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    DENND5A DENN domain containing 5A [ Homo sapiens (human) ]

    Gene ID: 23258, updated on 9-Dec-2024

    Summary

    Official Symbol
    DENND5Aprovided by HGNC
    Official Full Name
    DENN domain containing 5Aprovided by HGNC
    Primary source
    HGNC:HGNC:19344
    See related
    Ensembl:ENSG00000184014 MIM:617278; AllianceGenome:HGNC:19344
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    DEE49; EIEE49; RAB6IP1
    Summary
    This gene encodes a DENN-domain-containing protein that functions as a RAB-activating guanine nucleotide exchange factor (GEF). This protein catalyzes the conversion of GDP to GTP and thereby converts inactive GDP-bound Rab proteins into their active GTP-bound form. The encoded protein is recruited by RAB6 onto Golgi membranes and is therefore referred to as RAB6-interacting protein 1. This protein binds with RAB39 as well. Alternative splicing results in multiple transcript variants encoding distinct isoforms. Mutations in this gene are associated with early infantile epileptic encephalopathy-49. [provided by RefSeq, Feb 2017]
    Expression
    Ubiquitous expression in brain (RPKM 36.4), heart (RPKM 21.0) and 25 other tissues See more
    Orthologs
    NEW
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    Try the new Transcript table

    Genomic context

    See DENND5A in Genome Data Viewer
    Location:
    11p15.4
    Exon count:
    24
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (9138825..9265350, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (9223596..9350195, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (9160372..9286897, complement)

    Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:9116861-9117362 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:9117363-9117862 Neighboring gene keratin 8 pseudogene 41 Neighboring gene uncharacterized LOC105376542 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:9142475-9143138 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4401 Neighboring gene Sharpr-MPRA regulatory region 9656 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr11:9190693-9191892 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:9250779-9251379 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr11:9251982-9252582 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4402 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:9273812-9274511 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3121 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4403 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4404 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3122 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3123 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4405 Neighboring gene MPRA-validated peak1192 silencer Neighboring gene tRNA-Leu (CAA) 5-1 Neighboring gene transmembrane protein 41B Neighboring gene proline rich 13 pseudogene 2

    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

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • FLJ22354, FLJ33829, FLJ43455, KIAA1091

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    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 protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables small GTPase binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    Process Evidence Code Pubs
    involved_in negative regulation of neuron projection development ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in retrograde transport, endosome to Golgi IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in retrograde transport, endosome to Golgi IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    Component Evidence Code Pubs
    located_in Golgi membrane IEA
    Inferred from Electronic Annotation
    more info
     
    located_in cytosol TAS
    Traceable Author Statement
    more info
     
    part_of retromer complex IDA
    Inferred from Direct Assay
    more info
    PubMed 
    is_active_in trans-Golgi network IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in trans-Golgi network IDA
    Inferred from Direct Assay
    more info
    PubMed 

    General protein information

    Preferred Names
    DENN domain-containing protein 5A
    Names
    DENN/MADD domain containing 5A
    RAB6 interacting protein 1
    rab6-interacting protein 1

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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.

    Genomic

    1. NG_053019.1 RefSeqGene

      Range
      4986..131511
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001243254.2NP_001230183.1  DENN domain-containing protein 5A isoform 2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) uses an alternate donor splice site at the penultimate coding exon compared to variant 1. This results in a frame-shift, and a shorter isoform (2) with a distinct C-terminus compared to isoform 1.
      Source sequence(s)
      AC055845, AK295881, AL117448, DN999250
      Consensus CDS
      CCDS58119.1
      UniProtKB/TrEMBL
      A0A7P0T9Z2
      Related
      ENSP00000435866.1, ENST00000530044.5
      Conserved Domains (5) summary
      smart00801
      Location:513588
      dDENN; Domain always found downstream of DENN domain, found in a variety of signalling proteins
      smart00593
      Location:884947
      RUN; domain involved in Ras-like GTPase signaling
      smart00800
      Location:12138
      uDENN; Domain always found upstream of DENN domain, found in a variety of signalling proteins
      cd01757
      Location:9541062
      PLAT_RAB6IP1; PLAT/LH2 domain present in RAB6 interacting protein 1 (Rab6IP1)_like family. PLAT/LH2 domains consists of an eight stranded beta-barrel. In RabIP1 this domain may participate in lipid-mediated modulation of Rab6IP1's function via it's generally proposed ...
      pfam02141
      Location:202390
      DENN; DENN (AEX-3) domain
    2. NM_001348749.2NP_001335678.1  DENN domain-containing protein 5A isoform 3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) lacks an in-frame exon in the 5' coding region, compared to variant 1, and encodes a shorter isoform (3), compared to isoform 1.
      Source sequence(s)
      AC055845, AC079296, AP006259
      Consensus CDS
      CCDS91437.1
      UniProtKB/TrEMBL
      A0A7P0T9Z2, A0A7P0Z4N9
      Related
      ENSP00000506456.1, ENST00000681203.1
      Conserved Domains (5) summary
      smart00801
      Location:489564
      dDENN; Domain always found downstream of DENN domain, found in a variety of signalling proteins
      smart00800
      Location:12114
      uDENN; Domain always found upstream of DENN domain, found in a variety of signalling proteins
      cd01757
      Location:9301038
      PLAT_RAB6IP1; PLAT/LH2 domain present in RAB6 interacting protein 1 (Rab6IP1)_like family. PLAT/LH2 domains consists of an eight stranded beta-barrel. In RabIP1 this domain may participate in lipid-mediated modulation of Rab6IP1's function via it's generally proposed ...
      pfam02141
      Location:178366
      DENN; DENN (AEX-3) domain
      cl02689
      Location:771918
      RUN; RUN domain
    3. NM_001348750.2NP_001335679.1  DENN domain-containing protein 5A isoform 4

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) has an additional alternate exon in its 5' end which results in the use of a downstream in-frame start codon, compared to variant 1, and encodes a shorter isoform (4), compared to isoform 1.
      Source sequence(s)
      AC055845, AC079296, AP006259
      UniProtKB/TrEMBL
      B4DYK4
      Related
      ENSP00000505621.1, ENST00000680554.1
      Conserved Domains (5) summary
      smart00801
      Location:417492
      dDENN; Domain always found downstream of DENN domain, found in a variety of signalling proteins
      smart00800
      Location:142
      uDENN; Domain always found upstream of DENN domain, found in a variety of signalling proteins
      cd01757
      Location:858966
      PLAT_RAB6IP1; PLAT/LH2 domain present in RAB6 interacting protein 1 (Rab6IP1)_like family. PLAT/LH2 domains consists of an eight stranded beta-barrel. In RabIP1 this domain may participate in lipid-mediated modulation of Rab6IP1's function via it's generally proposed ...
      pfam02141
      Location:106294
      DENN; DENN (AEX-3) domain
      cl02689
      Location:699846
      RUN; RUN domain
    4. NM_015213.4NP_056028.2  DENN domain-containing protein 5A isoform 1

      See identical proteins and their annotated locations for NP_056028.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (1).
      Source sequence(s)
      AB029014, AC055845, AL117448, DN999250
      Consensus CDS
      CCDS31423.1
      UniProtKB/Swiss-Prot
      B4DJ15, E9PS91, Q6IQ26, Q96GN3, Q9H6U7, Q9UFV0, Q9UPR1
      UniProtKB/TrEMBL
      A0A7P0T9Z2
      Related
      ENSP00000328524.3, ENST00000328194.8
      Conserved Domains (5) summary
      smart00801
      Location:513588
      dDENN; Domain always found downstream of DENN domain, found in a variety of signalling proteins
      smart00800
      Location:12138
      uDENN; Domain always found upstream of DENN domain, found in a variety of signalling proteins
      cd01757
      Location:9541062
      PLAT_RAB6IP1; PLAT/LH2 domain present in RAB6 interacting protein 1 (Rab6IP1)_like family. PLAT/LH2 domains consists of an eight stranded beta-barrel. In RabIP1 this domain may participate in lipid-mediated modulation of Rab6IP1's function via it's generally proposed ...
      pfam02141
      Location:202390
      DENN; DENN (AEX-3) domain
      cl02689
      Location:795942
      RUN; RUN domain

    RNA

    1. NR_145966.2 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (6) differs in the 5' UTR and lacks an alternate internal exon, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AC055845, AC079296, AP006259
      Related
      ENST00000530780.2

    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_000011.10 Reference GRCh38.p14 Primary Assembly

      Range
      9138825..9265350 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060935.1 Alternate T2T-CHM13v2.0

      Range
      9223596..9350195 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)