RIMBP3 Gene (Protein Coding)

RIMS Binding Protein 3

GC22M018605
GIFtS:
29
See more...

Aliases for RIMBP3 Gene

Aliases for RIMBP3 Gene

  • RIMS Binding Protein 3 2 3 5
  • RIMBP3A 2 3 4
  • RIMS-Binding Protein 3A 3 4
  • RIM-BP3.1 3 4
  • RIM-BP3.A 3 4
  • RIMBP3.1 2 3
  • KIAA1666 2 4
  • RIMS Binding Protein 3.1 3
  • RIMS-Binding Protein 3.1 4
  • RIM-BP3 3
  • RIMBP3 5

External Ids for RIMBP3 Gene

Previous GeneCards Identifiers for RIMBP3 Gene

  • GC22M018843
  • GC22M020456
  • GC22M003946

Summaries for RIMBP3 Gene

GeneCards Summary for RIMBP3 Gene

RIMBP3 (RIMS Binding Protein 3) is a Protein Coding gene. Diseases associated with RIMBP3 include Retinitis Pigmentosa 43. An important paralog of this gene is RIMBP3C.

UniProtKB/Swiss-Prot Summary for RIMBP3 Gene

  • Probable component of the manchette, a microtubule-based structure which plays a key role in sperm head morphogenesis during late stages of sperm development.

Additional gene information for RIMBP3 Gene

No data available for Entrez Gene Summary , CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for RIMBP3 Gene

Genomics for RIMBP3 Gene

GeneHancer (GH) Regulatory Elements Pubs

Download GeneHancer 2017 data
Promoters and enhancers for RIMBP3 Gene
GeneHancer (GH) Identifier GH Type GH
Score		 GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites		 Gene Targets
GH22J018611 Promoter 0.4 Ensembl 600.7 +1.2 1218 2.6 ZBTB26 RIMBP3 piR-60428-001 piR-55218-001 TMEM191B
GH22J018572 Promoter 0.8 Ensembl 0.3 +36.1 36118 6.4 ARHGAP35 MTA2 YBX3 NKRF POLR2A EGR1 HDGF GATAD2A TRIM25 DPF2 UFD1 PI4KAP1 lnc-GGTLC3-4 piR-57460-432 RIMBP3 TMEM191B
GH22J018527 Promoter/Enhancer 1 Ensembl ENCODE 0.2 +82.8 82818 3.4 PRDM10 ZNF341 KLF9 SP2 EGR1 CTBP1 ZBTB40 CREB1 ZBTB26 ZBTB17 ENSG00000277690 NONHSAG033313.2 TMEM191B lnc-GGTLC3-2 RIMBP3
GH22J018591 Enhancer 0.3 Ensembl 0.4 +18.4 18418 5 CTCF KLF1 piR-57460-433 RF01210-015 RIMBP3 TMEM191B
GH22J018631 Enhancer 0.3 Ensembl 0.4 -20.0 -19982 0.2 GLIS1 ENSG00000286175 SUSD2P2 RIMBP3
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around RIMBP3 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for RIMBP3

Top Transcription factor binding sites by QIAGEN in the RIMBP3 gene promoter:
  • Brachyury
  • COMP1
  • Egr-2
  • ER-alpha
  • POU3F2
  • POU3F2 (N-Oct-5a)
  • POU3F2 (N-Oct-5b)
  • SRY
  • USF-1
  • USF1

Genomic Locations for RIMBP3 Gene

Genomic Locations for RIMBP3 Gene
chr22:18,605,815-18,611,919
(GRCh38/hg38)
Size:
6,105 bases
Orientation:
Minus strand
chr22:20,455,991-20,461,786
(GRCh37/hg19)
Size:
5,796 bases
Orientation:
Minus strand

Genomic View for RIMBP3 Gene

Genes around RIMBP3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
RIMBP3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for RIMBP3 Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for RIMBP3 Gene

Proteins for RIMBP3 Gene

Products:

  1. Antibody
  2. Protein
  3. Assay

  • Protein details for RIMBP3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9UFD9-RIM3A_HUMAN
    Recommended name:
    RIMS-binding protein 3A
    Protein Accession:
    Q9UFD9
    Secondary Accessions:
    • Q8IYP7
    • Q9BY94
    • Q9UFQ5

    Protein attributes for RIMBP3 Gene

    Size:
    1639 amino acids
    Molecular mass:
    180717 Da
    Quaternary structure:
    • Interacts with LRGUK (via guanylate kinase-like domain). Interacts (via C-terminus) with HOOK1 (via coiled-coil region).
    SequenceCaution:
    • Sequence=AAH35246.2; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305}; Sequence=BAB33336.1; Type=Frameshift; Evidence={ECO:0000305}; Sequence=CAB61362.2; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for RIMBP3 Gene

neXtProt entry for RIMBP3 Gene

Protein Expression for RIMBP3 Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Post-translational modifications for RIMBP3 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for RIMBP3 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for RIMBP3 Gene

Domains & Families for RIMBP3 Gene

Gene Families for RIMBP3 Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for RIMBP3 Gene

InterPro:
Blocks:
  • Variant SH3
ProtoNet:

Suggested Antigen Peptide Sequences for RIMBP3 Gene

GenScript: Design optimal peptide antigens:
  • RIMS-binding protein 3.1 (RIM3A_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q9UFD9

UniProtKB/Swiss-Prot:

RIM3A_HUMAN :
  • Belongs to the RIMBP family.
Family:
  • Belongs to the RIMBP family.
genes like me logo Genes that share domains with RIMBP3: view

Function for RIMBP3 Gene

Products:

  1. Animal Model
  2. CRISPR
  3. miRNA
  4. Inhibitory RNA
  5. Clone
  6. Cell Line

Molecular function for RIMBP3 Gene

UniProtKB/Swiss-Prot Function:
Probable component of the manchette, a microtubule-based structure which plays a key role in sperm head morphogenesis during late stages of sperm development.

Phenotypes From GWAS Catalog for RIMBP3 Gene

Gene Ontology (GO) - Molecular Function for RIMBP3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 24722188
GO:0030156 benzodiazepine receptor binding IBA 21873635
genes like me logo Genes that share ontologies with RIMBP3: view
genes like me logo Genes that share phenotypes with RIMBP3: view

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for RIMBP3

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , miRNA , Transcription Factor Targets and HOMER Transcription for RIMBP3 Gene

Localization for RIMBP3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for RIMBP3 Gene

Cytoplasm, cytoskeleton. Note=In elongating spermatids, localizes to the manchette. {ECO:0000250 UniProtKB:Q3V0F0}.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for RIMBP3 gene
Compartment Confidence
nucleus 4
cytoskeleton 3
cytosol 2

Subcellular locations from the

Human Protein Atlas (HPA)
  • Plasma membrane (1)
  • Vesicles (1)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for RIMBP3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0002177 colocalizes_with manchette IBA 21873635
GO:0005634 nucleus IBA 21873635
GO:0005737 cytoplasm IEA --
GO:0005856 cytoskeleton IEA --
GO:0045202 synapse IEA --
genes like me logo Genes that share ontologies with RIMBP3: view

Pathways & Interactions for RIMBP3 Gene

PathCards logo

SuperPathways for RIMBP3 Gene

No Data Available

Gene Ontology (GO) - Biological Process for RIMBP3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007274 NOT neuromuscular synaptic transmission IBA 21873635
GO:0007283 spermatogenesis IEA --
GO:0007286 spermatid development IBA 21873635
GO:0009566 fertilization IBA 21873635
GO:0030154 cell differentiation IEA --
genes like me logo Genes that share ontologies with RIMBP3: view

No data available for Pathways by source and SIGNOR curated interactions for RIMBP3 Gene

Drugs & Compounds for RIMBP3 Gene

Products:

  1. Drug
No Compound Related Data Available

Transcripts for RIMBP3 Gene

Products:

  1. CRISPR
  2. miRNA
  3. Inhibitory RNA
  4. Clone

mRNA/cDNA for RIMBP3 Gene

1 REFSEQ mRNAs :
4 NCBI additional mRNA sequence :
1 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for RIMBP3

Alternative Splicing Database (ASD) splice patterns (SP) for RIMBP3 Gene

No ASD Table

Relevant External Links for RIMBP3 Gene

GeneLoc Exon Structure for
RIMBP3

Expression for RIMBP3 Gene

Products:

  1. Primer
  2. Gene Expression Assay

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for RIMBP3 Gene

mRNA expression in normal human tissues for RIMBP3 Gene
mRNA expression by GTEx for RIMBP3 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for RIMBP3 Gene

This gene is overexpressed in Testis (x41.5).

Protein differential expression in normal tissues from HIPED for RIMBP3 Gene

This gene is overexpressed in Testis (43.1), Monocytes (13.1), and Pancreatic juice (12.8).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for RIMBP3 Gene



Protein tissue co-expression partners for RIMBP3 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for RIMBP3

SOURCE GeneReport for Unigene cluster for RIMBP3 Gene:

Hs.115429

Evidence on tissue expression from TISSUES for RIMBP3 Gene

  • Nervous system(4.2)
genes like me logo Genes that share expression patterns with RIMBP3: view

No data available for mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for RIMBP3 Gene

Orthologs for RIMBP3 Gene

This gene was present in the common ancestor of mammals.

Orthologs for RIMBP3 Gene

Organism Taxonomy Gene Similarity Type Details
Dog
(Canis familiaris)
 Mammalia LOC486445 30
  • 79.39 (n)
Cow
(Bos Taurus)
 Mammalia RIMBP3B 30
  • 75.55 (n)
Rat
(Rattus norvegicus)
 Mammalia Rimbp3 30
  • 73.95 (n)
Mouse
(Mus musculus)
 Mammalia Rimbp3 30
  • 73.68 (n)
Species where no ortholog for RIMBP3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Baker's yeast (Saccharomyces cerevisiae)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • Chicken (Gallus gallus)
  • Chimpanzee (Pan troglodytes)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Fission Yeast (Schizosaccharomyces pombe)
  • Fruit Fly (Drosophila melanogaster)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Lizard (Anolis carolinensis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Oppossum (Monodelphis domestica)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Platypus (Ornithorhynchus anatinus)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Squirt (Ciona savignyi)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Thale Cress (Arabidopsis thaliana)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Tropical Clawed Frog (Silurana tropicalis)
  • Wheat (Triticum aestivum)
  • Worm (Caenorhabditis elegans)
  • Zebrafish (Danio rerio)

Evolution for RIMBP3 Gene

ENSEMBL:
Gene Tree for RIMBP3 (if available)
TreeFam:
Gene Tree for RIMBP3 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for RIMBP3: view image

Paralogs for RIMBP3 Gene

Paralogs for RIMBP3 Gene

(2) SIMAP similar genes for RIMBP3 Gene using alignment to 1 proteins:

  • RIM3A_HUMAN
genes like me logo Genes that share paralogs with RIMBP3: view

Variants for RIMBP3 Gene

Products:

  1. SNP Genotyping and Copy Number Assay

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for RIMBP3 Gene

SNP ID Clinical significance and condition Chr 22 pos Variation AA Info Type
rs374395444 - p.Arg1513Cys

Additional dbSNP identifiers (rs#s) for RIMBP3 Gene

Structural Variations from Database of Genomic Variants (DGV) for RIMBP3 Gene

Variant ID Type Subtype PubMed ID
dgv1283e212 CNV gain 25503493
dgv16n31 CNV gain 19718026
dgv173e55 CNV gain 17911159
dgv2431n106 OTHER inversion 24896259
dgv4466n100 CNV gain+loss 25217958
dgv4467n100 CNV gain 25217958
dgv7963n54 CNV gain 21841781
dgv7964n54 CNV loss 21841781
dgv7965n54 CNV gain 21841781
dgv7989n54 CNV gain 21841781
dgv817e199 CNV deletion 23128226
dgv99e203 CNV gain+loss 21179565
esv22247 CNV gain+loss 19812545
esv26930 CNV gain+loss 19812545
esv2751935 CNV loss 17911159
esv2758824 CNV gain+loss 17122850
esv32687 CNV gain+loss 17666407
esv3381183 CNV duplication 20981092
esv3575418 CNV gain 25503493
nsv1055756 CNV gain 25217958
nsv1061694 CNV gain 25217958
nsv1071779 CNV deletion 25765185
nsv1144016 CNV deletion 24896259
nsv1146969 CNV duplication 26484159
nsv428385 CNV gain+loss 18775914
nsv469578 CNV gain 16826518
nsv471339 CNV gain 19718026
nsv471594 CNV gain+loss 15918152
nsv516997 CNV gain+loss 19592680
nsv588139 CNV loss 21841781
nsv820540 CNV duplication 20802225
nsv953028 CNV deletion 24416366
nsv962755 CNV duplication 23825009
nsv964588 CNV duplication 23825009

Variation tolerance for RIMBP3 Gene

Gene Damage Index Score: 7.84; 83.56% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for RIMBP3 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
RIMBP3

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for RIMBP3 Gene

Disorders for RIMBP3 Gene

MalaCards: The human disease database

(1) MalaCards diseases for RIMBP3 Gene - From: DISEASES

Disorder Aliases PubMed IDs
retinitis pigmentosa 43
  • rp43
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for RIMBP3

ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
genes like me logo Genes that share disorders with RIMBP3: view

No data available for UniProtKB/Swiss-Prot and Genatlas for RIMBP3 Gene

Publications for RIMBP3 Gene

  1. Identification of novel transcribed sequences on human chromosome 22 by expressed sequence tag mapping. (PMID: 11258795) Hirosawa M … Ohara O (DNA research : an international journal for rapid publication of reports on genes and genomes 2001) 2 3 4
  2. Structure and evolution of RIM-BP genes: identification of a novel family member. (PMID: 17855024) Mittelstaedt T … Schoch S (Gene 2007) 2 3
  3. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4
  4. The DNA sequence of human chromosome 22. (PMID: 10591208) Dunham I … O'Brien KP (Nature 1999) 3 4
  5. Extensive disruption of protein interactions by genetic variants across the allele frequency spectrum in human populations. (PMID: 31515488) Fragoza R … Yu H (Nature communications 2019) 3

ExternalLinks

View latest publications for RIMBP3 gene in Mastermind

Products for RIMBP3 Gene

Sources for RIMBP3 Gene