This gene encodes a guanine nucleotide exchange factor for the ras-related protein Rab3A. The encoded protein binds Rab3a and the inositol hexakisphosphate kinase InsP6K1. Alternative splicing results in multiple transcript variants. A related pseudogene has been identified on chromosome 7. [provided by RefSeq, Nov 2012] See more...

Aliases for RAB3IL1 Gene

Aliases for RAB3IL1 Gene

  • RAB3A Interacting Protein Like 1 2 3 5
  • Guanine Nucleotide Exchange Factor For Rab-3A 3 4
  • RAB3A Interacting Protein (Rabin3)-Like 1 2 3
  • Rab3A-Interacting-Like Protein 1 3 4
  • Rabin3-Like 1 3 4
  • GRAB 2 3
  • Guanine Nucleotide Exchange Factor For Rab3A 2
  • Rab-3A-Interacting-Like Protein 1 4
  • RAB3IL1 5

External Ids for RAB3IL1 Gene

Previous GeneCards Identifiers for RAB3IL1 Gene

  • GC11M064178
  • GC11M063240
  • GC11M061915
  • GC11M061440
  • GC11M061422
  • GC11M061664
  • GC11M057992

Summaries for RAB3IL1 Gene

Entrez Gene Summary for RAB3IL1 Gene

  • This gene encodes a guanine nucleotide exchange factor for the ras-related protein Rab3A. The encoded protein binds Rab3a and the inositol hexakisphosphate kinase InsP6K1. Alternative splicing results in multiple transcript variants. A related pseudogene has been identified on chromosome 7. [provided by RefSeq, Nov 2012]

GeneCards Summary for RAB3IL1 Gene

RAB3IL1 (RAB3A Interacting Protein Like 1) is a Protein Coding gene. Diseases associated with RAB3IL1 include Inflammatory Bowel Disease 2 and Spinocerebellar Ataxia 20. Among its related pathways are Vesicle-mediated transport and RAB GEFs exchange GTP for GDP on RABs. Gene Ontology (GO) annotations related to this gene include Rab guanyl-nucleotide exchange factor activity. An important paralog of this gene is RAB3IP.

UniProtKB/Swiss-Prot Summary for RAB3IL1 Gene

  • Guanine nucleotide exchange factor (GEF) which may activate RAB3A, a GTPase that regulates synaptic vesicle exocytosis. Promotes the exchange of GDP to GTP, converting inactive GDP-bound Rab proteins into their active GTP-bound form. May also activate RAB8A and RAB8B.

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for RAB3IL1 Gene

Genomics for RAB3IL1 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for RAB3IL1 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
GH11J061916 Promoter/Enhancer 2.5 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 278.8 +25.3 25252 9.7 IKZF1 MYC NCOR1 ZNF580 ZNF592 ZMYM3 POLR2A ZIC2 NFIC NONO RAB3IL1 CSKMT CPSF7 TUT1 TAF6L WDR74 GANAB SNHG1 FADS3 BEST1
GH11J061947 Enhancer 1 ENCODE dbSUPER 250.7 -1.7 -1668 0.9 ZNF207 ZNF654 ZNF600 ZNF592 ZIC2 NFIC CTCF REST DEK TRIM22 BEST1 RAB3IL1 lnc-FTH1-5 FTH1
GH11J061950 Enhancer 0.8 CraniofacialAtlas dbSUPER 250.7 -1.1 -1117 0.2 ZNF592 ZIC2 GABPB1 CTCF EP400 REST IKZF1 ZNF48 HDGF CTBP1 BEST1 RAB3IL1 lnc-FTH1-5 FTH1
GH11J061946 Promoter/Enhancer 0.5 EPDnew dbSUPER 250.7 0.0 -20 0.1 BEST1 RAB3IL1
GH11J061960 Promoter/Enhancer 2.7 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 11.8 -22.6 -22612 16.4 BCLAF1 SP1 NCOR1 MYC IKZF1 ZNF600 SSRP1 JUND ZNF592 KLF9 FTH1 HSALNG0084568 LOC399900 MN297049 lnc-RAB3IL1-2 CPSF7 NXF1 GANAB TMEM138 STX5-DT
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around RAB3IL1 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for RAB3IL1

Top Transcription factor binding sites by QIAGEN in the RAB3IL1 gene promoter:
  • AML1a
  • AP-2gamma
  • c-Ets-1
  • LyF-1
  • NF-E2 p45
  • NRF-2
  • Pax-5
  • STAT1
  • STAT1alpha
  • STAT1beta

Genomic Locations for RAB3IL1 Gene

Latest Assembly
chr11:61,897,299-61,946,312
(GRCh38/hg38)
Size:
49,014 bases
Orientation:
Minus strand

Previous Assembly
chr11:61,664,773-61,687,756
(GRCh37/hg19 by Entrez Gene)
Size:
22,984 bases
Orientation:
Minus strand

chr11:61,664,773-61,687,741
(GRCh37/hg19 by Ensembl)
Size:
22,969 bases
Orientation:
Minus strand

Genomic View for RAB3IL1 Gene

Genes around RAB3IL1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
RAB3IL1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for RAB3IL1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for RAB3IL1 Gene

Proteins for RAB3IL1 Gene

  • Protein details for RAB3IL1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q8TBN0-R3GEF_HUMAN
    Recommended name:
    Guanine nucleotide exchange factor for Rab-3A
    Protein Accession:
    Q8TBN0
    Secondary Accessions:
    • Q86V32
    • Q9P1Q8

    Protein attributes for RAB3IL1 Gene

    Size:
    382 amino acids
    Molecular mass:
    42637 Da
    Quaternary structure:
    • Interacts with RAB3A and IHPK1 through the coiled-coil domain. This interaction is competitive. IHPK1 kinase activity is not required for this interaction (By similarity).

    Three dimensional structures from OCA and Proteopedia for RAB3IL1 Gene

    Alternative splice isoforms for RAB3IL1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for RAB3IL1 Gene

Post-translational modifications for RAB3IL1 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for RAB3IL1 Gene

Domains & Families for RAB3IL1 Gene

Gene Families for RAB3IL1 Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for RAB3IL1 Gene

InterPro:
Blocks:
  • Protein kinase PKN/PRK1, effector

Suggested Antigen Peptide Sequences for RAB3IL1 Gene

GenScript: Design optimal peptide antigens:
  • Rabin3-like 1 (R3GEF_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q8TBN0

UniProtKB/Swiss-Prot:

R3GEF_HUMAN :
  • Belongs to the SEC2 family.
Family:
  • Belongs to the SEC2 family.
genes like me logo Genes that share domains with RAB3IL1: view

Function for RAB3IL1 Gene

Molecular function for RAB3IL1 Gene

UniProtKB/Swiss-Prot Function:
Guanine nucleotide exchange factor (GEF) which may activate RAB3A, a GTPase that regulates synaptic vesicle exocytosis. Promotes the exchange of GDP to GTP, converting inactive GDP-bound Rab proteins into their active GTP-bound form. May also activate RAB8A and RAB8B.
GENATLAS Biochemistry:
RAB3A interacting protein (rabin3)-like 1

Phenotypes From GWAS Catalog for RAB3IL1 Gene

Gene Ontology (GO) - Molecular Function for RAB3IL1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005085 guanyl-nucleotide exchange factor activity IBA,IDA 20937701
GO:0005515 protein binding IPI 16189514
GO:0042802 identical protein binding IPI 16189514
genes like me logo Genes that share ontologies with RAB3IL1: view
genes like me logo Genes that share phenotypes with RAB3IL1: view

miRNA for RAB3IL1 Gene

miRTarBase miRNAs that target RAB3IL1

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for RAB3IL1

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for RAB3IL1 Gene

Localization for RAB3IL1 Gene

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 RAB3IL1 gene
Compartment Confidence
cytosol 5
mitochondrion 2
nucleus 2
golgi apparatus 2
plasma membrane 1
extracellular 1
cytoskeleton 1
endoplasmic reticulum 1
endosome 1
lysosome 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Centriolar satellite (2)
  • Cytosol (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for RAB3IL1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005829 cytosol TAS --
GO:0070319 Golgi to plasma membrane transport vesicle IBA 21873635
genes like me logo Genes that share ontologies with RAB3IL1: view

No data available for Subcellular locations from UniProtKB/Swiss-Prot for RAB3IL1 Gene

Pathways & Interactions for RAB3IL1 Gene

genes like me logo Genes that share pathways with RAB3IL1: view

Pathways by source for RAB3IL1 Gene

Gene Ontology (GO) - Biological Process for RAB3IL1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006887 exocytosis IBA 21873635
GO:0015031 protein transport IEA --
GO:0050790 regulation of catalytic activity IEA --
genes like me logo Genes that share ontologies with RAB3IL1: view

No data available for SIGNOR curated interactions for RAB3IL1 Gene

Drugs & Compounds for RAB3IL1 Gene

(3) Drugs for RAB3IL1 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Guanosine diphosphate Experimental Pharma 0
Guanosine monophosphate Experimental Pharma 0
Guanosine triphosphate Experimental Pharma 0
genes like me logo Genes that share compounds with RAB3IL1: view

Transcripts for RAB3IL1 Gene

mRNA/cDNA for RAB3IL1 Gene

2 REFSEQ mRNAs :
6 NCBI additional mRNA sequence :
6 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 RAB3IL1

Alternative Splicing Database (ASD) splice patterns (SP) for RAB3IL1 Gene

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

Relevant External Links for RAB3IL1 Gene

GeneLoc Exon Structure for
RAB3IL1

Expression for RAB3IL1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for RAB3IL1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for RAB3IL1 Gene

This gene is overexpressed in Tlymphocyte (24.4), Testis (10.7), Uterus (8.5), Monocytes (6.4), and Pancreatic juice (6.2).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for RAB3IL1 Gene



Transcriptomic regulation report from SPP (The Signaling Pathways Project) for RAB3IL1

SOURCE GeneReport for Unigene cluster for RAB3IL1 Gene:

Hs.13759

Evidence on tissue expression from TISSUES for RAB3IL1 Gene

  • Intestine(4.3)
  • Liver(4.3)
  • Bone(4)
  • Blood(2.1)
  • Nervous system(2)
genes like me logo Genes that share expression patterns with RAB3IL1: view

Primer products for research

No data available for mRNA differential expression in normal tissues , Protein tissue co-expression partners , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for RAB3IL1 Gene

Orthologs for RAB3IL1 Gene

This gene was present in the common ancestor of animals.

Orthologs for RAB3IL1 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia RAB3IL1 29 30
  • 99.47 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia RAB3IL1 29 30
  • 89.36 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia RAB3IL1 29 30
  • 89.35 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Rab3il1 29
  • 85.28 (n)
Mouse
(Mus musculus)
Mammalia Rab3il1 29 16 30
  • 84.55 (n)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia RAB3IL1 30
  • 58 (a)
OneToOne
Chicken
(Gallus gallus)
Aves RAB3IL1 29 30
  • 72.8 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia RAB3IL1 30
  • 60 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia LOC100489083 29
  • 68.35 (n)
Zebrafish
(Danio rerio)
Actinopterygii LOC100331248 29
  • 69.72 (n)
RAB3IL1 30
  • 65 (a)
OneToOne
wufd02h10 29
Rainbow Trout
(Oncorhynchus mykiss)
Actinopterygii Omy.5564 29
Worm
(Caenorhabditis elegans)
Secernentea F54C9.11 29 30
  • 46.02 (n)
OneToMany
Sea Squirt
(Ciona savignyi)
Ascidiacea -- 30
  • 40 (a)
OneToMany
Species where no ortholog for RAB3IL1 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)
  • Oppossum (Monodelphis domestica)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • 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 RAB3IL1 Gene

ENSEMBL:
Gene Tree for RAB3IL1 (if available)
TreeFam:
Gene Tree for RAB3IL1 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for RAB3IL1: view image
Alliance of Genome Resources:
Additional Orthologs for RAB3IL1

Paralogs for RAB3IL1 Gene

Paralogs for RAB3IL1 Gene

(1) SIMAP similar genes for RAB3IL1 Gene using alignment to 3 proteins:

  • R3GEF_HUMAN
  • E9PK89_HUMAN
  • H0YD19_HUMAN

Pseudogenes.org Pseudogenes for RAB3IL1 Gene

genes like me logo Genes that share paralogs with RAB3IL1: view

Variants for RAB3IL1 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for RAB3IL1 Gene

SNP ID Clinical significance and condition Chr 11 pos Variation AA Info Type
rs174477 -- p.Gln49Arg
rs3815045 -- p.His323Tyr

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for RAB3IL1 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 RAB3IL1 Gene

Variant ID Type Subtype PubMed ID
nsv1070039 CNV deletion 25765185
nsv468585 CNV loss 19166990
nsv472106 CNV novel sequence insertion 20440878
nsv528697 CNV loss 19592680
nsv555171 CNV loss 21841781

Variation tolerance for RAB3IL1 Gene

Residual Variation Intolerance Score: 61.5% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 6.08; 75.33% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for RAB3IL1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
RAB3IL1
Leiden Open Variation Database (LOVD)
RAB3IL1

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for RAB3IL1 Gene

Disorders for RAB3IL1 Gene

MalaCards: The human disease database

(4) MalaCards diseases for RAB3IL1 Gene - From: COP

Disorder Aliases PubMed IDs
inflammatory bowel disease 2
  • ibd2
spinocerebellar ataxia 20
  • sca20
achondrogenesis
  • achondrogenesis syndrome
autoimmune lymphoproliferative syndrome
  • alps
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for RAB3IL1

genes like me logo Genes that share disorders with RAB3IL1: view

No data available for UniProtKB/Swiss-Prot and Genatlas for RAB3IL1 Gene

Publications for RAB3IL1 Gene

  1. Genome-wide association study identifies novel loci associated with circulating phospho- and sphingolipid concentrations. (PMID: 22359512) Demirkan A … EUROSPAN consortium (PLoS genetics 2012) 3 40
  2. Genetic loci associated with plasma phospholipid n-3 fatty acids: a meta-analysis of genome-wide association studies from the CHARGE Consortium. (PMID: 21829377) Lemaitre RN … Steffen LM (PLoS genetics 2011) 3 40
  3. Family-wide characterization of the DENN domain Rab GDP-GTP exchange factors. (PMID: 20937701) Yoshimura S … Barr FA (The Journal of cell biology 2010) 3 4
  4. GRAB: a physiologic guanine nucleotide exchange factor for Rab3A, which interacts with inositol hexakisphosphate kinase. (PMID: 11516400) Luo HR … Snyder SH (Neuron 2001) 2 3
  5. A reference map of the human binary protein interactome. (PMID: 32296183) Luck K … Calderwood MA (Nature 2020) 3

Products for RAB3IL1 Gene

  • Biorbyt antibodies for RAB3IL1

Sources for RAB3IL1 Gene