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    DENND10 DENN domain containing 10 [ Homo sapiens (human) ]

    Gene ID: 404636, updated on 10-Dec-2024

    Summary

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    Official Symbol
    DENND10provided by HGNC
    Official Full Name
    DENN domain containing 10provided by HGNC
    Primary source
    HGNC:HGNC:31793
    See related
    Ensembl:ENSG00000119979 AllianceGenome:HGNC:31793
    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
    FAM45A
    Summary
    Enables guanyl-nucleotide exchange factor activity and small GTPase binding activity. Involved in endosome transport via multivesicular body sorting pathway; protein transport; and regulation of early endosome to late endosome transport. Located in late endosome. [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Ubiquitous expression in thyroid (RPKM 10.5), esophagus (RPKM 8.9) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See DENND10 in Genome Data Viewer
    Location:
    10q26.11
    Exon count:
    11
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (119104113..119137984)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (119999563..120033391)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (120863625..120897496)

    Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene eukaryotic translation initiation factor 3 subunit A Neighboring gene small nucleolar RNA SNORA19 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:120826117-120826618 Neighboring gene small nucleolar RNA, H/ACA box 19 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2867 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:120840059-120840821 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:120852323-120852823 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2868 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:120865335-120865834 Neighboring gene Sharpr-MPRA regulatory region 2644 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:120901959-120902460 Neighboring gene sideroflexin 4 Neighboring gene ReSE screen-validated silencer GRCh37_chr10:120924677-120924863 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2869 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:120937203-120937847 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4104 Neighboring gene peroxiredoxin 3

    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. DENN domain-containing protein FAM45A regulates the homeostasis of late/multivesicular endosomes. Zhang J, et al. Biochim Biophys Acta Mol Cell Res, 2019 May. PMID 30771381
    2. Structure of the endosomal Commander complex linked to Ritscher-Schinzel syndrome. Healy MD, et al. Cell, 2023 May 11. PMID 37172566, Free PMC Article
    3. Mammalian APE1 controls miRNA processing and its interactome is linked to cancer RNA metabolism. Antoniali G, et al. Nat Commun, 2017 Oct 6. PMID 28986522, Free PMC Article
    4. Cell fixation improves performance of in situ crosslinking mass spectrometry while preserving cellular ultrastructure. Michael ARM, et al. Nat Commun, 2024 Oct 2. PMID 39358380, Free PMC Article
    5. hORFeome v3.1: a resource of human open reading frames representing over 10,000 human genes. Lamesch P, et al. Genomics, 2007 Mar. PMID 17207965, Free PMC Article

    See all (16) 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

    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

    • FLJ55853

    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 protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables small GTPase binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables small GTPase binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in endosome transport via multivesicular body sorting pathway IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in protein transport IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in protein transport IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in regulation of early endosome to late endosome transport IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in regulation of early endosome to late endosome transport IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    is_active_in late endosome IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in late endosome IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    DENN domain-containing protein 10
    Names
    family with sequence similarity 45 member A
    protein FAM45A

    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_001303111.2 → NP_001290040.1  DENN domain-containing protein 10 isoform 2

      See identical proteins and their annotated locations for NP_001290040.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) contains an alternate exon and uses an alternate splice site in the 5' region and initiates translation at an alternate start codon, compared to variant 1. The encoded isoform (2) has a distinct N-terminus and is shorter than isoform 1.
      Source sequence(s)
      AK293136, AL355598, BC022271, DA531569
      UniProtKB/Swiss-Prot
      Q5H9G7, Q6NSW5, Q9NZ36
      Conserved Domains (1) summary
      pfam08616
      Location:150 → 256
      SPA; Stabilization of polarity axis

    2. NM_001303112.2 → NP_001290041.1  DENN domain-containing protein 10 isoform 3

      See identical proteins and their annotated locations for NP_001290041.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) uses two alternate splice sites in the 5' region and initiates translation at an alternate start codon, compared to variant 1. The encoded isoform (3) has a distinct N-terminus and is shorter than isoform 1.
      Source sequence(s)
      AK297971, AL355598, BC022271, DA531569
      UniProtKB/TrEMBL
      B4DNL9
      Conserved Domains (1) summary
      pfam08616
      Location:85 → 191
      SPA; Stabilization of polarity axis

    3. NM_001303113.2 → NP_001290042.1  DENN domain-containing protein 10 isoform 4

      See identical proteins and their annotated locations for NP_001290042.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) uses an alternate splice site and lacks an exon in the 5' region and initiates translation at an alternate start codon, compared to variant 1. The encoded isoform (4) has a distinct N-terminus and is shorter than isoform 1.
      Source sequence(s)
      AK297633, AL355598, BC022271, DA531569
      UniProtKB/TrEMBL
      B4DMU4
      Conserved Domains (1) summary
      pfam08616
      Location:9 → 113
      SPA; Stabilization of polarity axis

    4. NM_207009.4 → NP_996892.1  DENN domain-containing protein 10 isoform 1

      See identical proteins and their annotated locations for NP_996892.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (1).
      Source sequence(s)
      AL355598, BC022271, DA531569
      Consensus CDS
      CCDS7609.1
      UniProtKB/Swiss-Prot
      B1AMV6, B4DDC3, D3DRC8, Q5H9G7, Q6NSW5, Q8TCE6, Q9NXW4, Q9NZ36
      Related
      ENSP00000354688.2, ENST00000361432.3
      Conserved Domains (1) summary
      pfam08616
      Location:158 → 264
      SPA; Stabilization of polarity axis

    RNA

    1. NR_130122.2 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (5) lacks an internal exon compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AK293365, AL355598, BC022271

    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_000010.11 Reference GRCh38.p14 Primary Assembly

      Range
      119104113..119137984
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006717849.5 → XP_006717912.1  DENN domain-containing protein 10 isoform X3

      See identical proteins and their annotated locations for XP_006717912.1

      UniProtKB/TrEMBL
      A0A3B3IRE4
      Conserved Domains (1) summary
      pfam08616
      Location:47 → 153
      SPA; Stabilization of polarity axis

    2. XM_017016264.3 → XP_016871753.1  DENN domain-containing protein 10 isoform X2

      UniProtKB/Swiss-Prot
      Q5H9G7, Q6NSW5, Q9NZ36
      Conserved Domains (1) summary
      pfam08616
      Location:158 → 264
      SPA; Stabilization of polarity axis

    3. XM_047425250.1 → XP_047281206.1  DENN domain-containing protein 10 isoform X3

      UniProtKB/TrEMBL
      A0A3B3IRE4

    4. XM_047425251.1 → XP_047281207.1  DENN domain-containing protein 10 isoform X3

      UniProtKB/TrEMBL
      A0A3B3IRE4

    5. XM_047425249.1 → XP_047281205.1  DENN domain-containing protein 10 isoform X1

      UniProtKB/Swiss-Prot
      Q5H9G7, Q6NSW5, Q9NZ36

    6. XM_047425252.1 → XP_047281208.1  DENN domain-containing protein 10 isoform X3

      UniProtKB/TrEMBL
      A0A3B3IRE4
      Related
      ENSP00000496780.1, ENST00000648560.1

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060934.1 Alternate T2T-CHM13v2.0

      Range
      119999563..120033391
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054365945.1 → XP_054221920.1  DENN domain-containing protein 10 isoform X3

      UniProtKB/TrEMBL
      A0A3B3IRE4

    2. XM_054365944.1 → XP_054221919.1  DENN domain-containing protein 10 isoform X2

      UniProtKB/Swiss-Prot
      Q5H9G7, Q6NSW5, Q9NZ36

    3. XM_054365946.1 → XP_054221921.1  DENN domain-containing protein 10 isoform X3

      UniProtKB/TrEMBL
      A0A3B3IRE4

    4. XM_054365947.1 → XP_054221922.1  DENN domain-containing protein 10 isoform X3

      UniProtKB/TrEMBL
      A0A3B3IRE4

    5. XM_054365943.1 → XP_054221918.1  DENN domain-containing protein 10 isoform X1

      UniProtKB/Swiss-Prot
      Q5H9G7, Q6NSW5, Q9NZ36

    6. XM_054365948.1 → XP_054221923.1  DENN domain-containing protein 10 isoform X3

      UniProtKB/TrEMBL
      A0A3B3IRE4
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8TCE6.1 GenPept UniProtKB/Swiss-Prot:Q8TCE6

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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