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    RAB5IF RAB5 interacting factor [ Homo sapiens (human) ]

    Gene ID: 55969, updated on 27-Nov-2024

    Summary

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    Official Symbol
    RAB5IFprovided by HGNC
    Official Full Name
    RAB5 interacting factorprovided by HGNC
    Primary source
    HGNC:HGNC:15870
    See related
    Ensembl:ENSG00000101084 MIM:619960; AllianceGenome:HGNC:15870
    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
    OPTI; RIP5; RCAF1; CFSMR2; PNAS-11; C20orf24
    Summary
    Involved in mitochondrial respirasome assembly and multi-pass transmembrane protein insertion into ER membrane. Located in mitochondrion. Part of multi-pass translocon complex. Implicated in craniofacial dysmorphism, skeletal anomalies, and impaired intellectual development syndrome 2. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Ubiquitous expression in bone marrow (RPKM 56.7), esophagus (RPKM 45.4) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See RAB5IF in Genome Data Viewer
    Location:
    20q11.23
    Exon count:
    5
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (36605779..36612557)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (38329630..38336422)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (35234182..35240960)

    Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene DLGAP4 antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12872 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:35170723-35171376 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:35171377-35172030 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:35172031-35172684 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:35172685-35173338 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:35175959-35176887 Neighboring gene NANOG hESC enhancer GRCh37_chr20:35191013-35191578 Neighboring gene myosin light chain 9 Neighboring gene OCT4-H3K27ac hESC enhancer GRCh37_chr20:35199946-35200498 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17809 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12873 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12874 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12875 Neighboring gene TGIF2-RAB5IF readthrough Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:35213881-35214870 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:35217734-35218362 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:35219932-35220810 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17810 Neighboring gene TGFB induced factor homeobox 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17811 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17812 Neighboring gene ReSE screen-validated silencer GRCh37_chr20:35233097-35233496 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17813 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12876 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr20:35235327-35236526 Neighboring gene heterogeneous nuclear ribonucleoprotein A3 pseudogene 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17814 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:35261429-35261930 Neighboring gene Src like adaptor 2 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr20:35271232-35271902 Neighboring gene NDRG family member 3 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:35305009-35305810 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:35324917-35325417 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:35373956-35374922

    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. Regulation of Mitochondrial Electron Transport Chain Assembly. Cogliati S, et al. J Mol Biol, 2018 Dec 7. PMID 30292820
    2. The GDP/GTP cycle of Rab5 in the regulation of endocytotic membrane traffic. Vitale G, et al. Cold Spring Harb Symp Quant Biol, 1995. PMID 8824393
    3. Rab5 affinity chromatography without nonhydrolyzable GTP analogues. Hagiwara M, et al. Z Naturforsch C J Biosci, 2009 Mar-Apr. PMID 19526728
    4. The Pivotal Role of Long Noncoding RNA RAB5IF in the Proliferation of Hepatocellular Carcinoma Via LGR5 Mediated β-Catenin and c-Myc Signaling. Koo JI, et al. Biomolecules, 2019 Nov 8. PMID 31717443, Free PMC Article
    5. RIP5 is a RIP-homologous inducer of cell death. Zha J, et al. Biochem Biophys Res Commun, 2004 Jun 25. PMID 15178406

    See all (29) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. The Pivotal Role of Long Noncoding RNA RAB5IF in the Proliferation of Hepatocellular Carcinoma Via LGR5 Mediated beta-Catenin and c-Myc Signaling.
      Title: The Pivotal Role of Long Noncoding RNA RAB5IF in the Proliferation of Hepatocellular Carcinoma Via LGR5 Mediated β-Catenin and c-Myc Signaling.
    2. This protein seems to play a role in mitochondrial respirasome assembly and function and we propose to rename it as RCAF1 (Respirasome Complex Assembly Factor 1).
      Title: Rewiring of the Human Mitochondrial Interactome during Neuronal Reprogramming Reveals Regulators of the Respirasome and Neurogenesis.
    3. Observational study of gene-disease association. (HuGE Navigator)
      Title: Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression.
    Submit: New GeneRIF Correction

    Phenotypes

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    Review eQTL and phenotype association data in this region using PheGenI

    Associated conditions

    Description Tests
    Craniofacial dysmorphism, skeletal anomalies, and impaired intellectual development syndrome 2
    MedGen: C5676895 OMIM: 616994 GeneReviews: Not available
    		not available

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    HIV-1 interactions

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    Protein interactions

    Protein Gene Interaction Pubs
    Envelope surface glycoprotein gp160, precursor env HIV-1 gp160 is identified to have a physical interaction with chromosome 20 open reading frame 24 (C20orf24) in human HEK293 and/or Jurkat cell lines by using affinity tagging and purification mass spectrometry analyses PubMed

    Go to the HIV-1, Human Interaction Database

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Readthrough TGIF2-RAB5IF

    Readthrough gene: TGIF2-RAB5IF, Included gene: TGIF2

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in mitochondrial respirasome assembly IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in multi-pass transmembrane protein insertion into ER membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in endoplasmic reticulum membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in mitochondrial inner membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in mitochondrion IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    part_of multi-pass translocon complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    GEL complex subunit OPTI
    Names
    obligate partner of TMCO1 insertase
    rab5-interacting protein
    respirasome complex assembly factor 1
    uncharacterized protein C20orf24

    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_001199534.2 → NP_001186463.1  GEL complex subunit OPTI isoform c

      See identical proteins and their annotated locations for NP_001186463.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) uses an alternate splice site that causes a frameshift in the 3' coding region, compared to variant 1. The resulting isoform (c) is longer and has a distinct C-terminus, compared to isoform a.
      Source sequence(s)
      AF112213, BC001871, BG395753, BI223439
      Consensus CDS
      CCDS56190.1
      UniProtKB/Swiss-Prot
      E1P5U0, O00605, Q5QPG6, Q5QPG7, Q9BT03, Q9BUV8, Q9BZU7, Q9UI05
      Related
      ENSP00000362958.5, ENST00000373852.9
      Conserved Domains (1) summary
      pfam07019
      Location:44 → 118
      Rab5ip; Rab5-interacting protein (Rab5ip)

    2. NM_001374178.1 → NP_001361107.1  GEL complex subunit OPTI isoform d

      Status: VALIDATED

      Source sequence(s)
      AL050318
      Conserved Domains (1) summary
      pfam07019
      Location:44 → 116
      Rab5ip; Rab5-interacting protein (Rab5ip)

    3. NM_018840.5 → NP_061328.1  GEL complex subunit OPTI isoform a

      See identical proteins and their annotated locations for NP_061328.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes the shortest isoform (a).
      Source sequence(s)
      AF112213, BG395753, BI223439
      Consensus CDS
      CCDS13280.1
      UniProtKB/Swiss-Prot
      Q9BUV8
      Related
      ENSP00000340164.3, ENST00000344795.8
      Conserved Domains (1) summary
      pfam07019
      Location:44 → 120
      Rab5ip; Rab5-interacting protein (Rab5ip)

    4. NM_199483.3 → NP_955777.1  GEL complex subunit OPTI isoform b

      See identical proteins and their annotated locations for NP_955777.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks an alternate exon that causes a frameshift in the 3' coding region, compared to variant 1. The resulting isoform (b) is longer and has a distinct C-terminus, compared to isoform a.
      Source sequence(s)
      AF112213, BG395753, BI223439, BU189639
      Consensus CDS
      CCDS13279.1
      UniProtKB/Swiss-Prot
      Q9BUV8
      Related
      ENSP00000341213.3, ENST00000342422.3
      Conserved Domains (1) summary
      pfam07019
      Location:44 → 79
      Rab5ip; Rab5-interacting protein (Rab5ip)

    RNA

    1. NR_026562.4 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) includes an additional internal exon, compared to variant 1. This variant is represented as non-coding because the use of the supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AF112213, AL050318, BG395753, BI223439
      Related
      ENST00000483815.5

    2. NR_164350.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AL050318
      Related
      ENST00000492721.5

    3. NR_164351.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AL050318

    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_000020.11 Reference GRCh38.p14 Primary Assembly

      Range
      36605779..36612557
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060944.1 Alternate T2T-CHM13v2.0

      Range
      38329630..38336422
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_199484.1: Suppressed sequence

      Description
      NM_199484.1: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.

    2. NM_199485.1: Suppressed sequence

      Description
      NM_199485.1: 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
    Q9BUV8.1 GenPept UniProtKB/Swiss-Prot:Q9BUV8

    Gene LinkOut

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

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