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    DENND4B DENN domain containing 4B [ Homo sapiens (human) ]

    Gene ID: 9909, updated on 3-Apr-2024

    Summary

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    Official Symbol
    DENND4Bprovided by HGNC
    Official Full Name
    DENN domain containing 4Bprovided by HGNC
    Primary source
    HGNC:HGNC:29044
    See related
    Ensembl:ENSG00000198837 MIM:619843; AllianceGenome:HGNC:29044
    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
    KIAA0476
    Summary
    Enables guanyl-nucleotide exchange factor activity. Involved in regulation of Rab protein signal transduction. Located in Golgi apparatus and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Ubiquitous expression in spleen (RPKM 20.1), lymph node (RPKM 17.2) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    Location:
    1q21.3
    Exon count:
    30
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (153929501..153946894, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (153066762..153084154, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (153901977..153919194, complement)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124904425 Neighboring gene GATA zinc finger domain containing 2B Neighboring gene adipose differentiation-related protein pseudogene Neighboring gene Sharpr-MPRA regulatory region 14566 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:153877149-153877650 Neighboring gene Sharpr-MPRA regulatory region 2699 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1345 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1755 Neighboring gene uncharacterized LOC101928059 Neighboring gene Sharpr-MPRA regulatory region 4321 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:153897582-153897755 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1756 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1757 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:153918384-153918884 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1758 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1759 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1760 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1761 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1347 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1762 Neighboring gene CREB regulated transcription coactivator 2 Neighboring gene solute carrier family 39 member 1 Neighboring gene microRNA 6737

    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. Molecular cloning, structural analysis, and expression of a human IRLB, MYC promoter-binding protein: new DENN domain-containing protein family emerges. Semova N, et al. Genomics, 2003 Sep. PMID 12906859
    2. Novel triplet repeat containing genes in human brain: cloning, expression, and length polymorphisms. Li SH, et al. Genomics, 1993 Jun. PMID 8325628
    3. Genome-wide association identifies genetic variants associated with lentiform nucleus volume in N = 1345 young and elderly subjects. Hibar DP, et al. Brain Imaging Behav, 2013 Jun. PMID 22903471, Free PMC Article
    4. Characterization of cDNA clones in size-fractionated cDNA libraries from human brain. Seki N, et al. DNA Res, 1997 Oct 31. PMID 9455484
    5. 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

    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 identifies genetic variants associated with lentiform nucleus volume in N = 1345 young and elderly subjects.
    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

    Clone Names

    • FLJ26202, DKFZp762N174

    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 regulation of Rab protein signal transduction IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in regulation of Rab protein signal transduction IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in Golgi apparatus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in cytoplasmic vesicle IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytosol TAS
    Traceable Author Statement
    more info
    		  
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		  

    General protein information

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    Preferred Names
    DENN domain-containing protein 4B
    Names
    DENN/MADD domain containing 4B

    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_001367466.1 → NP_001354395.1  DENN domain-containing protein 4B isoform 2

      Status: VALIDATED

      Source sequence(s)
      AL358472
      UniProtKB/TrEMBL
      E9PAK5

    2. NM_014856.3 → NP_055671.2  DENN domain-containing protein 4B isoform 1

      See identical proteins and their annotated locations for NP_055671.2

      Status: VALIDATED

      Source sequence(s)
      AB007945, AL358472
      Consensus CDS
      CCDS44228.1
      UniProtKB/Swiss-Prot
      O75064, Q5T4K0
      UniProtKB/TrEMBL
      E9PAK5
      Related
      ENSP00000354597.4, ENST00000361217.9
      Conserved Domains (5) summary
      smart00801
      Location:563 → 636
      dDENN; Domain always found downstream of DENN domain, found in a variety of signalling proteins
      smart00800
      Location:191 → 279
      uDENN; Domain always found upstream of DENN domain, found in a variety of signalling proteins
      sd00004
      Location:813 → 842
      PPR; PPR repeat [structural motif]
      pfam02141
      Location:313 → 497
      DENN; DENN (AEX-3) domain
      pfam13041
      Location:811 → 851
      PPR_2; PPR repeat family

    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_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      153929501..153946894 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047435925.1 → XP_047291881.1  DENN domain-containing protein 4B isoform X7

    2. XM_047435915.1 → XP_047291871.1  DENN domain-containing protein 4B isoform X2

    3. XM_011510219.2 → XP_011508521.2  DENN domain-containing protein 4B isoform X6

    4. XM_047435916.1 → XP_047291872.1  DENN domain-containing protein 4B isoform X3

    5. XM_047435912.1 → XP_047291868.1  DENN domain-containing protein 4B isoform X1

    6. XM_047435943.1 → XP_047291899.1  DENN domain-containing protein 4B isoform X5

    7. XM_047435921.1 → XP_047291877.1  DENN domain-containing protein 4B isoform X5

    8. XM_047435936.1 → XP_047291892.1  DENN domain-containing protein 4B isoform X10

    9. XM_047435917.1 → XP_047291873.1  DENN domain-containing protein 4B isoform X4

    10. XM_011510221.4 → XP_011508523.1  DENN domain-containing protein 4B isoform X13

      Conserved Domains (4) summary
      smart00801
      Location:361 → 434
      dDENN; Domain always found downstream of DENN domain, found in a variety of signalling proteins
      sd00004
      Location:611 → 640
      PPR; PPR repeat [structural motif]
      pfam02141
      Location:165 → 295
      DENN; DENN (AEX-3) domain
      pfam13041
      Location:609 → 649
      PPR_2; PPR repeat family

    11. XM_047435944.1 → XP_047291900.1  DENN domain-containing protein 4B isoform X11

    12. XM_011510220.3 → XP_011508522.1  DENN domain-containing protein 4B isoform X12

      See identical proteins and their annotated locations for XP_011508522.1

      Conserved Domains (4) summary
      smart00801
      Location:458 → 531
      dDENN; Domain always found downstream of DENN domain, found in a variety of signalling proteins
      sd00004
      Location:708 → 737
      PPR; PPR repeat [structural motif]
      pfam02141
      Location:208 → 392
      DENN; DENN (AEX-3) domain
      pfam13041
      Location:706 → 746
      PPR_2; PPR repeat family

    13. XM_047435933.1 → XP_047291889.1  DENN domain-containing protein 4B isoform X9

    14. XM_047435930.1 → XP_047291886.1  DENN domain-containing protein 4B isoform X8

      Related
      ENSP00000357635.2, ENST00000368646.6

    15. XM_011510222.2 → XP_011508524.2  DENN domain-containing protein 4B isoform X14

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      153066762..153084154 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054339917.1 → XP_054195892.1  DENN domain-containing protein 4B isoform X3

    2. XM_054339923.1 → XP_054195898.1  DENN domain-containing protein 4B isoform X5

    3. XM_054339922.1 → XP_054195897.1  DENN domain-containing protein 4B isoform X10

    4. XM_054339918.1 → XP_054195893.1  DENN domain-containing protein 4B isoform X4

    5. XM_054339919.1 → XP_054195894.1  DENN domain-containing protein 4B isoform X16

    6. XM_054339916.1 → XP_054195891.1  DENN domain-containing protein 4B isoform X15

    7. XM_054339926.1 → XP_054195901.1  DENN domain-containing protein 4B isoform X13

    8. XM_054339924.1 → XP_054195899.1  DENN domain-containing protein 4B isoform X11

    9. XM_054339925.1 → XP_054195900.1  DENN domain-containing protein 4B isoform X12

    10. XM_054339921.1 → XP_054195896.1  DENN domain-containing protein 4B isoform X9

    11. XM_054339920.1 → XP_054195895.1  DENN domain-containing protein 4B isoform X17

    12. XM_054339927.1 → XP_054195902.1  DENN domain-containing protein 4B isoform X18

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    O75064.4 GenPept UniProtKB/Swiss-Prot:O75064

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