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

Gene ID: 414918, updated on 5-Mar-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 involved in regulation of catalytic activity. Predicted to be located in cytosol. Predicted to be active in recycling endosome. [provided by Alliance of Genome Resources, Apr 2022]
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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Location:
22q13.33
Exon count:
21
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 22 NC_000022.11 (50309030..50327012, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 22 NC_060946.1 (50816794..50834878, complement)
105.20220307 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
  • 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. SUMOylation of DDX39A Alters Binding and Export of Antiviral Transcripts to Control Innate Immunity. Shi P, et al. J Immunol, 2020 Jul 1. PMID 32393512

See all (15) 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_2023_10

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

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