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DENND2A DENN domain containing 2A [ Homo sapiens (human) ]

Gene ID: 27147, updated on 5-Mar-2024

Summary

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Official Symbol
DENND2Aprovided by HGNC
Official Full Name
DENN domain containing 2Aprovided by HGNC
Primary source
HGNC:HGNC:22212
See related
Ensembl:ENSG00000146966 MIM:620120; AllianceGenome:HGNC:22212
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
FAM31D; KIAA1277
Summary
Enables guanyl-nucleotide exchange factor activity. Involved in retrograde transport, endosome to Golgi. Located in actin cytoskeleton. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Broad expression in endometrium (RPKM 6.4), ovary (RPKM 5.7) and 22 other tissues See more
Orthologs
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Genomic context

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See DENND2A in Genome Data Viewer
Location:
7q34
Exon count:
22
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (140518419..140641460, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (141832550..141955637, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (140218219..140341260, complement)

Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26781 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:140143760-140144260 Neighboring gene nucleoside diphosphate kinase, mitochondrial-like Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:140156257-140157110 Neighboring gene makorin ring finger protein 1 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:140178571-140179411 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:140179742-140180652 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26782 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:140206498-140207088 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:140207089-140207678 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:140227087-140227701 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:140244505-140245005 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:140253137-140253867 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:140255121-140255621 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:140269202-140269702 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:140269703-140270203 Neighboring gene Sharpr-MPRA regulatory region 5784 Neighboring gene Sharpr-MPRA regulatory region 9531 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:140324769-140325360 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:140325951-140326542 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:140327133-140327724 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:140327725-140328314 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:140332981-140333481 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:140334787-140335394 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:140335395-140336002 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:140336003-140336609 Neighboring gene Sharpr-MPRA regulatory region 2153 Neighboring gene uncharacterized LOC105375535 Neighboring gene ReSE screen-validated silencer GRCh37_chr7:140346933-140347108 Neighboring gene RNA, 7SL, cytoplasmic 771, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18715 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26783 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:140378691-140379191 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:140389463-140389963 Neighboring gene aarF domain containing kinase 2

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. DOCK11 and DENND2A play pivotal roles in the maintenance of hepatitis B virus in host cells. Hashimoto S, et al. PLoS One, 2021. PMID 33539396, Free PMC Article
  2. Genome-wide association identifies ATOH7 as a major gene determining human optic disc size. Macgregor S, et al. Hum Mol Genet, 2010 Jul 1. PMID 20395239, Free PMC Article
  3. Family-wide characterization of the DENN domain Rab GDP-GTP exchange factors. Yoshimura S, et al. J Cell Biol, 2010 Oct 18. PMID 20937701, Free PMC Article
  4. Prediction of the coding sequences of unidentified human genes. XV. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro. Nagase T, et al. DNA Res, 1999 Oct 29. PMID 10574462
  5. Proteomic Analysis of the EWS-Fli-1 Interactome Reveals the Role of the Lysosome in EWS-Fli-1 Turnover. Elzi DJ, et al. J Proteome Res, 2014 Aug 1. PMID 24999758, Free PMC Article

See all (14) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. DOCK11 and DENND2A play pivotal roles in the maintenance of hepatitis B virus in host cells.
    Title: DOCK11 and DENND2A play pivotal roles in the maintenance of hepatitis B virus in host cells.
  2. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
    Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
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

EBI GWAS Catalog

Description
Genome-wide association identifies ATOH7 as a major gene determining human optic disc size.
EBI GWAS Catalog

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

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
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
  
Process Evidence Code Pubs
involved_in protein transport IEA
Inferred from Electronic Annotation
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
is_active_in actin cytoskeleton IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in actin cytoskeleton IDA
Inferred from Direct Assay
more info
 PubMed 
located_in cytosol TAS
Traceable Author Statement
more info
  

General protein information

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Preferred Names
DENN domain-containing protein 2A
Names
DENN/MADD domain containing 2A

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_001318052.2 → NP_001304981.1  DENN domain-containing protein 2A isoform a

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1, 2 and 5 encode the same isoform (a).
    Source sequence(s)
    AB033103, AC006452, BC049193, DA401015
    Consensus CDS
    CCDS43659.1
    UniProtKB/Swiss-Prot
    C9JUI3, Q1RMD5, Q86XY0, Q9ULE3
    UniProtKB/TrEMBL
    A2RUF6
    Related
    ENSP00000275884.6, ENST00000275884.10
    Conserved Domains (3) summary
    smart00801
    Location:896 → 962
    dDENN; Domain always found downstream of DENN domain, found in a variety of signalling proteins
    smart00800
    Location:561 → 653
    uDENN; Domain always found upstream of DENN domain, found in a variety of signalling proteins
    pfam02141
    Location:660 → 816
    DENN; DENN (AEX-3) domain

  2. NM_001318053.2 → NP_001304982.1  DENN domain-containing protein 2A isoform b

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) lacks several exons, and its 3' terminal exon extends past a splice site that is used in variant 1. This results in a novel 3' coding region and 3' UTR, compared to variant 1. The encoded isoform (b) has a shorter and distinct C-terminus, compared to isoform a.
    Source sequence(s)
    AC069335, BC115004, DA401015
    Consensus CDS
    CCDS83233.1
    UniProtKB/TrEMBL
    F8WAT8
    Related
    ENSP00000419464.1, ENST00000492720.5
    Conserved Domains (2) summary
    smart00799
    Location:661 → 775
    DENN; Domain found in a variety of signalling proteins, always encircled by uDENN and dDENN
    smart00800
    Location:561 → 653
    uDENN; Domain always found upstream of DENN domain, found in a variety of signalling proteins

  3. NM_001362678.2 → NP_001349607.1  DENN domain-containing protein 2A isoform a

    Status: VALIDATED

    Description
    Transcript Variant: This variant (5) differs in the 5' UTR compared to variant 1. Variants 1, 2 and 5 encode the same isoform (a).
    Source sequence(s)
    AB033103, AC006452, BC049193, DA401015, DC322559
    Consensus CDS
    CCDS43659.1
    UniProtKB/Swiss-Prot
    C9JUI3, Q1RMD5, Q86XY0, Q9ULE3
    UniProtKB/TrEMBL
    A2RUF6
    Conserved Domains (3) summary
    smart00801
    Location:896 → 962
    dDENN; Domain always found downstream of DENN domain, found in a variety of signalling proteins
    smart00800
    Location:561 → 653
    uDENN; Domain always found upstream of DENN domain, found in a variety of signalling proteins
    pfam02141
    Location:660 → 816
    DENN; DENN (AEX-3) domain

  4. NM_015689.5 → NP_056504.3  DENN domain-containing protein 2A isoform a

    See identical proteins and their annotated locations for NP_056504.3

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longer isoform (a). Variants 1, 2 and 5 encode the same isoform (a).
    Source sequence(s)
    AB033103, AC006452, AI040169, AK290056, BC049193, BC115004, DA401015
    Consensus CDS
    CCDS43659.1
    UniProtKB/Swiss-Prot
    C9JUI3, Q1RMD5, Q86XY0, Q9ULE3
    UniProtKB/TrEMBL
    A2RUF6
    Related
    ENSP00000419654.1, ENST00000496613.6
    Conserved Domains (3) summary
    smart00801
    Location:896 → 962
    dDENN; Domain always found downstream of DENN domain, found in a variety of signalling proteins
    smart00800
    Location:561 → 653
    uDENN; Domain always found upstream of DENN domain, found in a variety of signalling proteins
    pfam02141
    Location:660 → 816
    DENN; DENN (AEX-3) domain

RNA

  1. NR_134477.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) lacks several 5' exons, and uses an alternate splice site in a 3' 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)
    AI040169, BC049193, BC115004, BC144190, DA401015
    Related
    ENST00000461883.5

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_000007.14 Reference GRCh38.p14 Primary Assembly

    Range
    140518419..140641460 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060931.1 Alternate T2T-CHM13v2.0

    Range
    141832550..141955637 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9ULE3.4 GenPept UniProtKB/Swiss-Prot:Q9ULE3

Gene LinkOut

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