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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
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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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