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

Gene ID: 23258, updated on 24-Nov-2020

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
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

Genomic context

See DENND5A in Genome Data Viewer
Location:
11p15.4
Exon count:
24
Annotation release Status Assembly Chr Location
109.20201120 current GRCh38.p13 (GCF_000001405.39) 11 NC_000011.10 (9138825..9265350, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (9160372..9286882, complement)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene keratin 8 pseudogene 41 Neighboring gene uncharacterized LOC105376542 Neighboring gene Sharpr-MPRA regulatory region 9656 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

Homology

Clone Names

  • FLJ22354, FLJ33829, FLJ43455, KIAA1091

Gene Ontology Provided by GOA

Function Evidence Code Pubs
guanyl-nucleotide exchange factor activity IDA
Inferred from Direct Assay
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
negative regulation of neuron projection development ISS
Inferred from Sequence or Structural Similarity
more info
 
retrograde transport, endosome to Golgi IMP
Inferred from Mutant Phenotype
more info
PubMed 
Component Evidence Code Pubs
Golgi membrane IEA
Inferred from Electronic Annotation
more info
 
cytosol TAS
Traceable Author Statement
more info
 
colocalizes_with retromer complex IDA
Inferred from Direct Assay
more info
PubMed 
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)

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/Swiss-Prot
    Q6IQ26
    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
    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
    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
    Q6IQ26
    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

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20201120

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000011.10 Reference GRCh38.p13 Primary Assembly

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