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

    Gene ID: 160518, updated on 10-Dec-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, Dec 2024]
    Expression
    Broad expression in ovary (RPKM 8.9), testis (RPKM 6.8) and 21 other tissues See more
    Orthologs
    mouse all
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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: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 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)

    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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