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

    Gene ID: 27147, updated on 28-Oct-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, Oct 2024]
    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_2024_08 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (140518419..140641460, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (141832550..141955637, complement)
    RS_2024_09 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 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
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    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_2024_08

    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

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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