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    DENND6A DENN domain containing 6A [ Homo sapiens (human) ]

    Gene ID: 201627, updated on 10-Dec-2024

    Summary

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    Official Symbol
    DENND6Aprovided by HGNC
    Official Full Name
    DENN domain containing 6Aprovided by HGNC
    Primary source
    HGNC:HGNC:26635
    See related
    Ensembl:ENSG00000174839 MIM:620561; AllianceGenome:HGNC:26635
    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
    AFI1A; FAM116A
    Summary
    Enables guanyl-nucleotide exchange factor activity. Involved in positive regulation of cell-cell adhesion mediated by cadherin. Located in recycling endosome. [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Ubiquitous expression in ovary (RPKM 8.9), thyroid (RPKM 8.0) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See DENND6A in Genome Data Viewer
    Location:
    3p14.3
    Exon count:
    24
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (57625454..57693077, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (57665829..57733445, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (57611181..57678804, complement)

    Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene phosphodiesterase 12 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr3:57582608-57583807 Neighboring gene ARF4 antisense RNA 1 Neighboring gene RNA, U6atac small nuclear 26, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14481 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:57678132-57678632 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14483 Neighboring gene DENND6A divergent transcript Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr3:57737311-57738510 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancers GRCh37_chr3:57741142-57742044 and GRCh37_chr3:57742045-57742946 Neighboring gene MPRA-validated peak4671 silencer Neighboring gene sarcolemma associated protein Neighboring gene PDHA1 pseudogene 1

    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. DENN domain proteins: regulators of Rab GTPases. Marat AL, et al. J Biol Chem, 2011 Apr 22. PMID 21330364, Free PMC Article
    2. Rab14 and its exchange factor FAM116 link endocytic recycling and adherens junction stability in migrating cells. Linford A, et al. Dev Cell, 2012 May 15. PMID 22595670, Free PMC Article
    3. BioID reveals an ATG9A interaction with ATG13-ATG101 in the degradation of p62/SQSTM1-ubiquitin clusters. Kannangara AR, et al. EMBO Rep, 2021 Oct 5. PMID 34369648, Free PMC Article
    4. Integrative analysis of kinase networks in TRAIL-induced apoptosis provides a source of potential targets for combination therapy. So J, et al. Sci Signal, 2015 Apr 7. PMID 25852190
    5. E3 ubiquitin ligase RNF123 targets lamin B1 and lamin-binding proteins. Khanna R, et al. FEBS J, 2018 Jun. PMID 29676528

    See all (21) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. FAM116 and Rab14 therefore define an endocytic recycling pathway needed for ADAM protease trafficking and regulation of cell-cell junctions.
      Title: Rab14 and its exchange factor FAM116 link endocytic recycling and adherens junction stability in migrating cells.
    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

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ34969

    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 positive regulation of cell-cell adhesion mediated by cadherin IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cytosol TAS
    Traceable Author Statement
    more info
    		  
    located_in intracellular membrane-bounded organelle IDA
    Inferred from Direct Assay
    more info
    		  
    is_active_in recycling endosome IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in recycling endosome IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    protein DENND6A
    Names
    DENN domain-containing protein 6A
    DENN/MADD domain containing 6A
    family with sequence similarity 116, member A
    protein FAM116A

    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_152678.3 → NP_689891.1  protein DENND6A

      See identical proteins and their annotated locations for NP_689891.1

      Status: VALIDATED

      Source sequence(s)
      AA605125, AC114480, AK074156, BC040291
      Consensus CDS
      CCDS33773.1
      UniProtKB/Swiss-Prot
      Q7Z5T4, Q8IWF6, Q8N235, Q8TEG8
      Related
      ENSP00000311401.5, ENST00000311128.10
      Conserved Domains (3) summary
      cl11519
      Location:171 → 359
      DENN; DENN (AEX-3) domain
      cl40631
      Location:270 → 373
      SPA; Stabilization of polarity axis
      cl40632
      Location:64 → 201
      Avl9; Transport protein Avl9

    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_000003.12 Reference GRCh38.p14 Primary Assembly

      Range
      57625454..57693077 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006713019.4 → XP_006713082.1  protein DENND6A isoform X1

      Conserved Domains (2) summary
      pfam08616
      Location:269 → 372
      SPA; Stabilization of polarity axis
      cl11519
      Location:170 → 358
      DENN; DENN (AEX-3) domain

    2. XM_047447670.1 → XP_047303626.1  protein DENND6A isoform X2

    RNA

    1. XR_007095649.1 RNA Sequence

    2. XR_245100.2 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060927.1 Alternate T2T-CHM13v2.0

      Range
      57665829..57733445 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054345650.1 → XP_054201625.1  protein DENND6A isoform X1

    2. XM_054345651.1 → XP_054201626.1  protein DENND6A isoform X2

    RNA

    1. XR_008486678.1 RNA Sequence

    2. XR_008486677.1 RNA Sequence

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8IWF6.1 GenPept UniProtKB/Swiss-Prot:Q8IWF6

    Gene LinkOut

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

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