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    RAB3IP RAB3A interacting protein [ Homo sapiens (human) ]

    Gene ID: 117177, updated on 27-Nov-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 several processes, including positive regulation of cilium assembly; protein localization to motile cilium; and protein targeting to membrane. Located in centrosome; cytosol; and nucleus. [provided by Alliance of Genome Resources, Nov 2024]
    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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    See RAB3IP in Genome Data Viewer
    Location:
    12q15
    Exon count:
    17
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (69738242..69823204)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (69717376..69802330)
    RS_2024_09 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. GAS64, the first amplified and putative non-translated gene. Fischer U, et al. Int J Oncol, 2002 Jan. PMID 11743660
    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. Crystal structure of tetrameric human Rabin8 GEF domain. Vetter M, et al. Proteins, 2018 Apr. PMID 29318657
    4. Comparative perinatal mortality under medical care foundations and other delivery models. Newport J, et al. Inquiry, 1975 Mar. PMID 123217
    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 (61) 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)

    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 IBA
    Inferred from Biological aspect of Ancestor
    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 identical protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in Golgi to plasma membrane transport TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in ciliary basal body-plasma membrane docking TAS
    Traceable Author Statement
    more info
    		  
    involved_in cilium assembly IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in cilium assembly TAS
    Traceable Author Statement
    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 localization to organelle 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
    located_in centrosome IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in centrosome IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in ciliary basal body TAS
    Traceable Author Statement
    more info
    		 PubMed 
    is_active_in cytosol IBA
    Inferred from Biological aspect of Ancestor
    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_2024_08

    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

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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