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    DENND6B DENN domain containing 6B [ Homo sapiens (human) ]

    Gene ID: 414918, updated on 2-Nov-2024

    Summary

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    Official Symbol
    DENND6Bprovided by HGNC
    Official Full Name
    DENN domain containing 6Bprovided by HGNC
    Primary source
    HGNC:HGNC:32690
    See related
    Ensembl:ENSG00000205593 MIM:620562; AllianceGenome:HGNC:32690
    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
    AFI1B; FAM116B
    Summary
    Enables guanyl-nucleotide exchange factor activity. Predicted to be located in cytosol. Predicted to be active in recycling endosome. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Broad expression in brain (RPKM 4.5), testis (RPKM 3.3) and 24 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See DENND6B in Genome Data Viewer
    Location:
    22q13.33
    Exon count:
    21
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 22 NC_000022.11 (50309030..50327012, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 22 NC_060946.1 (50816794..50834878, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 22 NC_000022.10 (50747459..50765441, complement)

    Chromosome 22 - NC_000022.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13964 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13965 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13966 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:50710106-50710645 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:50710646-50711186 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13968 Neighboring gene mitogen-activated protein kinase 11 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr22:50720546-50721745 Neighboring gene plexin B2 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13969 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19312 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:50738869-50739425 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:50739426-50739982 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13970 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr22:50743729-50744928 Neighboring gene ReSE screen-validated silencer GRCh37_chr22:50745236-50745386 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13971 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13972 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13973 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13974 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19314 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:50753063-50753811 Neighboring gene uncharacterized LOC105373096 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:50755814-50756314 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:50756315-50756815 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:50759389-50759889 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13975 Neighboring gene ReSE screen-validated silencer GRCh37_chr22:50770723-50770912 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19316 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19317 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:50780464-50781110 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13976 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13977 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13978 Neighboring gene protein phosphatase 6 regulatory subunit 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19318 Neighboring gene RNA, 7SL, cytoplasmic 500, pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:50836255-50836755 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:50838165-50838761 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr22:50844619-50845818 Neighboring gene microRNA 12114

    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. 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. The MEKK1 PHD ubiquitinates TAB1 to activate MAPKs in response to cytokines. Charlaftis N, et al. EMBO J, 2014 Nov 3. PMID 25260751, Free PMC Article
    4. Genome-wide association study identifies three novel susceptibility loci for severe Acne vulgaris. Navarini AA, et al. Nat Commun, 2014 Jun 13. PMID 24927181
    5. High-resolution photocatalytic mapping of SARS-CoV-2 spike interactions on the cell surface. Datta S, et al. Cell Chem Biol, 2023 Oct 19. PMID 37499664

    See all (18) citations in PubMed

    GeneRIFs: Gene References Into Functions

    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 study identifies three novel susceptibility loci for severe Acne vulgaris.
    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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    Homology

    Clone Names

    • MGC33692

    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
    		  
    Component Evidence Code Pubs
    located_in cytosol TAS
    Traceable Author Statement
    more info
    		  
    is_active_in recycling endosome IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    protein DENND6B
    Names
    DENN domain-containing protein 6B
    DENN/MADD domain containing 6B
    family with sequence similarity 116, member B
    protein FAM116B

    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_001001794.4 → NP_001001794.3  protein DENND6B

      See identical proteins and their annotated locations for NP_001001794.3

      Status: VALIDATED

      Source sequence(s)
      AA864612, BC031069, CR932344
      Consensus CDS
      CCDS46732.1
      UniProtKB/Swiss-Prot
      A6X8I5, Q8NEG7
      Related
      ENSP00000391524.2, ENST00000413817.8
      Conserved Domains (2) summary
      pfam08616
      Location:250 → 356
      SPA; Stabilization of polarity axis
      cl11519
      Location:151 → 311
      DENN; DENN (AEX-3) domain

    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_000022.11 Reference GRCh38.p14 Primary Assembly

      Range
      50309030..50327012 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011530693.4 → XP_011528995.1  protein DENND6B isoform X3

      Conserved Domains (2) summary
      pfam08616
      Location:250 → 356
      SPA; Stabilization of polarity axis
      cl11519
      Location:151 → 311
      DENN; DENN (AEX-3) domain

    2. XM_005261914.5 → XP_005261971.1  protein DENND6B isoform X2

      Conserved Domains (2) summary
      pfam08616
      Location:299 → 405
      SPA; Stabilization of polarity axis
      cl11519
      Location:201 → 360
      DENN; DENN (AEX-3) domain

    3. XM_011530692.4 → XP_011528994.1  protein DENND6B isoform X1

      Conserved Domains (2) summary
      pfam08616
      Location:299 → 405
      SPA; Stabilization of polarity axis
      cl11519
      Location:201 → 360
      DENN; DENN (AEX-3) domain

    4. XM_047441364.1 → XP_047297320.1  protein DENND6B isoform X4

    5. XM_047441365.1 → XP_047297321.1  protein DENND6B isoform X5

    RNA

    1. XR_007067972.1 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060946.1 Alternate T2T-CHM13v2.0

      Range
      50816794..50834878 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054325617.1 → XP_054181592.1  protein DENND6B isoform X3

    2. XM_054325616.1 → XP_054181591.1  protein DENND6B isoform X2

    3. XM_054325615.1 → XP_054181590.1  protein DENND6B isoform X1

    4. XM_054325618.1 → XP_054181593.1  protein DENND6B isoform X4

    5. XM_054325619.1 → XP_054181594.1  protein DENND6B isoform X5

    RNA

    1. XR_008485397.1 RNA Sequence

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8NEG7.1 GenPept UniProtKB/Swiss-Prot:Q8NEG7

    Gene LinkOut

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