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RAB5IF RAB5 interacting factor [ Homo sapiens (human) ]

Gene ID: 55969, updated on 5-Mar-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. Located in mitochondrial respirasome. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in bone marrow (RPKM 56.7), esophagus (RPKM 45.4) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
20q11.23
Exon count:
5
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (36605779..36612557)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (38329630..38336422)
105.20220307 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 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
  3. Rab5 affinity chromatography without nonhydrolyzable GTP analogues. Hagiwara M, et al. Z Naturforsch C J Biosci, 2009 Mar-Apr. PMID 19526728
  4. 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
  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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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

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)

Genotypes

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 molecular_function ND
No biological Data available
more info
  
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 respirasome 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_2023_10

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

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