Rbp3 (retinol binding protein 3) - Rat Genome Database

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Gene: Rbp3 (retinol binding protein 3) Rattus norvegicus
Analyze
Symbol: Rbp3
Name: retinol binding protein 3
RGD ID: 3545
Description: Enables retinol binding activity. Predicted to be involved in retinoid metabolic process. Located in interphotoreceptor matrix. Human ortholog(s) of this gene implicated in retinitis pigmentosa 66. Orthologous to human RBP3 (retinol binding protein 3); PARTICIPATES IN altered retinoid cycle metabolic pathway; retinitis pigmentosa pathway; retinoid cycle metabolic pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; acetamide; ammonium chloride.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: interphotoreceptor retinoid binding protein; interphotoreceptor retinol- binding protein; Irbp; retinol binding protein 3, interstitial; retinol-binding protein 2; retinol-binding protein 3; Retinol-binding protein 3 interstitial
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2169,267,538 - 9,276,006 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl169,267,538 - 9,276,006 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx169,287,011 - 9,295,469 (+)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.01610,431,722 - 10,440,180 (+)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.0169,282,080 - 9,290,538 (+)NCBIRnor_WKY
Rnor_6.01610,277,775 - 10,286,243 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1610,277,775 - 10,286,243 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0168,598,417 - 8,606,885 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4169,578,549 - 9,587,017 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1169,581,408 - 9,587,667 (+)NCBI
Celera165,934,735 - 5,943,197 (-)NCBICelera
Cytogenetic Map16p16NCBI
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

Biological Process

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. Genes and mutations causing retinitis pigmentosa. Daiger SP, etal., Clin Genet. 2013 Aug;84(2):132-41. doi: 10.1111/cge.12203. Epub 2013 Jun 19.
2. 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.
3. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
4. Differential expression of interphotoreceptor retinoid-binding protein, opsin, cellular retinaldehyde-binding protein, and basic fibroblastic growth factor. Gonzalez-Fernandez F, etal., Exp Eye Res 1993 Apr;56(4):411-27.
5. Regulation of the interphotoreceptor retinoid-binding protein content of the retina by vitamin A. Katz ML, etal., Exp Eye Res. 1993 Oct;57(4):393-401.
6. Key enzymes of the retinoid (visual) cycle in vertebrate retina. Kiser PD, etal., Biochim Biophys Acta. 2012 Jan;1821(1):137-51. Epub 2011 Apr 5.
7. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
8. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
9. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
10. Susceptibility to retinal light damage in transgenic rats with rhodopsin mutations. Organisciak DT, etal., Invest Ophthalmol Vis Sci 2003 Feb;44(2):486-92.
11. GOA pipeline RGD automated data pipeline
12. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
13. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
14. Photoreceptor degeneration: genetic and mechanistic dissection of a complex trait. Wright AF, etal., Nat Rev Genet. 2010 Apr;11(4):273-84. doi: 10.1038/nrg2717.
Additional References at PubMed
PMID:1703544   PMID:10764531   PMID:10862357   PMID:12082125   PMID:15008417   PMID:16551580   PMID:21935947   PMID:23486466   PMID:24769233  


Genomics

Comparative Map Data
Rbp3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2169,267,538 - 9,276,006 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl169,267,538 - 9,276,006 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx169,287,011 - 9,295,469 (+)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.01610,431,722 - 10,440,180 (+)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.0169,282,080 - 9,290,538 (+)NCBIRnor_WKY
Rnor_6.01610,277,775 - 10,286,243 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1610,277,775 - 10,286,243 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0168,598,417 - 8,606,885 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4169,578,549 - 9,587,017 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1169,581,408 - 9,587,667 (+)NCBI
Celera165,934,735 - 5,943,197 (-)NCBICelera
Cytogenetic Map16p16NCBI
RBP3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381047,348,363 - 47,357,881 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl1047,348,363 - 47,357,881 (+)EnsemblGRCh38hg38GRCh38
GRCh371048,381,481 - 48,390,999 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361048,001,493 - 48,010,997 (-)NCBINCBI36Build 36hg18NCBI36
Build 341048,001,486 - 48,011,005NCBI
Celera1044,805,391 - 44,814,895 (-)NCBICelera
Cytogenetic Map10q11.22NCBI
HuRef1043,133,968 - 43,143,472 (-)NCBIHuRef
CHM1_11048,546,535 - 48,556,039 (-)NCBICHM1_1
T2T-CHM13v2.01048,239,660 - 48,249,178 (+)NCBIT2T-CHM13v2.0
Rbp3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391433,675,960 - 33,686,176 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1433,675,960 - 33,686,173 (+)EnsemblGRCm39 Ensembl
GRCm381433,954,003 - 33,964,219 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1433,954,003 - 33,964,216 (+)EnsemblGRCm38mm10GRCm38
MGSCv371434,767,208 - 34,777,402 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361432,783,114 - 32,793,308 (+)NCBIMGSCv36mm8
Celera1430,220,252 - 30,230,440 (+)NCBICelera
Cytogenetic Map14BNCBI
cM Map1420.8NCBI
Rbp3
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555562,217,440 - 2,225,501 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049555562,217,528 - 2,225,369 (+)NCBIChiLan1.0ChiLan1.0
RBP3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Mhudiblu_PPA_v01046,543,196 - 46,558,978 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
RBP3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1434,974,559 - 34,983,460 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl434,974,638 - 34,982,907 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha434,938,826 - 34,947,174 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0435,334,972 - 35,343,320 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl435,335,051 - 35,343,320 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1435,166,726 - 35,175,057 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0435,347,836 - 35,356,183 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0435,855,515 - 35,863,870 (-)NCBIUU_Cfam_GSD_1.0
Rbp3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440721381,319,474 - 81,330,738 (+)NCBIHiC_Itri_2
SpeTri2.0NW_0049365547,329,155 - 7,340,434 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
RBP3
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1488,490,013 - 88,504,510 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11488,491,701 - 88,503,388 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21496,117,157 - 96,130,134 (-)NCBISscrofa10.2Sscrofa10.2susScr3
RBP3
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1944,111,494 - 44,124,352 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl944,114,562 - 44,123,932 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_0236660483,882,027 - 3,896,363 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0

Variants

.
Variants in Rbp3
61 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:122
Count of miRNA genes:96
Interacting mature miRNAs:106
Transcripts:ENSRNOT00000027446
Prediction methods:Microtar, 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 (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1357403Slep4Serum leptin concentration QTL 43.91blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)1619639137Rat
1600369Hcas8Hepatocarcinoma susceptibility QTL 8liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)16122477621Rat
631830Alc7Alcohol consumption QTL 72.9consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)16126727669Rat
634355Rends4Renal damage susceptibility QTL 40.05kidney blood vessel morphology trait (VT:0000530)organ lesion measurement (CMO:0000677)16126727669Rat
1582235Insul8Insulin level QTL 83.30.0063blood insulin amount (VT:0001560)calculated serum insulin level (CMO:0000359)16126727669Rat
9590151Scort8Serum corticosterone level QTL 88.450.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)16130836262Rat
2302380Slep6Serum leptin concentration QTL 63.36blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)16132139025Rat
2307172Activ4Activity QTL 43.710.00023locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)16133418960Rat
1354584Despr6Despair related QTL 63.10.0067locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)16139533930Rat
2303566Bw90Body weight QTL 902body mass (VT:0001259)body weight (CMO:0000012)16139533930Rat
631561Hcuc2Hepatic copper content QTL 22.8hepatic copper amount (VT:0003065)liver total copper weight (CMO:0001507)16139533949Rat
6903319Bw114Body weight QTL 1142.70.0037body mass (VT:0001259)body weight (CMO:0000012)16143534949Rat
7411664Foco30Food consumption QTL 30110.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)16144588133Rat
1354625Despr7Despair related QTL 73.160.016locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)16144977551Rat
1600378Arunc4Aerobic running capacity QTL 40.03exercise endurance trait (VT:0002332)maximum distance run on treadmill (CMO:0001406)1638024580345693Rat
2293343Glom16Glomerulus QTL 167.4kidney glomerulus integrity trait (VT:0010546)kidney sclerotic glomeruli count to total glomeruli count ratio (CMO:0001269)1683223646053497Rat
2312660Bw95Body weight QTL 950.05inguinal fat pad mass (VT:0010424)inguinal fat pad weight to body weight ratio (CMO:0001253)1683223659492508Rat
2312663Slep9Serum leptin concentration QTL 90.001blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)1683223659492508Rat
2312666Insul16Insulin level QTL 160.01blood insulin amount (VT:0001560)serum insulin level (CMO:0000358)1683223659492508Rat
2312669Stl23Serum triglyceride level QTL 230.01blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)1683223659492508Rat
2301406Kidm39Kidney mass QTL 390.002kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)16285170915884239Rat
1300133Rf24Renal function QTL 243.64blood creatinine amount (VT:0005328)creatinine clearance (CMO:0000765)16338015021361552Rat
2306902Bp339Blood pressure QTL 3390.01arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)16338015043025077Rat
737825Alc13Alcohol consumption QTL 134.5consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)16422760916039848Rat
70183BpQTLcluster13Blood pressure QTL cluster 133.654arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)16422760943025077Rat
70183BpQTLcluster13Blood pressure QTL cluster 133.654arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)16422760943025077Rat
70183BpQTLcluster13Blood pressure QTL cluster 133.654arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)16422760943025077Rat
737819Hcas4Hepatocarcinoma susceptibility QTL 44.43liver integrity trait (VT:0010547)volume of individual liver tumorous lesion (CMO:0001078)16422760946975965Rat
61405Niddm6Non-insulin dependent diabetes mellitus QTL 63.660.001blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)16422760948972724Rat
61338Bp23Blood pressure QTL 234.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)16422760949227609Rat
737826Alc11Alcohol consumption QTL 113.2consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)16422760960252231Rat
61372Bp40Blood pressure QTL 402.2blood pressure trait (VT:0000183)systolic blood pressure (CMO:0000004)16422773017696785Rat

Markers in Region
BE095712  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2169,267,985 - 9,268,205 (+)MAPPERmRatBN7.2
Rnor_6.01610,278,223 - 10,278,442NCBIRnor6.0
Rnor_5.0168,598,865 - 8,599,084UniSTSRnor5.0
RGSC_v3.4169,578,997 - 9,579,216UniSTSRGSC3.4
Celera165,942,530 - 5,942,749UniSTS
RH 3.4 Map1692.0UniSTS
Cytogenetic Map16p16UniSTS
RH139342  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2169,276,434 - 9,276,658 (+)MAPPERmRatBN7.2
Rnor_6.01610,286,672 - 10,286,895NCBIRnor6.0
Rnor_5.0168,607,314 - 8,607,537UniSTSRnor5.0
RGSC_v3.4169,587,446 - 9,587,669UniSTSRGSC3.4
Celera165,934,083 - 5,934,306UniSTS
RH 3.4 Map18365.4UniSTS
Cytogenetic Map16p16UniSTS


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

circulatory system endocrine system exocrine system hepatobiliary system nervous system reproductive system respiratory system
High
Medium
Low 9 9 9 1 5
Below cutoff 2 32 32 32 20 12 1

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000090679   ⟹   ENSRNOP00000068670
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl169,267,538 - 9,276,006 (+)Ensembl
Rnor_6.0 Ensembl1610,277,775 - 10,286,243 (+)Ensembl
RefSeq Acc Id: NM_001191832   ⟹   NP_001178761
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2169,267,538 - 9,276,006 (+)NCBI
Rnor_6.01610,277,775 - 10,286,243 (+)NCBI
Rnor_5.0168,598,417 - 8,606,885 (+)NCBI
Celera165,934,735 - 5,943,197 (-)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_001178761   ⟸   NM_001191832
- Peptide Label: precursor
- UniProtKB: G3V8Q4 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000068670   ⟸   ENSRNOT00000090679
Protein Domains
TSPc

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-G3V8Q4-F1-model_v2 AlphaFold G3V8Q4 1-1234 view protein structure

Transcriptome

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

Promoters
RGD ID:13699953
Promoter ID:EPDNEW_R10477
Type:single initiation site
Name:Rbp3_1
Description:retinol binding protein 3
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_6.01610,277,722 - 10,277,782EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:3545 AgrOrtholog
BioCyc Gene G2FUF-12082 BioCyc
BioCyc Pathway PWY-6861 [the visual cycle I (vertebrates)] BioCyc
Ensembl Genes ENSRNOG00000051911 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000068670 ENTREZGENE
  ENSRNOP00000068670.1 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000090679 ENTREZGENE
  ENSRNOT00000090679.2 UniProtKB/TrEMBL
InterPro ClpP/crotonase-like_dom UniProtKB/TrEMBL
  Interphotoreceptor_retinol-bd UniProtKB/TrEMBL
KEGG Report rno:24711 UniProtKB/TrEMBL
NCBI Gene 24711 ENTREZGENE
Pfam Peptidase_S41 UniProtKB/TrEMBL
PhenoGen Rbp3 PhenoGen
SMART TSPc UniProtKB/TrEMBL
Superfamily-SCOP SSF52096 UniProtKB/TrEMBL
UniProt A0A8A1UAJ7_RAT UniProtKB/TrEMBL
  A0A8A1UD18_RAT UniProtKB/TrEMBL
  A0A8A1UF31_RAT UniProtKB/TrEMBL
  A0A8A1UFU8_RAT UniProtKB/TrEMBL
  A0A8A1UIS1_RAT UniProtKB/TrEMBL
  G3V8Q4 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2015-12-09 Rbp3  retinol binding protein 3  Rbp3  retinol binding protein 3, interstitial  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2004-09-10 Rbp3  retinol binding protein 3, interstitial    retinol binding protein 3  Name updated 1299863 APPROVED
2002-06-10 Rbp3  Retinol-binding protein 3, interstitial      Symbol and Name status set to approved 70586 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_expression decreased retinal expression is detected in response to light induced retinal damage in rats transgenic for rhodopsin mutations 1299193