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    RABGEF1 RAB guanine nucleotide exchange factor 1 [ Homo sapiens (human) ]

    Gene ID: 27342, updated on 13-Mar-2020

    Summary

    Official Symbol
    RABGEF1provided by HGNC
    Official Full Name
    RAB guanine nucleotide exchange factor 1provided by HGNC
    Primary source
    HGNC:HGNC:17676
    See related
    Ensembl:ENSG00000154710 MIM:609700
    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
    RAP1; RABEX5; rabex-5
    Summary
    RABGEF1 forms a complex with rabaptin-5 (RABPT5; MIM 603616) that is required for endocytic membrane fusion, and it serves as a specific guanine nucleotide exchange factor (GEF) for RAB5 (RAB5A; MIM 179512) (Horiuchi et al., 1997 [PubMed 9323142]).[supplied by OMIM, Mar 2010]
    Expression
    Ubiquitous expression in bone marrow (RPKM 17.2), testis (RPKM 15.3) and 25 other tissues See more
    Orthologs

    Genomic context

    See RABGEF1 in Genome Data Viewer
    Location:
    7q11.21
    Exon count:
    24
    Annotation release Status Assembly Chr Location
    109.20200228 current GRCh38.p13 (GCF_000001405.39) 7 NC_000007.14 (66654567..66811464)
    105 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (66147151..66276451)

    Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene ribosomal protein L35 pseudogene 5 Neighboring gene uncharacterized LOC100996437 Neighboring gene potassium channel tetramerization domain containing 7 Neighboring gene uncharacterized LOC107986707 Neighboring gene GrpE like 1, mitochondrial pseudogene Neighboring gene GTF2I repeat domain containing 1 pseudogene 1 Neighboring gene general transcription factor IIi pseudogene 23 Neighboring gene uncharacterized LOC107983971 Neighboring gene RNA, U6 small nuclear 1254, pseudogene

    Genomic regions, transcripts, and products

    Expression

    • 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    NHGRI GWAS Catalog

    Description
    Genome-wide joint SNP and CNV analysis of aortic root diameter in African Americans: the HyperGEN study.
    NHGRI GWA Catalog

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Homology

    Clone Names

    • FLJ32302

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    DNA binding IEA
    Inferred from Electronic Annotation
    more info
     
    Rab GTPase binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Rab guanyl-nucleotide exchange factor activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    Rab guanyl-nucleotide exchange factor activity IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    zinc ion binding IEA
    Inferred from Electronic Annotation
    more info
     
    Process Evidence Code Pubs
    endocytosis IEA
    Inferred from Electronic Annotation
    more info
     
    protein targeting to membrane IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    Component Evidence Code Pubs
    cytosol IDA
    Inferred from Direct Assay
    more info
     
    cytosol TAS
    Traceable Author Statement
    more info
     
    early endosome IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    early endosome membrane TAS
    Traceable Author Statement
    more info
     
    nucleolus IDA
    Inferred from Direct Assay
    more info
     
    recycling endosome IEA
    Inferred from Electronic Annotation
    more info
     

    General protein information

    Preferred Names
    rab5 GDP/GTP exchange factor
    Names
    RAB guanine nucleotide exchange factor (GEF) 1
    rabaptin-5-associated exchange factor for Rab5

    NCBI Reference Sequences (RefSeq)

    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_001287060.2NP_001273989.1  rab5 GDP/GTP exchange factor isoform a

      See identical proteins and their annotated locations for NP_001273989.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes isoform a. Variants 1 and 6-8 all encode the same isoform (a).
      Source sequence(s)
      AC027644, AC079588
      Consensus CDS
      CCDS75610.1
      UniProtKB/Swiss-Prot
      Q9UJ41
      UniProtKB/TrEMBL
      A0A0A0MSJ3, B3KMF1
      Related
      ENSP00000390480.3, ENST00000437078.6
      Conserved Domains (1) summary
      pfam02204
      Location:78178
      VPS9; Vacuolar sorting protein 9 (VPS9) domain
    2. NM_001287061.2NP_001273990.1  rab5 GDP/GTP exchange factor isoform b

      See identical proteins and their annotated locations for NP_001273990.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) contains alternate 5' exon structure and includes an additional internal exon, and it thus differs in its 5' UTR and initiates translation at an alternate start codon, compared to variant 1. The encoded isoform (b) is longer at the N-terminus, compared to isoform a.
      Source sequence(s)
      AC027644
      Consensus CDS
      CCDS69308.1
      UniProtKB/Swiss-Prot
      Q9UJ41
      UniProtKB/TrEMBL
      B3KMF1
      Related
      ENSP00000370208.3, ENST00000380828.6
      Conserved Domains (2) summary
      pfam01754
      Location:3154
      zf-A20; A20-like zinc finger
      pfam02204
      Location:284384
      VPS9; Vacuolar sorting protein 9 (VPS9) domain
    3. NM_001287062.2NP_001273991.1  rab5 GDP/GTP exchange factor isoform c

      See identical proteins and their annotated locations for NP_001273991.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) contains alternate 5' exon structure and includes an additional internal exon, and it thus differs in its 5' UTR and initiates translation at an alternate start codon, compared to variant 1. The encoded isoform (c) is longer at the N-terminus, compared to isoform a. Variants 3, 4, and 9-20 all encode the same isoform (c).
      Source sequence(s)
      AC027644
      Consensus CDS
      CCDS5535.1
      UniProtKB/Swiss-Prot
      Q9UJ41
      UniProtKB/TrEMBL
      A0A024RDL6, A8K3R3, B3KMF1
      Related
      ENSP00000415815.1, ENST00000450873.6
      Conserved Domains (2) summary
      pfam01754
      Location:1740
      zf-A20; A20-like zinc finger
      pfam02204
      Location:270370
      VPS9; Vacuolar sorting protein 9 (VPS9) domain
    4. NM_001367722.1NP_001354651.1  rab5 GDP/GTP exchange factor isoform a

      Status: VALIDATED

      Description
      Transcript Variant: This variant (6), as well as variants 1, 7, and 8, encodes isoform a.
      Source sequence(s)
      AC006001, AC027644
    5. NM_001367723.1NP_001354652.1  rab5 GDP/GTP exchange factor isoform a

      Status: VALIDATED

      Description
      Transcript Variant: This variant (7), as well as variants 1, 6, and 8, encodes isoform a.
      Source sequence(s)
      AC027644, AC079588
    6. NM_001367724.1NP_001354653.1  rab5 GDP/GTP exchange factor isoform a

      Status: VALIDATED

      Description
      Transcript Variant: This variant (8), as well as variants 1, 6, and 7, encodes isoform a.
      Source sequence(s)
      AC027644
    7. NM_001367725.1NP_001354654.1  rab5 GDP/GTP exchange factor isoform c

      Status: VALIDATED

      Description
      Transcript Variant: This variant (9), as well as variants 3, 4, and 10-20, encodes isoform c.
      Source sequence(s)
      AC006001, AC027644
    8. NM_001367726.1NP_001354655.1  rab5 GDP/GTP exchange factor isoform c

      Status: VALIDATED

      Description
      Transcript Variant: This variant (10), as well as variants 3, 4, 9, and 11-20, encodes isoform c.
      Source sequence(s)
      AC006001, AC027644
    9. NM_001367727.1NP_001354656.1  rab5 GDP/GTP exchange factor isoform c

      Status: VALIDATED

      Description
      Transcript Variant: This variant (11), as well as variants 3, 4, 9, 10, and 12-20, encodes isoform c.
      Source sequence(s)
      AC006001, AC027644
    10. NM_001367728.1NP_001354657.1  rab5 GDP/GTP exchange factor isoform c

      Status: VALIDATED

      Description
      Transcript Variant: This variant (12), as well as variants 3, 4, 9-11, and 13-20, encodes isoform c.
      Source sequence(s)
      AC006001, AC027644
    11. NM_001367729.1NP_001354658.1  rab5 GDP/GTP exchange factor isoform c

      Status: VALIDATED

      Description
      Transcript Variant: This variant (13), as well as variants 3, 4, 9-12, and 14-20, encodes isoform c.
      Source sequence(s)
      AC027644, AC079588
    12. NM_001367730.1NP_001354659.1  rab5 GDP/GTP exchange factor isoform c

      Status: VALIDATED

      Description
      Transcript Variant: This variant (14), as well as variants 3, 4, 9-13, and 15-20, encodes isoform c.
      Source sequence(s)
      AC027644, AC079588
    13. NM_001367731.1NP_001354660.1  rab5 GDP/GTP exchange factor isoform c

      Status: VALIDATED

      Description
      Transcript Variant: This variant (15), as well as variants 3, 4, 9-14, and 16-20, encodes isoform c.
      Source sequence(s)
      AC027644, AC079588
    14. NM_001367732.1NP_001354661.1  rab5 GDP/GTP exchange factor isoform c

      Status: VALIDATED

      Description
      Transcript Variant: This variant (16), as well as variants 3, 4, 9-15, and 17-20, encodes isoform c.
      Source sequence(s)
      AC027644, AC079588
    15. NM_001367733.1NP_001354662.1  rab5 GDP/GTP exchange factor isoform c

      Status: VALIDATED

      Description
      Transcript Variant: This variant (17), as well as variants 3, 4, 9-16, and 18-20, encodes isoform c.
      Source sequence(s)
      AC027644, AC079588
    16. NM_001367734.1NP_001354663.1  rab5 GDP/GTP exchange factor isoform c

      Status: VALIDATED

      Description
      Transcript Variant: This variant (18), as well as variants 3, 4, 9-17, 19, and 20, encodes isoform c.
      Source sequence(s)
      AC027644
    17. NM_001367735.1NP_001354664.1  rab5 GDP/GTP exchange factor isoform c

      Status: VALIDATED

      Description
      Transcript Variant: This variant (19), as well as variants 3, 4, 9-18, and 20, encodes isoform c.
      Source sequence(s)
      AC027644
    18. NM_001367736.1NP_001354665.1  rab5 GDP/GTP exchange factor isoform c

      Status: VALIDATED

      Description
      Transcript Variant: This variant (20), as well as variants 3, 4, and 9-19, encodes isoform c.
      Source sequence(s)
      AC027644
    19. NM_001367737.1NP_001354666.1  rab5 GDP/GTP exchange factor isoform d

      Status: VALIDATED

      Description
      Transcript Variant: This variant (21), as well as variants 22-24, encodes isoform d.
      Source sequence(s)
      AC006001, AC027644
    20. NM_001367738.1NP_001354667.1  rab5 GDP/GTP exchange factor isoform d

      Status: VALIDATED

      Description
      Transcript Variant: This variant (22), as well as variants 21, 23, and 24, encodes isoform d.
      Source sequence(s)
      AC027644, AC079588
    21. NM_001367739.1NP_001354668.1  rab5 GDP/GTP exchange factor isoform d

      Status: VALIDATED

      Description
      Transcript Variant: This variant (23), as well as variants 21, 22, and 24, encodes isoform d.
      Source sequence(s)
      AC027644
    22. NM_001367740.1NP_001354669.1  rab5 GDP/GTP exchange factor isoform d

      Status: VALIDATED

      Description
      Transcript Variant: This variant (24), as well as variants 21-23, encodes isoform d.
      Source sequence(s)
      AC027644, AC079588
    23. NM_001367741.1NP_001354670.1  rab5 GDP/GTP exchange factor isoform e

      Status: VALIDATED

      Description
      Transcript Variant: This variant (25), as well as variant 26, encodes isoform e.
      Source sequence(s)
      AC006001, AC027644
    24. NM_001367742.1NP_001354671.1  rab5 GDP/GTP exchange factor isoform e

      Status: VALIDATED

      Description
      Transcript Variant: This variant (26), as well as variant 25, encodes isoform e.
      Source sequence(s)
      AC027644
    25. NM_001367743.1NP_001354672.1  rab5 GDP/GTP exchange factor isoform f precursor

      Status: VALIDATED

      Description
      Transcript Variant: This variant (27), as well as variant 28, encodes isoform f.
      Source sequence(s)
      AC027644
    26. NM_001367744.1NP_001354673.1  rab5 GDP/GTP exchange factor isoform f precursor

      Status: VALIDATED

      Description
      Transcript Variant: This variant (28), as well as variant 27, encodes isoform f.
      Source sequence(s)
      AC027644
    27. NM_001367745.1NP_001354674.1  rab5 GDP/GTP exchange factor isoform g

      Status: VALIDATED

      Description
      Transcript Variant: This variant (29), as well as variants 30-32, encodes isoform g.
      Source sequence(s)
      AC027644, AC079588
    28. NM_001367746.1NP_001354675.1  rab5 GDP/GTP exchange factor isoform g

      Status: VALIDATED

      Description
      Transcript Variant: This variant (30), as well as variants 29, 31, and 32, encodes isoform g.
      Source sequence(s)
      AC027644, AC079588
    29. NM_001367747.1NP_001354676.1  rab5 GDP/GTP exchange factor isoform g

      Status: VALIDATED

      Description
      Transcript Variant: This variant (31), as well as variants 29, 30, and 32, encodes isoform g.
      Source sequence(s)
      AC027644
    30. NM_001367748.1NP_001354677.1  rab5 GDP/GTP exchange factor isoform g

      Status: VALIDATED

      Description
      Transcript Variant: This variant (32), as well as variants 29-31, encodes isoform g.
      Source sequence(s)
      AC027644
    31. NM_001367749.1NP_001354678.1  rab5 GDP/GTP exchange factor isoform h

      Status: VALIDATED

      Description
      Transcript Variant: This variant (33), as well as variants 34 and 35, encodes isoform h.
      Source sequence(s)
      AC027644
    32. NM_001367750.1NP_001354679.1  rab5 GDP/GTP exchange factor isoform h

      Status: VALIDATED

      Description
      Transcript Variant: This variant (34), as well as variants 33 and 35, encodes isoform h.
      Source sequence(s)
      AC027644
    33. NM_001367751.1NP_001354680.1  rab5 GDP/GTP exchange factor isoform h

      Status: VALIDATED

      Description
      Transcript Variant: This variant (35), as well as variants 33 and 34, encodes isoform h.
      Source sequence(s)
      AC027644
    34. NM_001367752.1NP_001354681.1  rab5 GDP/GTP exchange factor isoform i

      Status: VALIDATED

      Source sequence(s)
      AC006001, AC027644
    35. NM_001367753.1NP_001354682.1  rab5 GDP/GTP exchange factor isoform j

      Status: VALIDATED

      Source sequence(s)
      AC027644
      Related
      ENSP00000421124.3, ENST00000510829.6
    36. NM_001367754.1NP_001354683.1  rab5 GDP/GTP exchange factor isoform k

      Status: VALIDATED

      Source sequence(s)
      AC027644
    37. NM_001367755.1NP_001354684.1  rab5 GDP/GTP exchange factor isoform l

      Status: VALIDATED

      Source sequence(s)
      AC027644
    38. NM_001367756.1NP_001354685.1  rab5 GDP/GTP exchange factor isoform m

      Status: VALIDATED

      Source sequence(s)
      AC027644
    39. NM_014504.3NP_055319.1  rab5 GDP/GTP exchange factor isoform c

      See identical proteins and their annotated locations for NP_055319.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) contains alternate 5' exon structure and includes an additional internal exon, and it thus differs in its 5' UTR and initiates translation at an alternate start codon, compared to variant 1. The encoded isoform (c) is longer at the N-terminus, compared to isoform a. Variants 3, 4, and 9-20 all encode the same isoform (c).
      Source sequence(s)
      AC027644
      Consensus CDS
      CCDS5535.1
      UniProtKB/Swiss-Prot
      Q9UJ41
      UniProtKB/TrEMBL
      A0A024RDL6
      Related
      ENSP00000284957.4, ENST00000284957.9
      Conserved Domains (2) summary
      pfam01754
      Location:1740
      zf-A20; A20-like zinc finger
      pfam02204
      Location:270370
      VPS9; Vacuolar sorting protein 9 (VPS9) domain

    RNA

    1. NR_104676.2 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (5) includes the same 5' terminal exon but lacks the remaining exons found in variant 1, and it instead contains an alternate 3' terminal exon. This variant is represented as non-coding because it lacks the entire coding region found in variant 1.
      Source sequence(s)
      AC027644, AC079588
    2. NR_160287.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC027644

    RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.

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

    Reference GRCh38.p13 Primary Assembly

    Genomic

    1. NC_000007.14 Reference GRCh38.p13 Primary Assembly

      Range
      66654567..66811464
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
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