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RAB3IP RAB3A interacting protein [ Homo sapiens (human) ]

Gene ID: 117177, updated on 11-Apr-2024

Summary

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Official Symbol
RAB3IPprovided by HGNC
Official Full Name
RAB3A interacting proteinprovided by HGNC
Primary source
HGNC:HGNC:16508
See related
Ensembl:ENSG00000127328 MIM:608686; AllianceGenome:HGNC:16508
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
RABIN3; RABIN8
Summary
Enables guanyl-nucleotide exchange factor activity and identical protein binding activity. Involved in cilium assembly; protein localization to organelle; and protein targeting to membrane. Located in centrosome; cytosol; and nucleus. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Broad expression in brain (RPKM 6.7), kidney (RPKM 6.6) and 24 other tissues See more
Orthologs
mouse all
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Genomic context

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Location:
12q15
Exon count:
17
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (69738242..69823204)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (69717376..69802330)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (70132640..70216984)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105369823 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6654 Neighboring gene leucine rich repeat containing 10 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr12:70082106-70083305 Neighboring gene bestrophin 3 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:70083432-70084000 Neighboring gene ReSE screen-validated silencer GRCh37_chr12:70087234-70087434 Neighboring gene uncharacterized LOC101928002 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4654 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:70153303-70153894 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_30842 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_30867 Neighboring gene myelin regulatory factor like Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:70272467-70273004 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:70273005-70273542 Neighboring gene MPRA-validated peak1788 silencer Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr12:70289930-70290500 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr12:70290501-70291069 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6656 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr12:70325891-70326586 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:70332766-70333393 Neighboring gene MPRA-validated peak1789 silencer Neighboring gene MPRA-validated peak1793 silencer Neighboring gene MPRA-validated peak1794 silencer Neighboring gene uncharacterized LOC124902959 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr12:70463098-70463693

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. Crystal structure of tetrameric human Rabin8 GEF domain. Vetter M, et al. Proteins, 2018 Apr. PMID 29318657
  2. Activation of Rab8 guanine nucleotide exchange factor Rabin8 by ERK1/2 in response to EGF signaling. Wang J, et al. Proc Natl Acad Sci U S A, 2015 Jan 6. PMID 25535387, Free PMC Article
  3. GAS64, the first amplified and putative non-translated gene. Fischer U, et al. Int J Oncol, 2002 Jan. PMID 11743660
  4. Rab3IP interacts with SSX2 and enhances the invasiveness of gastric cancer cells. Ren H, et al. Biochem Biophys Res Commun, 2018 Sep 18. PMID 30005870
  5. Rabin8 suppresses autophagosome formation independently of its guanine nucleotide-exchange activity towards Rab8. Amagai Y, et al. J Biochem, 2015 Aug. PMID 25787272

See all (59) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. LINC00943 knockdown attenuates MPP(+)-induced neuronal damage via miR-15b-5p/RAB3IP axis in SK-N-SH cells.
    Title: LINC00943 knockdown attenuates MPP(+)-induced neuronal damage via miR-15b-5p/RAB3IP axis in SK-N-SH cells.
  2. Long noncoding RNA NEAT1 knockdown inhibits MPP(+)-induced apoptosis, in fl ammation and cytotoxicity in SK-N-SH cells by regulating miR-212-5p/RAB3IP axis.
    Title: Long noncoding RNA NEAT1 knockdown inhibits MPP(+)-induced apoptosis, inflammation and cytotoxicity in SK-N-SH cells by regulating miR-212-5p/RAB3IP axis.
  3. Rab8 and Rabin8-Mediated Tumor Formation by Hyperactivated EGFR Signaling via FGFR Signaling.
    Title: Rab8 and Rabin8-Mediated Tumor Formation by Hyperactivated EGFR Signaling via FGFR Signaling.
  4. C7orf43 directly binds to Rabin8 and that C7orf43 knockdown diminishes Rabin8 preciliary centrosome accumulation.
    Title: The C7orf43/TRAPPC14 component links the TRAPPII complex to Rabin8 for preciliary vesicle tethering at the mother centriole during ciliogenesis.
  5. The crystal structure of tetrameric Rabin8, guanine nucleotide exchange factors (GEFs) domain reveals an occluded Rab8 binding site suggesting that this oligomer is enzymatically inactive, a notion that's verified experimentally using Rabin8/Rab8 GEF assays.
    Title: Crystal structure of tetrameric human Rabin8 GEF domain.
  6. role of Rab3IP in inducing an invasive phenotype in gastric cancer cells, in addition to its involvement in EMT.
    Title: Rab3IP interacts with SSX2 and enhances the invasiveness of gastric cancer cells.
  7. Authors show that Rab11-GMPPNP-FIP3-Rabin8 is more stable than Rab11-GMPPNP-Rabin8, owing to direct interaction between Rabin8 and FIP3 within the dual effector-bound complex.
    Title: Structure of Rab11-FIP3-Rabin8 reveals simultaneous binding of FIP3 and Rabin8 effectors to Rab11.
  8. the role of Rabin8 (a mammalian ortholog of Sec2p) with Rab8-nucleotide-exchange factor activity in autophagy in mammalian cells, was examined.
    Title: Rabin8 suppresses autophagosome formation independently of its guanine nucleotide-exchange activity towards Rab8.
  9. Rab11-FIP3 coordinates the interactions of ASAP1 and Rab11a with Rabin8.
    Title: The Arf and Rab11 effector FIP3 acts synergistically with ASAP1 to direct Rabin8 in ciliary receptor targeting.
  10. Rabin8 was identified as a direct phospho-substrate of ERK1/2 in response to EGF signaling.
    Title: Activation of Rab8 guanine nucleotide exchange factor Rabin8 by ERK1/2 in response to EGF signaling.
Submit: New GeneRIF Correction See all GeneRIFs (11)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ14660, FLJ22548, MGC71495

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables GTPase binding IEA
Inferred from Electronic Annotation
more info
  
enables guanyl-nucleotide exchange factor activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables guanyl-nucleotide exchange factor activity TAS
Traceable Author Statement
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in ciliary basal body-plasma membrane docking TAS
Traceable Author Statement
more info
  
involved_in cilium assembly TAS
Traceable Author Statement
more info
  
involved_in exocytosis IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in negative regulation of filopodium assembly IEA
Inferred from Electronic Annotation
more info
  
involved_in positive regulation of cilium assembly IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in protein localization to motile cilium IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in protein targeting to membrane IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in protein transport IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
is_active_in Golgi to plasma membrane transport vesicle IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in centrosome IEA
Inferred from Electronic Annotation
more info
  
located_in cytosol IDA
Inferred from Direct Assay
more info
 PubMed 
located_in cytosol TAS
Traceable Author Statement
more info
  
located_in lamellipodium IEA
Inferred from Electronic Annotation
more info
  
located_in nucleus IDA
Inferred from Direct Assay
more info
 PubMed 
located_in perinuclear region of cytoplasm IEA
Inferred from Electronic Annotation
more info
  
located_in proximal dendrite IEA
Inferred from Electronic Annotation
more info
  
is_active_in trans-Golgi network membrane IC
Inferred by Curator
more info
 PubMed 

General protein information

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Preferred Names
rab-3A-interacting protein
Names
SSX2 interacting protein
rab3A-interacting protein
rabin-3

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_001024647.3 → NP_001019818.1  rab-3A-interacting protein isoform A

    See identical proteins and their annotated locations for NP_001019818.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (A) has multiple differences, which result in a distinct 5' UTR and cause translation initiation at a downstream start codon, compared to variant alpha 2. The resulting isoform (A) has a shorter N-terminus, compared to isoform alpha 2. Variants A and B encode the same isoform A.
    Source sequence(s)
    AC025263, AI912718, BC014553, DN912041
    Consensus CDS
    CCDS44942.1
    UniProtKB/Swiss-Prot
    Q96QF0
    Related
    ENSP00000448773.1, ENST00000551641.5
    Conserved Domains (1) summary
    cd21068
    Location:60 → 252
    Rab11BD_RAB3IP; Rab11 binding domain of Rab-3A-interacting protein (RAB3IP)

  2. NM_001278402.1 → NP_001265331.1  rab-3A-interacting protein isoform A

    See identical proteins and their annotated locations for NP_001265331.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (B) has multiple differences, which result in a distinct 5' UTR and cause translation initiation at a downstream start codon, compared to variant alpha 2. The resulting isoform (A) has a shorter N-terminus, compared to isoform alpha 2. Variants A and B encode the same isoform A.
    Source sequence(s)
    AC025263, AI912718, AK027671, BC015548, DN912041
    Consensus CDS
    CCDS44942.1
    UniProtKB/Swiss-Prot
    Q96QF0
    Related
    ENSP00000448027.1, ENST00000553099.5
    Conserved Domains (1) summary
    cd21068
    Location:60 → 252
    Rab11BD_RAB3IP; Rab11 binding domain of Rab-3A-interacting protein (RAB3IP)

  3. NM_022456.5 → NP_071901.2  rab-3A-interacting protein isoform alpha 1

    See identical proteins and their annotated locations for NP_071901.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (alpha 1) has a distinct 5' UTR and lacks an in-frame portion of the 5' coding region, compared to variant alpha 2. The resulting isoform (alpha 1) has a shorter N-terminus, compared to isoform alpha 2.
    Source sequence(s)
    AC025263, AI912718, AJ312896, DB460944
    Consensus CDS
    CCDS8995.1
    UniProtKB/Swiss-Prot
    Q96QF0
    Related
    ENSP00000247833.7, ENST00000247833.12
    Conserved Domains (2) summary
    COG4372
    Location:104 → 240
    COG4372; Uncharacterized conserved protein, contains DUF3084 domain [Function unknown]
    pfam06428
    Location:173 → 241
    Sec2p; GDP/GTP exchange factor Sec2p

  4. NM_175623.4 → NP_783322.1  rab-3A-interacting protein isoform alpha 2

    See identical proteins and their annotated locations for NP_783322.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (alpha 2) encodes the longest isoform (alpha 2).
    Source sequence(s)
    AC025263, AI912718, AJ312897, DA874650
    Consensus CDS
    CCDS8993.1
    UniProtKB/Swiss-Prot
    B7WPJ6, Q6PCE4, Q96A24, Q96QE6, Q96QE7, Q96QE8, Q96QE9, Q96QF0, Q96QF1, Q9H673
    Related
    ENSP00000447300.1, ENST00000550536.5
    Conserved Domains (2) summary
    COG4372
    Location:120 → 256
    COG4372; Uncharacterized conserved protein, contains DUF3084 domain [Function unknown]
    pfam06428
    Location:189 → 257
    Sec2p; GDP/GTP exchange factor Sec2p

  5. NM_175624.4 → NP_783323.1  rab-3A-interacting protein isoform beta 1

    See identical proteins and their annotated locations for NP_783323.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (beta 1) has a distinct 5' UTR and multiple coding region differences, compared to variant alpha 2. These differences cause translation initiation at a downstream AUG and a frameshift in the 3' coding region. The resulting isoform (beta 1) is shorter and has a shorter N-terminus and a distinct C-terminus, compared to isoform alpha 2.
    Source sequence(s)
    AC025263, AI912718, AJ312898, DB460944
    Consensus CDS
    CCDS8996.1
    UniProtKB/TrEMBL
    J3KPG1
    Related
    ENSP00000419216.2, ENST00000483530.6
    Conserved Domains (2) summary
    pfam06428
    Location:173 → 254
    Sec2p; GDP/GTP exchange factor Sec2p
    cl26472
    Location:104 → 240
    DUF3084; Protein of unknown function (DUF3084)

  6. NM_175625.4 → NP_783324.1  rab-3A-interacting protein isoform beta 2

    See identical proteins and their annotated locations for NP_783324.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (beta 2) lacks an exon in the 3' coding region, which results in a frameshift, compared to variant alpha 2. The resulting isoform (beta 2) is shorter and has a distinct C-terminus, compared to isoform alpha 2.
    Source sequence(s)
    AC025263, AI912718, AJ312899, DA874650
    Consensus CDS
    CCDS41811.1
    UniProtKB/TrEMBL
    J3KPG1
    Related
    ENSP00000355381.5, ENST00000362025.9
    Conserved Domains (2) summary
    pfam06428
    Location:189 → 270
    Sec2p; GDP/GTP exchange factor Sec2p
    cl26472
    Location:120 → 256
    DUF3084; Protein of unknown function (DUF3084)

RNA

  1. NR_103519.2 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (gamma 1) has an alternate 5' exon and lacks an internal exon in the 3' region, compared to variant alpha 2. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant alpha 2, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AC025263, AI912718, AJ312900, BC014553, DB460944

  2. NR_103520.2 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (gamma 2) lacks an internal exon in the 3' region, compared to variant alpha 2. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant alpha 2, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AC025263, AI912718, AJ312901, BC014553, DA874650

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000012.12 Reference GRCh38.p14 Primary Assembly

    Range
    69738242..69823204
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047428268.1 → XP_047284224.1  rab-3A-interacting protein isoform X4

  2. XM_017018775.2 → XP_016874264.1  rab-3A-interacting protein isoform X6

  3. XM_047428266.1 → XP_047284222.1  rab-3A-interacting protein isoform X2

  4. XM_047428267.1 → XP_047284223.1  rab-3A-interacting protein isoform X3

    Related
    ENSP00000368086.4, ENST00000378809.8

  5. XM_006719226.4 → XP_006719289.3  rab-3A-interacting protein isoform X1

  6. XM_047428269.1 → XP_047284225.1  rab-3A-interacting protein isoform X5

  7. XM_024448832.2 → XP_024304600.1  rab-3A-interacting protein isoform X5

RNA

  1. XR_007063038.1 RNA Sequence

  2. XR_007063039.1 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    69717376..69802330
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054371035.1 → XP_054227010.1  rab-3A-interacting protein isoform X4

  2. XM_054371038.1 → XP_054227013.1  rab-3A-interacting protein isoform X6

  3. XM_054371033.1 → XP_054227008.1  rab-3A-interacting protein isoform X2

  4. XM_054371034.1 → XP_054227009.1  rab-3A-interacting protein isoform X3

  5. XM_054371032.1 → XP_054227007.1  rab-3A-interacting protein isoform X1

  6. XM_054371039.1 → XP_054227014.1  rab-3A-interacting protein isoform X7

  7. XM_054371037.1 → XP_054227012.1  rab-3A-interacting protein isoform X5

  8. XM_054371036.1 → XP_054227011.1  rab-3A-interacting protein isoform X5

RNA

  1. XR_008488521.1 RNA Sequence

  2. XR_008488522.1 RNA Sequence

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_175626.1: Suppressed sequence

    Description
    NM_175626.1: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.

  2. NM_175627.1: Suppressed sequence

    Description
    NM_175627.1: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q96QF0.1 GenPept UniProtKB/Swiss-Prot:Q96QF0

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