Aliases for RIMBP3B Gene

Aliases for RIMBP3B Gene

  • RIMS Binding Protein 3B 2 3 5
  • RIMS-Binding Protein 3B 3 4
  • RIM-BP3.2 3 4
  • RIM-BP3.B 3 4
  • RIMS Binding Protein 3.2 3
  • RIMS-Binding Protein 3.2 4
  • RIMBP3.2 3

External Ids for RIMBP3B Gene

Previous GeneCards Identifiers for RIMBP3B Gene

  • GC22P020067
  • GC22P021738
  • GC22P021759
  • GC22P021775
  • GC22P021797
  • GC22P021451
  • GC22P021489
  • GC22P022093
  • GC22P022136
  • GC22P021512
  • GC22P021558
  • GC22P021851
  • GC22P021890
  • GC22P021928
  • GC22P021964
  • GC22P022001
  • GC22P022051

Summaries for RIMBP3B Gene

GeneCards Summary for RIMBP3B Gene

RIMBP3B (RIMS Binding Protein 3B) is a Protein Coding gene. An important paralog of this gene is RIMBP3C.

UniProtKB/Swiss-Prot Summary for RIMBP3B 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 RIMBP3B Gene

No data available for Entrez Gene Summary , CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for RIMBP3B Gene

Genomics for RIMBP3B Gene

GeneHancer (GH) Regulatory Elements for RIMBP3B Gene

Promoters and enhancers for RIMBP3B 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
GH22J021383 Promoter 0.3 Ensembl 750.6 +1.2 1227 2.8 RIMBP3B piR-60428-002 piR-55218-002
GH22J022109 Enhancer 1 Ensembl ENCODE 4.7 +728.8 728827 5.6 CTCF RUNX1 RELA RAD21 ZFX MLLT1 ZNF687 CAVIN1 IKZF1 PRDM10 ABHD17AP5 TOP3B ENSG00000272779 IGLV5-52 ENSG00000234630 IGLV2-14 PPIL2 IGLC2 YPEL1 IGLV8-61
GH22J021386 Promoter 0.3 Ensembl 0.6 +2.9 2927 0.2 piR-42948-002 piR-60428-002 piR-55218-002 RIMBP3B
GH22J021388 Enhancer 0.2 Ensembl 0.4 +6.3 6327 2.6 ENSG00000252020 RN7SKP63 RF00283-002 piR-42948-002 lnc-RIMBP3-1-002 RIMBP3B
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around RIMBP3B on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the RIMBP3B gene promoter:
  • Brachyury
  • COMP1
  • Egr-2
  • ER-alpha
  • POU3F2
  • POU3F2 (N-Oct-5a)
  • POU3F2 (N-Oct-5b)
  • SRY
  • USF-1
  • USF1

Genomic Locations for RIMBP3B Gene

Genomic Locations for RIMBP3B Gene
chr22:21,383,374-21,389,478
(GRCh38/hg38)
Size:
6,105 bases
Orientation:
Plus strand
chr22:21,737,663-21,743,458
(GRCh37/hg19)
Size:
5,796 bases
Orientation:
Plus strand

Genomic View for RIMBP3B Gene

Genes around RIMBP3B on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
RIMBP3B Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for RIMBP3B Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for RIMBP3B Gene

Proteins for RIMBP3B Gene

  • Protein details for RIMBP3B Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    A6NNM3-RIM3B_HUMAN
    Recommended name:
    RIMS-binding protein 3B
    Protein Accession:
    A6NNM3

    Protein attributes for RIMBP3B Gene

    Size:
    1639 amino acids
    Molecular mass:
    180952 Da
    Quaternary structure:
    • Interacts with LRGUK (via guanylate kinase-like domain). Interacts (via C-terminus) with HOOK1 (via coiled-coil region).

neXtProt entry for RIMBP3B Gene

Post-translational modifications for RIMBP3B Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for RIMBP3B Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for RIMBP3B Gene

Domains & Families for RIMBP3B Gene

Gene Families for RIMBP3B Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for RIMBP3B Gene

Suggested Antigen Peptide Sequences for RIMBP3B Gene

GenScript: Design optimal peptide antigens:
  • RIMS-binding protein 3.2 (RIM3B_HUMAN)

Graphical View of Domain Structure for InterPro Entry

A6NNM3

UniProtKB/Swiss-Prot:

RIM3B_HUMAN :
  • Belongs to the RIMBP family.
Family:
  • Belongs to the RIMBP family.
genes like me logo Genes that share domains with RIMBP3B: view

Function for RIMBP3B Gene

Molecular function for RIMBP3B 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.

Gene Ontology (GO) - Molecular Function for RIMBP3B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IEA --
GO:0030156 benzodiazepine receptor binding IBA 21873635
genes like me logo Genes that share ontologies with RIMBP3B: view

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for RIMBP3B

No data available for Enzyme Numbers (IUBMB) , Phenotypes From GWAS Catalog , Phenotypes , Human Phenotype Ontology , Animal Models , miRNA , Transcription Factor Targets and HOMER Transcription for RIMBP3B Gene

Localization for RIMBP3B Gene

Subcellular locations from UniProtKB/Swiss-Prot for RIMBP3B Gene

Cytoplasm, cytoskeleton.

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 RIMBP3B 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 RIMBP3B 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 --
genes like me logo Genes that share ontologies with RIMBP3B: view

Pathways & Interactions for RIMBP3B Gene

PathCards logo

SuperPathways for RIMBP3B Gene

No Data Available

Gene Ontology (GO) - Biological Process for RIMBP3B 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 RIMBP3B: view

No data available for Pathways by source and SIGNOR curated interactions for RIMBP3B Gene

Drugs & Compounds for RIMBP3B Gene

No Compound Related Data Available

Transcripts for RIMBP3B Gene

mRNA/cDNA for RIMBP3B Gene

(1) REFSEQ mRNAs :
(2) Additional mRNA sequences :
(37) Selected AceView cDNA sequences:
(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 RIMBP3B

Alternative Splicing Database (ASD) splice patterns (SP) for RIMBP3B Gene

No ASD Table

Relevant External Links for RIMBP3B Gene

GeneLoc Exon Structure for
RIMBP3B
ECgene alternative splicing isoforms for
RIMBP3B

Expression for RIMBP3B Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for RIMBP3B Gene

mRNA differential expression in normal tissues according to GTEx for RIMBP3B Gene

This gene is overexpressed in Testis (x42.8).

NURSA nuclear receptor signaling pathways regulating expression of RIMBP3B Gene:

RIMBP3B

SOURCE GeneReport for Unigene cluster for RIMBP3B Gene:

Hs.568257
genes like me logo Genes that share expression patterns with RIMBP3B: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , Protein differential expression in normal tissues , Protein expression , Protein tissue co-expression partners , mRNA Expression by UniProt/SwissProt , Evidence on tissue expression from TISSUES and Phenotype-based relationships between genes and organs from Gene ORGANizer for RIMBP3B Gene

Orthologs for RIMBP3B Gene

This gene was present in the common ancestor of mammals.

Orthologs for RIMBP3B Gene

Organism Taxonomy Gene Similarity Type Details
dog
(Canis familiaris)
Mammalia LOC486445 32
  • 79.31 (n)
cow
(Bos Taurus)
Mammalia RIMBP3B 32
  • 75.6 (n)
rat
(Rattus norvegicus)
Mammalia Rimbp3 32
  • 73.97 (n)
mouse
(Mus musculus)
Mammalia Rimbp3 32
  • 73.66 (n)
Species where no ortholog for RIMBP3B was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya 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 squirt (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 RIMBP3B Gene

ENSEMBL:
Gene Tree for RIMBP3B (if available)
TreeFam:
Gene Tree for RIMBP3B (if available)

Paralogs for RIMBP3B Gene

Paralogs for RIMBP3B Gene

(2) SIMAP similar genes for RIMBP3B Gene using alignment to 1 proteins:

  • RIM3B_HUMAN
genes like me logo Genes that share paralogs with RIMBP3B: view

Variants for RIMBP3B Gene

Sequence variations from dbSNP and Humsavar for RIMBP3B Gene

SNP ID Clin Chr 22 pos Variation AA Info Type
rs1007518731 -- 21,388,296(+) G/C coding_sequence_variant, missense_variant
rs1025949559 -- 21,388,668(+) A/G coding_sequence_variant, missense_variant
rs1036275509 -- 21,389,182(+) T/G downstream_transcript_variant
rs1043176614 -- 21,383,096(+) C/T upstream_transcript_variant
rs1052037670 -- 21,388,193(+) G/A coding_sequence_variant, synonymous_variant

Structural Variations from Database of Genomic Variants (DGV) for RIMBP3B Gene

Variant ID Type Subtype PubMed ID
dgv4486n100 CNV gain 25217958
dgv4487n100 CNV gain 25217958
dgv4488n100 CNV gain 25217958
dgv4489n100 CNV gain 25217958
dgv4491n100 CNV gain 25217958
dgv7996n54 CNV gain 21841781
dgv819e199 CNV deletion 23128226
dgv820e199 CNV deletion 23128226
esv25508 CNV gain+loss 19812545
esv2661723 CNV deletion 23128226
esv2678291 CNV deletion 23128226
esv2760719 CNV gain 21179565
esv2763699 CNV gain+loss 21179565
esv28075 CNV gain+loss 19812545
esv3584494 CNV gain 24956385
esv3893444 CNV gain 25118596
nsv1066391 CNV gain 25217958
nsv1072204 CNV deletion 25765185
nsv1072625 CNV deletion 25765185
nsv1118945 CNV deletion 24896259
nsv1160729 CNV duplication 26073780
nsv1160730 CNV deletion 26073780
nsv428386 CNV loss 18775914
nsv436864 CNV insertion 17901297
nsv437849 CNV loss 16327808
nsv442791 CNV gain 18776908
nsv469545 CNV gain 16826518
nsv471490 CNV gain 19718026
nsv471596 CNV gain+loss 15918152
nsv511071 OTHER inversion 20534489
nsv7350 OTHER inversion 18451855
nsv834145 CNV loss 17160897
nsv953041 CNV deletion 24416366
nsv953042 CNV deletion 24416366
nsv962765 CNV duplication 23825009
nsv966082 CNV duplication 23825009

Variation tolerance for RIMBP3B Gene

Gene Damage Index Score: 1.18; 23.80% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for RIMBP3B Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
RIMBP3B

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for RIMBP3B Gene

Disorders for RIMBP3B Gene

Additional Disease Information for RIMBP3B

No disorders were found for RIMBP3B Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for RIMBP3B Gene

Publications for RIMBP3B Gene

  1. Structure and evolution of RIM-BP genes: identification of a novel family member. (PMID: 17855024) Mittelstaedt T … Schoch S (Gene 2007) 2 3 56
  2. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. (PMID: 21873635) Gaudet P … Thomas PD (Briefings in bioinformatics 2011) 3 56
  3. Toward a confocal subcellular atlas of the human proteome. (PMID: 18029348) Barbe L … Andersson-Svahn H (Molecular & cellular proteomics : MCP 2008) 3 56
  4. The DNA sequence of human chromosome 22. (PMID: 10591208) Dunham I … O'Brien KP (Nature 1999) 4 56

Products for RIMBP3B Gene

Sources for RIMBP3B Gene