.032,910,083 - 2,913,362 (+)NCBI
Rnor_5.032,891,496 - 2,894,775 (+)NCBI
RGSC_v3.433,858,161 - 3,861,440 (+)RGD
Celera33,330,587 - 3,333,866 (+)RGD
Sequence:
RefSeq Acc Id: XM_063284542   ⟹   XP_063140612
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8328,904,024 - 28,907,391 (+)NCBI
RefSeq Acc Id: XM_063284543   ⟹   XP_063140613
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8328,904,024 - 28,907,391 (+)NCBI
RefSeq Acc Id: XM_063284544   ⟹   XP_063140614
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8328,904,024 - 28,907,391 (+)NCBI
Protein Sequences
Protein RefSeqs NP_001121611 (Get FASTA)   NCBI Sequence Viewer  
  XP_063140612 (Get FASTA)   NCBI Sequence Viewer  
  XP_063140613 (Get FASTA)   NCBI Sequence Viewer  
  XP_063140614 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein ABG24236 (Get FASTA)   NCBI Sequence Viewer  
  EDL93545 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000062414.1
RefSeq Acc Id: NP_001121611   ⟸   NM_001128139
- Peptide Label: precursor
- UniProtKB: B3EY84 (UniProtKB/TrEMBL),   A6JTA2 (UniProtKB/TrEMBL),   F7EU54 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000062414   ⟸   ENSRNOT00000064745
RefSeq Acc Id: XP_063140612   ⟸   XM_063284542
- Peptide Label: isoform X1
RefSeq Acc Id: XP_063140614   ⟸   XM_063284544
- Peptide Label: isoform X2
- UniProtKB: A6JTA2 (UniProtKB/TrEMBL),   B3EY84 (UniProtKB/TrEMBL),   F7EU54 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063140613   ⟸   XM_063284543
- Peptide Label: isoform X2
- UniProtKB: A6JTA2 (UniProtKB/TrEMBL),   B3EY84 (UniProtKB/TrEMBL),   F7EU54 (UniProtKB/TrEMBL)
Protein Domains
Lipocalin/cytosolic fatty-acid binding

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-B3EY84-F1-model_v2 AlphaFold B3EY84 1-176 view protein structure

Transcriptome

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


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1588212 AgrOrtholog
BioCyc Gene G2FUF-50426 BioCyc
Ensembl Genes ENSRNOG00000042407 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000064745.2 UniProtKB/TrEMBL
Gene3D-CATH 2.40.128.20 UniProtKB/TrEMBL
InterPro Calycin UniProtKB/TrEMBL
  Lipocalin UniProtKB/TrEMBL
  Lipocln_cytosolic_FA_bd UniProtKB/TrEMBL
  vonEbner_gland UniProtKB/TrEMBL
KEGG Report rno:680754 UniProtKB/TrEMBL
NCBI Gene 680754 ENTREZGENE
PANTHER ODORANT-BINDING PROTEIN 2A UniProtKB/TrEMBL
  PTHR11430 UniProtKB/TrEMBL
Pfam Lipocalin UniProtKB/TrEMBL
PhenoGen Obp2a PhenoGen
PRINTS VNEBNERGLAND UniProtKB/TrEMBL
RatGTEx ENSRNOG00000042407 RatGTEx
Superfamily-SCOP Calycin UniProtKB/TrEMBL
UniProt A6JTA2 ENTREZGENE, UniProtKB/TrEMBL
  B3EY84 ENTREZGENE
  F7EU54 ENTREZGENE, UniProtKB/TrEMBL
UniProt Secondary B3EY84 UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2012-10-05 Obp2a  odorant binding protein 2A  Obp2b  odorant binding protein 2B  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2010-04-20 Obp2b  odorant binding protein 2B  Lcn13  lipocalin 13  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-03-05 Lcn13  lipocalin 13  LOC680754  similar to lipocalin 13  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-01-09 LOC680754  similar to lipocalin 13  LOC687323  similar to lipocalin 13  Data merged from RGD:1586574 1643240 APPROVED
2006-11-19 LOC680754  similar to lipocalin 13      Symbol and Name status set to provisional 70820 PROVISIONAL
2006-11-19 LOC687323  similar to lipocalin 13      Symbol and Name status set to provisional 70820 PROVISIONAL