Aliases for RAB3IP Gene

Aliases for RAB3IP Gene

  • RAB3A Interacting Protein 2 3 5
  • RABIN8 2 3 4
  • Rab-3A-Interacting Protein 3 4
  • Rab3A-Interacting Protein 3 4
  • Rabin-3 3 4
  • RABIN3 2 3
  • SSX2 Interacting Protein 3
  • SSX2-Interacting Protein 4
  • FLJ22548 2
  • Rabin3 2
  • RAB3IP 5

External Ids for RAB3IP Gene

Previous GeneCards Identifiers for RAB3IP Gene

  • GC00U991125
  • GC12U900020
  • GC12P069849
  • GC12P068418
  • GC12P070132
  • GC12P067181

Summaries for RAB3IP Gene

GeneCards Summary for RAB3IP Gene

RAB3IP (RAB3A Interacting Protein) is a Protein Coding gene. Diseases associated with RAB3IP include Nephronophthisis 15 and Bardet-Biedl Syndrome 3. Among its related pathways are Vesicle-mediated transport and Organelle biogenesis and maintenance. Gene Ontology (GO) annotations related to this gene include Rab guanyl-nucleotide exchange factor activity. An important paralog of this gene is RAB3IL1.

UniProtKB/Swiss-Prot Summary for RAB3IP Gene

  • Guanine nucleotide exchange factor (GEF) which may activate RAB8A and RAB8B (PubMed:12221131, PubMed:26824392). Promotes the exchange of GDP to GTP, converting inactive GDP-bound Rab proteins into their active GTP-bound form (PubMed:12221131, PubMed:26824392). Mediates the release of GDP from RAB8A and RAB8B but not from RAB3A or RAB5 (PubMed:20937701, PubMed:26824392). Modulates actin organization and promotes polarized transport of RAB8A-specific vesicles to the cell surface (PubMed:12221131). Together with RAB11A, RAB8A, the exocyst complex, PARD3, PRKCI, ANXA2, CDC42 and DNMBP promotes transcytosis of PODXL to the apical membrane initiation sites (AMIS), apical surface formation and lumenogenesis (PubMed:20890297).

Gene Wiki entry for RAB3IP Gene

No data available for Entrez Gene Summary , CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for RAB3IP Gene

Genomics for RAB3IP Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for RAB3IP 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
GH12J069738 Promoter/Enhancer 2 EPDnew Ensembl ENCODE CraniofacialAtlas 263 +1.6 1594 3.2 SP1 ZNF600 ATF2 KLF9 CEBPA ATF3 POLR2A ZIC2 YY1 CTCF LOC101928002 RAB3IP MYRFL CPSF6 PRANCR HSALNG0092280 ENSG00000258052
GH12J069778 Promoter/Enhancer 1.2 EPDnew Ensembl ENCODE 250.3 +41.5 41458 1.3 CTCF RAD21 ZNF143 CREB1 FOS TRIM22 BACH1 piR-45874-053 piR-52680-077 piR-57394-049 piR-55361-128 RAB3IP HSALNG0092280 ENSG00000258052
GH12J069801 Promoter 0.3 EPDnew 250.2 +63.6 63605 0.1 ENSG00000258052 RAB3IP piR-57394-049
GH12J069820 Promoter 0.3 EPDnew 250.2 +82.0 82040 0.1 piR-52823 RAB3IP MYRFL HSALNG0092285 ENSG00000258052
GH12J069685 Promoter/Enhancer 1.3 EPDnew Ensembl ENCODE 21.1 -50.3 -50306 7 ZNF600 IKZF1 JUND ZNF592 ZIC2 DEK ELK1 MAX ELF1 SAP130 BEST3 lnc-LRRC10-3 RAB3IP LOC101928002 LYZ MDM2 RF00017-1075 LOC105369823 lnc-CCT2-2 LRRC10
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around RAB3IP on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for RAB3IP

Top Transcription factor binding sites by QIAGEN in the RAB3IP gene promoter:
  • E4BP4
  • HOXA3
  • POU2F1
  • POU2F1a
  • STAT5A

Genomic Locations for RAB3IP Gene

Latest Assembly
chr12:69,738,007-69,823,204
(GRCh38/hg38)
Size:
85,198 bases
Orientation:
Plus strand

Previous Assembly
chr12:70,132,640-70,216,984
(GRCh37/hg19 by Entrez Gene)
Size:
84,345 bases
Orientation:
Plus strand

chr12:70,132,461-70,216,984
(GRCh37/hg19 by Ensembl)
Size:
84,524 bases
Orientation:
Plus strand

Genomic View for RAB3IP Gene

Genes around RAB3IP on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
RAB3IP Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for RAB3IP Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for RAB3IP Gene

Proteins for RAB3IP Gene

  • Protein details for RAB3IP Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q96QF0-RAB3I_HUMAN
    Recommended name:
    Rab-3A-interacting protein
    Protein Accession:
    Q96QF0
    Secondary Accessions:
    • B7WPJ6
    • Q6PCE4
    • Q96A24
    • Q96QE6
    • Q96QE7
    • Q96QE8
    • Q96QE9
    • Q96QF1
    • Q9H673

    Protein attributes for RAB3IP Gene

    Size:
    476 amino acids
    Molecular mass:
    53021 Da
    Quaternary structure:
    • Interacts with the N-terminal region of SSX2 (PubMed:12007189). Interacts with the GDP-bound forms of RAB8A and RAB8B (PubMed:26824392, PubMed:12221131). The interaction with RAB8A is prevented by phosphorylation of RAB8A at 'Thr-72' (PubMed:26824392). Interacts with the GDP-bound forms of RAB3A and RAB3D (PubMed:12221131). Interacts with DCDC1 (PubMed:22159412, PubMed:12007189, PubMed:12221131, PubMed:26824392). Interacts (via the N-terminal region) with TRAPPC14; this interaction mediates RAB3IP association with the TRAPP II complex (PubMed:31467083).

    Three dimensional structures from OCA and Proteopedia for RAB3IP Gene

    Alternative splice isoforms for RAB3IP Gene

neXtProt entry for RAB3IP Gene

Post-translational modifications for RAB3IP Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for RAB3IP Gene

Domains & Families for RAB3IP Gene

Gene Families for RAB3IP Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for RAB3IP Gene

Suggested Antigen Peptide Sequences for RAB3IP Gene

GenScript: Design optimal peptide antigens:
  • SSX2-interacting protein (RAB3I_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q96QF0

UniProtKB/Swiss-Prot:

RAB3I_HUMAN :
  • Belongs to the SEC2 family.
Family:
  • Belongs to the SEC2 family.
genes like me logo Genes that share domains with RAB3IP: view

Function for RAB3IP Gene

Molecular function for RAB3IP Gene

UniProtKB/Swiss-Prot Function:
Guanine nucleotide exchange factor (GEF) which may activate RAB8A and RAB8B (PubMed:12221131, PubMed:26824392). Promotes the exchange of GDP to GTP, converting inactive GDP-bound Rab proteins into their active GTP-bound form (PubMed:12221131, PubMed:26824392). Mediates the release of GDP from RAB8A and RAB8B but not from RAB3A or RAB5 (PubMed:20937701, PubMed:26824392). Modulates actin organization and promotes polarized transport of RAB8A-specific vesicles to the cell surface (PubMed:12221131). Together with RAB11A, RAB8A, the exocyst complex, PARD3, PRKCI, ANXA2, CDC42 and DNMBP promotes transcytosis of PODXL to the apical membrane initiation sites (AMIS), apical surface formation and lumenogenesis (PubMed:20890297).

Phenotypes From GWAS Catalog for RAB3IP Gene

Gene Ontology (GO) - Molecular Function for RAB3IP Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005085 guanyl-nucleotide exchange factor activity IEA,IDA 20937701
GO:0005515 protein binding IPI 12007189
GO:0042802 identical protein binding IPI --
genes like me logo Genes that share ontologies with RAB3IP: view
genes like me logo Genes that share phenotypes with RAB3IP: view

Animal Models for RAB3IP Gene

MGI Knock Outs for RAB3IP:
  • Rab3ip Rab3ip<tm1.1(KOMP)Vlcg>

miRNA for RAB3IP Gene

miRTarBase miRNAs that target RAB3IP

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for RAB3IP

Clone products for research

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for RAB3IP Gene

Localization for RAB3IP Gene

Subcellular locations from UniProtKB/Swiss-Prot for RAB3IP Gene

Cytoplasm. Nucleus. Cytoplasm, cytoskeleton. Cell projection, lamellipodium. Vesicle. Cytoplasm, cytoskeleton, microtubule organizing center, centrosome. Note=Predominantly cytoplasmic but a small proportion colocalizes with SSX2 in the nucleus. Activation of protein kinase C results in redistribution to the periphery of lamellipodia. {ECO:0000269 PubMed:12007189}.

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 RAB3IP gene
Compartment Confidence
cytoskeleton 5
nucleus 5
cytosol 5
plasma membrane 2
endosome 2
golgi apparatus 2
extracellular 1
mitochondrion 1
endoplasmic reticulum 1
lysosome 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Intermediate filaments (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for RAB3IP Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA,IDA 12007189
GO:0005737 cytoplasm IEA --
GO:0005813 centrosome IDA --
GO:0005829 cytosol TAS --
GO:0005856 cytoskeleton IEA --
genes like me logo Genes that share ontologies with RAB3IP: view

Pathways & Interactions for RAB3IP Gene

genes like me logo Genes that share pathways with RAB3IP: view

SIGNOR curated interactions for RAB3IP Gene

Is activated by:

Gene Ontology (GO) - Biological Process for RAB3IP Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006612 protein targeting to membrane IDA 23382462
GO:0006887 exocytosis IBA 21873635
GO:0006893 Golgi to plasma membrane transport TAS --
GO:0015031 protein transport IEA --
GO:0033365 protein localization to organelle IMP --
genes like me logo Genes that share ontologies with RAB3IP: view

Drugs & Compounds for RAB3IP Gene

No Compound Related Data Available

Transcripts for RAB3IP Gene

mRNA/cDNA for RAB3IP Gene

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

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for RAB3IP

Clone products for research

Alternative Splicing Database (ASD) splice patterns (SP) for RAB3IP Gene

ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5a · 5b · 5c ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11a · 11b ^ 12 ^ 13
SP1: - - - - -
SP2: - - - -
SP3: - - - - -
SP4: - - - - - -
SP5: - -
SP6: -
SP7:

Relevant External Links for RAB3IP Gene

GeneLoc Exon Structure for
RAB3IP

Expression for RAB3IP Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for RAB3IP Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for RAB3IP Gene

This gene is overexpressed in Brain - Cerebellar Hemisphere (x6.6) and Brain - Cerebellum (x4.8).

Protein differential expression in normal tissues from HIPED for RAB3IP Gene

This gene is overexpressed in Retina (29.5), Fetal Brain (9.1), Fetal ovary (9.0), and Islet of Langerhans (9.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for RAB3IP Gene



Protein tissue co-expression partners for RAB3IP Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for RAB3IP

SOURCE GeneReport for Unigene cluster for RAB3IP Gene:

Hs.258209

mRNA Expression by UniProt/SwissProt for RAB3IP Gene:

Q96QF0-RAB3I_HUMAN
Tissue specificity: Expressed in brain, kidney, heart, pancreas and placenta. Not detected in skeletal muscle or liver.

Evidence on tissue expression from TISSUES for RAB3IP Gene

  • Nervous system(4.8)
  • Liver(4.4)
  • Lung(2.7)
  • Kidney(2.5)
  • Eye(2.1)
genes like me logo Genes that share expression patterns with RAB3IP: view

Primer products for research

No data available for Phenotype-based relationships between genes and organs from Gene ORGANizer for RAB3IP Gene

Orthologs for RAB3IP Gene

This gene was present in the common ancestor of animals.

Orthologs for RAB3IP Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia RAB3IP 29 30
  • 99.93 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia -- 30
  • 97 (a)
OneToMany
RAB3IP 29
  • 94.37 (n)
Cow
(Bos Taurus)
Mammalia RAB3IP 29 30
  • 93.12 (n)
OneToMany
Platypus
(Ornithorhynchus anatinus)
Mammalia -- 30
  • 89 (a)
OneToMany
Oppossum
(Monodelphis domestica)
Mammalia -- 30
  • 88 (a)
OneToMany
Rat
(Rattus norvegicus)
Mammalia Rab3ip 29
  • 85.14 (n)
Mouse
(Mus musculus)
Mammalia Rab3ip 29 16 30
  • 84.97 (n)
OneToMany
Chicken
(Gallus gallus)
Aves -- 30
  • 86 (a)
OneToMany
RAB3IP 29
  • 82.08 (n)
Lizard
(Anolis carolinensis)
Reptilia -- 30
  • 79 (a)
OneToMany
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia rab3ip 29
  • 73.3 (n)
Zebrafish
(Danio rerio)
Actinopterygii rab3ip 29 30
  • 66.67 (n)
OneToMany
Dr.11691 29
Worm
(Caenorhabditis elegans)
Secernentea F54C9.11 30
  • 28 (a)
OneToMany
Sea Squirt
(Ciona savignyi)
Ascidiacea -- 30
  • 36 (a)
OneToMany
Species where no ortholog for RAB3IP 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)
  • 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)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • 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 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)
  • Wheat (Triticum aestivum)

Evolution for RAB3IP Gene

ENSEMBL:
Gene Tree for RAB3IP (if available)
TreeFam:
Gene Tree for RAB3IP (if available)
Aminode:
Evolutionary constrained regions (ECRs) for RAB3IP: view image
Alliance of Genome Resources:
Additional Orthologs for RAB3IP

Paralogs for RAB3IP Gene

Paralogs for RAB3IP Gene

(1) SIMAP similar genes for RAB3IP Gene using alignment to 8 proteins:

  • RAB3I_HUMAN
  • F8VNX9_HUMAN
  • F8VTR6_HUMAN
  • H0YD03_HUMAN
  • H0YHP4_HUMAN
  • H0YI02_HUMAN
  • H0YI66_HUMAN
  • J3KPG1_HUMAN
genes like me logo Genes that share paralogs with RAB3IP: view

Variants for RAB3IP Gene

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for RAB3IP Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

Structural Variations from Database of Genomic Variants (DGV) for RAB3IP Gene

Variant ID Type Subtype PubMed ID
esv1958700 CNV deletion 18987734
esv2746020 CNV deletion 23290073
nsv52529 CNV deletion 16902084

Variation tolerance for RAB3IP Gene

Residual Variation Intolerance Score: 12.5% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.29; 40.99% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for RAB3IP Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
RAB3IP
Leiden Open Variation Database (LOVD)
RAB3IP

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for RAB3IP Gene

Disorders for RAB3IP Gene

MalaCards: The human disease database

(11) MalaCards diseases for RAB3IP Gene - From: COP

- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for RAB3IP

genes like me logo Genes that share disorders with RAB3IP: view

No data available for UniProtKB/Swiss-Prot and Genatlas for RAB3IP Gene

Publications for RAB3IP Gene

  1. The cancer-related protein SSX2 interacts with the human homologue of a Ras-like GTPase interactor, RAB3IP, and a novel nuclear protein, SSX2IP. (PMID: 12007189) de Bruijn DR … van Kessel AG (Genes, chromosomes & cancer 2002) 3 4 22
  2. A Rab8-specific GDP/GTP exchange factor is involved in actin remodeling and polarized membrane transport. (PMID: 12221131) Hattula K … Peränen J (Molecular biology of the cell 2002) 2 3 4
  3. The C7orf43/TRAPPC14 component links the TRAPPII complex to Rabin8 for preciliary vesicle tethering at the mother centriole during ciliogenesis. (PMID: 31467083) Cuenca A … Westlake CJ (The Journal of biological chemistry 2019) 3 4
  4. Phosphoproteomics reveals that Parkinson's disease kinase LRRK2 regulates a subset of Rab GTPases. (PMID: 26824392) Steger M … Mann M (eLife 2016) 3 4
  5. Linking cytoplasmic dynein and transport of Rab8 vesicles to the midbody during cytokinesis by the doublecortin domain-containing 5 protein. (PMID: 22159412) Kaplan A … Reiner O (Journal of cell science 2011) 3 4

Products for RAB3IP Gene

Sources for RAB3IP Gene