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DENND5B DENN domain containing 5B [ Homo sapiens (human) ]

Gene ID: 160518, updated on 28-Oct-2024

Summary

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Official Symbol
DENND5Bprovided by HGNC
Official Full Name
DENN domain containing 5Bprovided by HGNC
Primary source
HGNC:HGNC:28338
See related
Ensembl:ENSG00000170456 MIM:617279; AllianceGenome:HGNC:28338
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
Summary
Enables guanyl-nucleotide exchange factor activity. Predicted to be involved in positive regulation of triglyceride transport. Predicted to be located in cytosol. [provided by Alliance of Genome Resources, Oct 2024]
Expression
Broad expression in ovary (RPKM 8.9), testis (RPKM 6.8) and 21 other tissues See more
Orthologs
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Genomic context

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See DENND5B in Genome Data Viewer
Location:
12p11.21
Exon count:
27
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (31382226..31591136, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (31258770..31467670, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (31535160..31744070, complement)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene SIN3-HDAC complex associated factor Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:31478173-31479104 Neighboring gene uncharacterized LOC79857 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:31517453-31517952 Neighboring gene U6 spliceosomal RNA Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:31523276-31523883 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:31523884-31524492 Neighboring gene long intergenic non-protein coding RNA 2387 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6164 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6165 Neighboring gene RNA, U6 small nuclear 618, pseudogene Neighboring gene small nucleolar RNA U13 Neighboring gene TAF10 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 30kDa pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6166 Neighboring gene mitochondrial ribosomal protein L30 pseudogene 2 Neighboring gene NANOG-H3K27ac hESC enhancers GRCh37_chr12:31671414-31671951 and GRCh37_chr12:31671952-31672488 Neighboring gene ANKRD49 pseudogene 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6167 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:31724314-31724814 Neighboring gene MPRA-validated peak1655 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6168 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4323 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4324 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4325 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6169 Neighboring gene DENND5B antisense RNA 1 Neighboring gene RNA, U5F small nuclear 4, pseudogene Neighboring gene ribosomal protein L31 pseudogene 50

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. De novo variants in DENND5B cause a neurodevelopmental disorder. Scala M, et al. Am J Hum Genet, 2024 Mar 7. PMID 38387458, Free PMC Article
  2. DENND5B Regulates Intestinal Triglyceride Absorption and Body Mass. Gordon SM, et al. Sci Rep, 2019 Mar 5. PMID 30837651, Free PMC Article
  3. 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
  4. POH1 contributes to hyperactivation of TGF-β signaling and facilitates hepatocellular carcinoma metastasis through deubiquitinating TGF-β receptors and caveolin-1. Wang B, et al. EBioMedicine, 2019 Mar. PMID 30745168, Free PMC Article
  5. Estrogen-regulated feedback loop limits the efficacy of estrogen receptor-targeted breast cancer therapy. Xiao T, et al. Proc Natl Acad Sci U S A, 2018 Jul 31. PMID 29987050, Free PMC Article

See all (17) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. De novo variants in DENND5B cause a neurodevelopmental disorder.
    Title: De novo variants in DENND5B cause a neurodevelopmental disorder.
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)

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

  • FLJ41648, FLJ43333, MGC24039, DKFZp686P1174

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables guanyl-nucleotide exchange factor activity IBA
Inferred from Biological aspect of Ancestor
more info
  
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 small GTPase binding IBA
Inferred from Biological aspect of Ancestor
more info
  
Process Evidence Code Pubs
involved_in positive regulation of triglyceride transport IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
located_in cytosol TAS
Traceable Author Statement
more info
  
located_in membrane IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
DENN domain-containing protein 5B
Names
DENN/MADD domain containing 5B
rab6IP1-like protein

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_001308339.2 → NP_001295268.1  DENN domain-containing protein 5B isoform 2

    See identical proteins and their annotated locations for NP_001295268.1

    Status: VALIDATED

    Source sequence(s)
    AC022080, AC068792, AK125323, BC068580, BM676905
    Consensus CDS
    CCDS76542.1
    UniProtKB/TrEMBL
    G3V1S3
    Related
    ENSP00000444889.1, ENST00000536562.5
    Conserved Domains (6) summary
    smart00801
    Location:534 → 609
    dDENN; Domain always found downstream of DENN domain, found in a variety of signalling proteins
    smart00800
    Location:82 → 155
    uDENN; Domain always found upstream of DENN domain, found in a variety of signalling proteins
    cd01757
    Location:971 → 1079
    PLAT_RAB6IP1; PLAT/LH2 domain present in RAB6 interacting protein 1 (Rab6IP1)_like family. PLAT/LH2 domains consists of an eight stranded beta-barrel. In RabIP1 this domain may participate in lipid-mediated modulation of Rab6IP1's function via it's generally proposed ...
    pfam02141
    Location:222 → 410
    DENN; DENN (AEX-3) domain
    pfam02759
    Location:815 → 959
    RUN; RUN domain
    cl02689
    Location:1162 → 1299
    RUN; RUN domain

  2. NM_001366890.1 → NP_001353819.1  DENN domain-containing protein 5B isoform 3

    Status: VALIDATED

    Source sequence(s)
    AC022080, AC068792
    Consensus CDS
    CCDS91679.1
    Related
    ENSP00000346238.4, ENST00000354285.8
    Conserved Domains (3) summary
    smart00801
    Location:521 → 596
    dDENN; Domain always found downstream of DENN domain, found in a variety of signalling proteins
    smart00800
    Location:19 → 142
    uDENN; Domain always found upstream of DENN domain, found in a variety of signalling proteins
    pfam02141
    Location:209 → 397
    DENN; DENN (AEX-3) domain

  3. NM_001366891.1 → NP_001353820.1  DENN domain-containing protein 5B isoform 4

    Status: VALIDATED

    Source sequence(s)
    AC022080, AC068792

  4. NM_001366892.1 → NP_001353821.1  DENN domain-containing protein 5B isoform 5

    Status: VALIDATED

    Source sequence(s)
    AC022080, AC068792
    UniProtKB/TrEMBL
    H0YGE5
    Related
    ENSP00000442938.1, ENST00000546299.1
    Conserved Domains (2) summary
    smart00800
    Location:19 → 120
    uDENN; Domain always found upstream of DENN domain, found in a variety of signalling proteins
    pfam02141
    Location:187 → 375
    DENN; DENN (AEX-3) domain

  5. NM_001366893.1 → NP_001353822.1  DENN domain-containing protein 5B isoform 6

    Status: VALIDATED

    Source sequence(s)
    AC022080, AC068792
    UniProtKB/TrEMBL
    H0YGE5
    Conserved Domains (2) summary
    smart00800
    Location:19 → 142
    uDENN; Domain always found upstream of DENN domain, found in a variety of signalling proteins
    pfam02141
    Location:209 → 397
    DENN; DENN (AEX-3) domain

  6. NM_144973.4 → NP_659410.3  DENN domain-containing protein 5B isoform 1

    See identical proteins and their annotated locations for NP_659410.3

    Status: VALIDATED

    Source sequence(s)
    AB209341, AC022080, AC068792, AI762929, BC020855, BF513808, BM676905
    Consensus CDS
    CCDS44857.1
    UniProtKB/Swiss-Prot
    B5ME75, Q59FW8, Q68CZ7, Q6NUJ0, Q6ZUT9, Q7Z3F9, Q8N973, Q8WUC8
    Related
    ENSP00000373734.5, ENST00000389082.10
    Conserved Domains (6) summary
    smart00801
    Location:499 → 574
    dDENN; Domain always found downstream of DENN domain, found in a variety of signalling proteins
    smart00800
    Location:19 → 120
    uDENN; Domain always found upstream of DENN domain, found in a variety of signalling proteins
    cd01757
    Location:936 → 1044
    PLAT_RAB6IP1; PLAT/LH2 domain present in RAB6 interacting protein 1 (Rab6IP1)_like family. PLAT/LH2 domains consists of an eight stranded beta-barrel. In RabIP1 this domain may participate in lipid-mediated modulation of Rab6IP1's function via it's generally proposed ...
    pfam02141
    Location:187 → 375
    DENN; DENN (AEX-3) domain
    pfam02759
    Location:780 → 924
    RUN; RUN domain
    cl02689
    Location:1127 → 1264
    RUN; RUN 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_000012.12 Reference GRCh38.p14 Primary Assembly

    Range
    31382226..31591136 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047428429.1 → XP_047284385.1  DENN domain-containing protein 5B isoform X17

  2. XM_047428424.1 → XP_047284380.1  DENN domain-containing protein 5B isoform X12

  3. XM_047428430.1 → XP_047284386.1  DENN domain-containing protein 5B isoform X18

  4. XM_047428421.1 → XP_047284377.1  DENN domain-containing protein 5B isoform X8

  5. XM_005253327.4 → XP_005253384.1  DENN domain-containing protein 5B isoform X3

    Conserved Domains (6) summary
    smart00801
    Location:499 → 574
    dDENN; Domain always found downstream of DENN domain, found in a variety of signalling proteins
    smart00800
    Location:19 → 120
    uDENN; Domain always found upstream of DENN domain, found in a variety of signalling proteins
    cd01757
    Location:973 → 1081
    PLAT_RAB6IP1; PLAT/LH2 domain present in RAB6 interacting protein 1 (Rab6IP1)_like family. PLAT/LH2 domains consists of an eight stranded beta-barrel. In RabIP1 this domain may participate in lipid-mediated modulation of Rab6IP1's function via it's generally proposed ...
    pfam02141
    Location:187 → 375
    DENN; DENN (AEX-3) domain
    pfam02759
    Location:817 → 961
    RUN; RUN domain
    cl02689
    Location:1164 → 1301
    RUN; RUN domain

  6. XM_047428427.1 → XP_047284383.1  DENN domain-containing protein 5B isoform X15

  7. XM_005253330.4 → XP_005253387.1  DENN domain-containing protein 5B isoform X11

    Conserved Domains (6) summary
    smart00801
    Location:344 → 419
    dDENN; Domain always found downstream of DENN domain, found in a variety of signalling proteins
    smart00799
    Location:146 → 220
    DENN; Domain found in a variety of signalling proteins, always encircled by uDENN and dDENN
    smart00800
    Location:19 → 142
    uDENN; Domain always found upstream of DENN domain, found in a variety of signalling proteins
    cd01757
    Location:818 → 926
    PLAT_RAB6IP1; PLAT/LH2 domain present in RAB6 interacting protein 1 (Rab6IP1)_like family. PLAT/LH2 domains consists of an eight stranded beta-barrel. In RabIP1 this domain may participate in lipid-mediated modulation of Rab6IP1's function via it's generally proposed ...
    pfam02759
    Location:662 → 806
    RUN; RUN domain
    cl02689
    Location:1009 → 1146
    RUN; RUN domain

  8. XM_047428428.1 → XP_047284384.1  DENN domain-containing protein 5B isoform X16

  9. XM_006719040.4 → XP_006719103.1  DENN domain-containing protein 5B isoform X4

    See identical proteins and their annotated locations for XP_006719103.1

    Conserved Domains (6) summary
    smart00801
    Location:521 → 596
    dDENN; Domain always found downstream of DENN domain, found in a variety of signalling proteins
    smart00800
    Location:19 → 142
    uDENN; Domain always found upstream of DENN domain, found in a variety of signalling proteins
    cd01757
    Location:958 → 1066
    PLAT_RAB6IP1; PLAT/LH2 domain present in RAB6 interacting protein 1 (Rab6IP1)_like family. PLAT/LH2 domains consists of an eight stranded beta-barrel. In RabIP1 this domain may participate in lipid-mediated modulation of Rab6IP1's function via it's generally proposed ...
    pfam02141
    Location:209 → 397
    DENN; DENN (AEX-3) domain
    pfam02759
    Location:802 → 946
    RUN; RUN domain
    cl02689
    Location:1149 → 1286
    RUN; RUN domain

  10. XM_005253326.3 → XP_005253383.1  DENN domain-containing protein 5B isoform X2

    Conserved Domains (6) summary
    smart00801
    Location:521 → 596
    dDENN; Domain always found downstream of DENN domain, found in a variety of signalling proteins
    smart00800
    Location:19 → 142
    uDENN; Domain always found upstream of DENN domain, found in a variety of signalling proteins
    cd01757
    Location:995 → 1103
    PLAT_RAB6IP1; PLAT/LH2 domain present in RAB6 interacting protein 1 (Rab6IP1)_like family. PLAT/LH2 domains consists of an eight stranded beta-barrel. In RabIP1 this domain may participate in lipid-mediated modulation of Rab6IP1's function via it's generally proposed ...
    pfam02141
    Location:209 → 397
    DENN; DENN (AEX-3) domain
    pfam02759
    Location:839 → 983
    RUN; RUN domain
    cl02689
    Location:1186 → 1323
    RUN; RUN domain

  11. XM_047428420.1 → XP_047284376.1  DENN domain-containing protein 5B isoform X7

  12. XM_047428419.1 → XP_047284375.1  DENN domain-containing protein 5B isoform X7

  13. XM_017018899.2 → XP_016874388.2  DENN domain-containing protein 5B isoform X13

  14. XM_047428422.1 → XP_047284378.1  DENN domain-containing protein 5B isoform X9

  15. XM_047428425.1 → XP_047284381.1  DENN domain-containing protein 5B isoform X14

  16. XM_047428423.1 → XP_047284379.1  DENN domain-containing protein 5B isoform X10

  17. XM_047428418.1 → XP_047284374.1  DENN domain-containing protein 5B isoform X6

  18. XM_047428416.1 → XP_047284372.1  DENN domain-containing protein 5B isoform X5

  19. XM_047428415.1 → XP_047284371.1  DENN domain-containing protein 5B isoform X1

  20. XM_011520590.3 → XP_011518892.1  DENN domain-containing protein 5B isoform X19

    Conserved Domains (5) summary
    smart00801
    Location:226 → 301
    dDENN; Domain always found downstream of DENN domain, found in a variety of signalling proteins
    smart00799
    Location:24 → 102
    DENN; Domain found in a variety of signalling proteins, always encircled by uDENN and dDENN
    cd01757
    Location:700 → 808
    PLAT_RAB6IP1; PLAT/LH2 domain present in RAB6 interacting protein 1 (Rab6IP1)_like family. PLAT/LH2 domains consists of an eight stranded beta-barrel. In RabIP1 this domain may participate in lipid-mediated modulation of Rab6IP1's function via it's generally proposed ...
    pfam02759
    Location:544 → 688
    RUN; RUN domain
    cl02689
    Location:891 → 1028
    RUN; RUN domain

  21. XM_047428431.1 → XP_047284387.1  DENN domain-containing protein 5B isoform X20

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    31258770..31467670 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054371277.1 → XP_054227252.1  DENN domain-containing protein 5B isoform X17

  2. XM_054371272.1 → XP_054227247.1  DENN domain-containing protein 5B isoform X12

  3. XM_054371278.1 → XP_054227253.1  DENN domain-containing protein 5B isoform X18

  4. XM_054371268.1 → XP_054227243.1  DENN domain-containing protein 5B isoform X8

  5. XM_054371262.1 → XP_054227237.1  DENN domain-containing protein 5B isoform X3

  6. XM_054371275.1 → XP_054227250.1  DENN domain-containing protein 5B isoform X15

  7. XM_054371271.1 → XP_054227246.1  DENN domain-containing protein 5B isoform X11

  8. XM_054371276.1 → XP_054227251.1  DENN domain-containing protein 5B isoform X16

  9. XM_054371263.1 → XP_054227238.1  DENN domain-containing protein 5B isoform X4

  10. XM_054371261.1 → XP_054227236.1  DENN domain-containing protein 5B isoform X2

  11. XM_054371267.1 → XP_054227242.1  DENN domain-containing protein 5B isoform X7

  12. XM_054371266.1 → XP_054227241.1  DENN domain-containing protein 5B isoform X7

  13. XM_054371273.1 → XP_054227248.1  DENN domain-containing protein 5B isoform X13

  14. XM_054371269.1 → XP_054227244.1  DENN domain-containing protein 5B isoform X9

  15. XM_054371274.1 → XP_054227249.1  DENN domain-containing protein 5B isoform X14

  16. XM_054371270.1 → XP_054227245.1  DENN domain-containing protein 5B isoform X10

  17. XM_054371265.1 → XP_054227240.1  DENN domain-containing protein 5B isoform X6

  18. XM_054371264.1 → XP_054227239.1  DENN domain-containing protein 5B isoform X5

  19. XM_054371260.1 → XP_054227235.1  DENN domain-containing protein 5B isoform X1

  20. XM_054371279.1 → XP_054227254.1  DENN domain-containing protein 5B isoform X19

  21. XM_054371280.1 → XP_054227255.1  DENN domain-containing protein 5B isoform X20

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q6ZUT9.2 GenPept UniProtKB/Swiss-Prot:Q6ZUT9

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