Rimbp3 (RIMS binding protein 3) - Rat Genome Database

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Gene: Rimbp3 (RIMS binding protein 3) Rattus norvegicus
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Symbol: Rimbp3
Name: RIMS binding protein 3
RGD ID: 1563657
Description: Predicted to enable benzodiazepine receptor binding activity. Predicted to be involved in fertilization and spermatid development. Predicted to be located in cytoplasm and cytoskeleton. Predicted to be active in nucleus. Predicted to colocalize with manchette. Orthologous to several human genes including RIMBP3C (RIMS binding protein 3C); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; gentamycin; paracetamol.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC303785; RGD1563657; RIMS-binding protein 3; similar to hypothetical protein DKFZp434H177.1 - human (fragment)
RGD Orthologs
Human
Mouse
Bonobo
Dog
Pig
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81197,288,041 - 97,293,616 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1197,273,234 - 97,303,170 (-)EnsemblGRCr8
mRatBN7.21183,783,816 - 83,789,391 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1183,784,244 - 83,789,082 (-)EnsemblmRatBN7.2
Rnor_6.01188,033,213 - 88,039,002 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1188,033,180 - 88,038,518 (-)Ensemblrn6Rnor6.0
Rnor_5.01191,087,058 - 91,092,550 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41185,786,898 - 85,792,478 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1182,546,116 - 82,551,905 (-)NCBICelera
Cytogenetic Map11q23NCBI
JBrowse:




Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
cytoskeleton  (IEA)
manchette  (IBA,ISO)
nucleus  (IBA,ISO)

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. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:17662146   PMID:19091768  


Genomics

Comparative Map Data
Rimbp3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81197,288,041 - 97,293,616 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1197,273,234 - 97,303,170 (-)EnsemblGRCr8
mRatBN7.21183,783,816 - 83,789,391 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1183,784,244 - 83,789,082 (-)EnsemblmRatBN7.2
Rnor_6.01188,033,213 - 88,039,002 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1188,033,180 - 88,038,518 (-)Ensemblrn6Rnor6.0
Rnor_5.01191,087,058 - 91,092,550 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41185,786,898 - 85,792,478 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1182,546,116 - 82,551,905 (-)NCBICelera
Cytogenetic Map11q23NCBI
RIMBP3C
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh382221,545,666 - 21,551,461 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl2221,545,666 - 21,551,461 (-)Ensemblhg38GRCh38
GRCh372221,899,955 - 21,905,750 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 362220,229,646 - 20,235,750 (-)NCBIBuild 36Build 36hg18NCBI36
Cytogenetic Map22q11.21NCBI
HuRef223,946,770 - 3,952,565 (-)NCBIHuRef
CHM1_12221,900,248 - 21,905,951 (-)NCBICHM1_1
T2T-CHM13v2.02221,796,920 - 21,802,715 (+)NCBIT2T-CHM13v2.0
Rimbp3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391617,025,999 - 17,031,846 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1617,026,467 - 17,031,846 (+)EnsemblGRCm39 EnsemblGRCm39
GRCm381617,208,135 - 17,213,982 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1617,208,603 - 17,213,982 (+)Ensemblmm10GRCm38
MGSCv371617,208,228 - 17,214,075 (+)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv361617,122,548 - 17,127,484 (+)NCBIMGSCv36mm8
Celera1617,780,950 - 17,786,797 (+)NCBICelera
Cytogenetic Map16A3NCBI
cM Map1610.67NCBI
RIMBP3C
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v22331,090,385 - 31,096,194 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan12233,639,177 - 33,644,959 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0223,668,133 - 3,673,619 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
LOC486445
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12630,819,266 - 30,824,791 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2630,776,985 - 30,782,513 (-)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.02632,224,478 - 32,230,006 (-)NCBIROS_Cfam_1.0ROS_Cfam_1.0
UMICH_Zoey_3.12630,273,966 - 30,279,493 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02629,897,997 - 29,903,525 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02630,987,818 - 30,993,345 (-)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
LOC100153093
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.11450,323,037 - 50,331,111 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21453,775,028 - 53,780,751 (+)NCBISscrofa10.2Sscrofa10.2susScr3
Rimbp3c
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247471,110,596 - 1,115,995 (-)NCBIHetGla 1.0HetGla 1.0hetGla2

miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:52
Count of miRNA genes:48
Interacting mature miRNAs:51
Transcripts:ENSRNOT00000051991
Prediction methods: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 (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
10058954Gmadr7Adrenal mass QTL 72.490.0049adrenal gland mass (VT:0010420)both adrenal glands wet weight to body weight ratio (CMO:0002411)117385089499753367Rat
4889859Pur28Proteinuria QTL 2819.50.001urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)115892833699753367Rat
724561Plsm4Polydactyly-luxate syndrome (PLS) morphotypes QTL 40.0003forelimb integrity trait (VT:0010562)front foot phalanges count (CMO:0001947)116796218499753367Rat
631506Bp104Blood pressure QTL 1042.8arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)117330831599753367Rat
7411658Foco27Food consumption QTL 2716.20.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)116985594399753367Rat
1549848Bvd6Brain ventricular dilatation QTL 63.10.0001brain ventricle morphology trait (VT:0000822)hydrocephalus severity score (CMO:0001881)117961851999753367Rat


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
16 11 66 159 76 75 44 79 44 6 311 177 11 138 66 91 31 16 16

Sequence


Ensembl Acc Id: ENSRNOT00000051991   ⟹   ENSRNOP00000054476
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1197,284,878 - 97,294,477 (-)Ensembl
mRatBN7.2 Ensembl1183,784,244 - 83,789,082 (-)Ensembl
Rnor_6.0 Ensembl1188,033,180 - 88,038,518 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000134105   ⟹   ENSRNOP00000103542
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1197,275,016 - 97,303,170 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000156318   ⟹   ENSRNOP00000108650
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1197,273,234 - 97,303,170 (-)Ensembl
RefSeq Acc Id: NM_001408780   ⟹   NP_001395709
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81197,288,041 - 97,293,616 (-)NCBI
mRatBN7.21183,783,816 - 83,789,391 (-)NCBI
Protein Sequences
Protein RefSeqs NP_001395709 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000054476
  ENSRNOP00000054476.3
  ENSRNOP00000103542.1
  ENSRNOP00000108650.1
Ensembl Acc Id: ENSRNOP00000054476   ⟸   ENSRNOT00000051991
RefSeq Acc Id: NP_001395709   ⟸   NM_001408780
- UniProtKB: D4A7Z1 (UniProtKB/TrEMBL)
Ensembl Acc Id: ENSRNOP00000108650   ⟸   ENSRNOT00000156318
Ensembl Acc Id: ENSRNOP00000103542   ⟸   ENSRNOT00000134105
Protein Domains
Fibronectin type-III   SH3

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D4A7Z1-F1-model_v2 AlphaFold D4A7Z1 1-1612 view protein structure

Transcriptome

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

Promoters
RGD ID:13698350
Promoter ID:EPDNEW_R8857
Type:single initiation site
Name:Rimbp3_1
Description:RIMS 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_6.01188,038,515 - 88,038,575EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1563657 AgrOrtholog
BioCyc Gene G2FUF-20581 BioCyc
Ensembl Genes ENSRNOG00000030452 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000051991 ENTREZGENE
  ENSRNOT00000051991.6 UniProtKB/TrEMBL
  ENSRNOT00000134105.1 UniProtKB/TrEMBL
  ENSRNOT00000156318.1 UniProtKB/TrEMBL
Gene3D-CATH 2.60.40.10 UniProtKB/TrEMBL
  SH3 Domains UniProtKB/TrEMBL
InterPro FN3_sf UniProtKB/TrEMBL
  FN_III UniProtKB/TrEMBL
  Ig-like_fold UniProtKB/TrEMBL
  RIMBP1/2/3 UniProtKB/TrEMBL
  SH3-like_dom UniProtKB/TrEMBL
  SH3_domain UniProtKB/TrEMBL
NCBI Gene 303785 ENTREZGENE
PANTHER PTHR14234 UniProtKB/TrEMBL
  PTHR14234:SF21 UniProtKB/TrEMBL
Pfam fn3 UniProtKB/TrEMBL
  Ig_RIMBP2 UniProtKB/TrEMBL
  RIMB1_N UniProtKB/TrEMBL
  SH3_2 UniProtKB/TrEMBL
PhenoGen Rimbp3 PhenoGen
PROSITE FN3 UniProtKB/TrEMBL
  SH3 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000030452 RatGTEx
SMART FN3 UniProtKB/TrEMBL
  SH3 UniProtKB/TrEMBL
Superfamily-SCOP FN_III-like UniProtKB/TrEMBL
  SH3 UniProtKB/TrEMBL
UniProt D4A7Z1 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-03-31 Rimbp3  RIMS binding protein 3  RGD1563657_predicted  similar to hypothetical protein DKFZp434H177.1 - human (fragment) (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-07 RGD1563657_predicted  similar to hypothetical protein DKFZp434H177.1 - human (fragment) (predicted)  LOC303785  similar to hypothetical protein DKFZp434H177.1 - human (fragment)  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC303785  similar to hypothetical protein DKFZp434H177.1 - human (fragment)      Symbol and Name status set to provisional 70820 PROVISIONAL