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    HEATR3 HEAT repeat containing 3 [ Homo sapiens (human) ]

    Gene ID: 55027, updated on 10-Dec-2024

    Summary

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    Official Symbol
    HEATR3provided by HGNC
    Official Full Name
    HEAT repeat containing 3provided by HGNC
    Primary source
    HGNC:HGNC:26087
    See related
    Ensembl:ENSG00000155393 MIM:614951; AllianceGenome:HGNC:26087
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    SYO1; DBA21
    Summary
    The protein encoded by this gene plays a role in ribosomal protein transport and in the assembly of the 5S ribonucleoprotein particle (5S RNP). The encoded protein also may be involved in NOD2-mediated NF-kappaB signaling. [provided by RefSeq, Jul 2016]
    Expression
    Ubiquitous expression in appendix (RPKM 5.5), spleen (RPKM 4.5) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See HEATR3 in Genome Data Viewer
    Location:
    16q12.1
    Exon count:
    17
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (50065970..50107272)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (55863712..55905022)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (50099881..50141183)

    Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene regulation of nuclear pre-mRNA domain containing 1A pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:50080479-50080979 Neighboring gene HEATR3 antisense RNA 1 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:50094586-50094761 Neighboring gene actin gamma 1 pseudogene 16 Neighboring gene Sharpr-MPRA regulatory region 4020 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7469 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7468 Neighboring gene MPRA-validated peak2588 silencer Neighboring gene RNY4 pseudogene 3 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7470 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7471 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:50157041-50157541 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:50177493-50177653 Neighboring gene uncharacterized LOC124900375 Neighboring gene ribosomal protein L10 pseudogene 14

    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. Symportin 1 chaperones 5S RNP assembly during ribosome biogenesis by occupying an essential rRNA-binding site. Calviño FR, et al. Nat Commun, 2015 Apr 7. PMID 25849277, Free PMC Article
    2. HEATR3 involved in the cell proliferation, metastasis and cell cycle development of bladder cancer acts as a tumor suppressor. Dou X, et al. Mol Genet Genomics, 2023 Nov. PMID 37518364
    3. HEATR3 variants impair nuclear import of uL18 (RPL5) and drive Diamond-Blackfan anemia. O'Donohue MF, et al. Blood, 2022 May 26. PMID 35213692, Free PMC Article
    4. Genetic variants at 6p21, 10q23, 16q21 and 22q12 are associated with esophageal cancer risk in a Chinese Han population. Jia X, et al. Int J Clin Exp Med, 2015. PMID 26770579, Free PMC Article
    5. Extended haplotype association study in Crohn's disease identifies a novel, Ashkenazi Jewish-specific missense mutation in the NF-κB pathway gene, HEATR3. Zhang W, et al. Genes Immun, 2013 Jul-Aug. PMID 23615072, Free PMC Article

    See all (53) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. HEATR3 involved in the cell proliferation, metastasis and cell cycle development of bladder cancer acts as a tumor suppressor.
      Title: HEATR3 involved in the cell proliferation, metastasis and cell cycle development of bladder cancer acts as a tumor suppressor.
    2. HEATR3 variants impair nuclear import of uL18 (RPL5) and drive Diamond-Blackfan anemia.
      Title: HEATR3 variants impair nuclear import of uL18 (RPL5) and drive Diamond-Blackfan anemia.
    3. Data indicate that HEATR3 plays a positive role in NOD2-mediated NF-kappaB signaling.
      Title: Extended haplotype association study in Crohn's disease identifies a novel, Ashkenazi Jewish-specific missense mutation in the NF-κB pathway gene, HEATR3.
    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

    Associated conditions

    Description Tests
    Diamond-Blackfan anemia 21
    MedGen: C5774230 OMIM: 620072 GeneReviews: Not available
    		not available

    EBI GWAS Catalog

    Description
    Genome-wide association analyses of esophageal squamous cell carcinoma in Chinese identify multiple susceptibility loci and gene-environment interactions.
    EBI GWAS Catalog
    Identification of nine new susceptibility loci for testicular cancer, including variants near DAZL and PRDM14.
    EBI GWAS Catalog
    Meta-analysis identifies four new loci associated with testicular germ cell tumor.
    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)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ20718

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables unfolded protein binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Process Evidence Code Pubs
    involved_in erythrocyte maturation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in protein import into nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in protein import into nucleus IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in ribosomal large subunit biogenesis IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in ribosomal large subunit biogenesis IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    HEAT repeat-containing protein 3
    Names
    symportin 1

    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_001329729.2 → NP_001316658.1  HEAT repeat-containing protein 3 isoform b

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2), as well as variant 3, encodes isoform b.
      Source sequence(s)
      AC007610
      UniProtKB/TrEMBL
      A0A8I5KR70
      Conserved Domains (1) summary
      cd13394
      Location:1 → 556
      Syo1_like; Fungal symportin 1 (syo1) and similar proteins

    2. NM_001329730.2 → NP_001316659.1  HEAT repeat-containing protein 3 isoform b

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3), as well as variant 2, encodes isoform b.
      Source sequence(s)
      AC007610
      UniProtKB/TrEMBL
      A0A8I5KR70
      Conserved Domains (1) summary
      cd13394
      Location:1 → 556
      Syo1_like; Fungal symportin 1 (syo1) and similar proteins

    3. NM_001329731.2 → NP_001316660.1  HEAT repeat-containing protein 3 isoform c

      Status: REVIEWED

      Source sequence(s)
      AC007610
      Conserved Domains (1) summary
      cd13394
      Location:134 → 442
      Syo1_like; Fungal symportin 1 (syo1) and similar proteins

    4. NM_182922.4 → NP_891552.1  HEAT repeat-containing protein 3 isoform a

      See identical proteins and their annotated locations for NP_891552.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (a).
      Source sequence(s)
      AC007610
      Consensus CDS
      CCDS10739.1
      UniProtKB/Swiss-Prot
      A8K1N4, Q7Z4Q2, Q8N525, Q8WV56, Q96CC9, Q9NWN7
      Related
      ENSP00000299192.7, ENST00000299192.8
      Conserved Domains (2) summary
      cd13394
      Location:2 → 673
      Syo1_like; Fungal symportin 1 (syo1) and similar proteins
      sd00043
      Location:69 → 108
      ARM; armadillo repeat [structural motif]

    RNA

    1. NR_138092.2 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC007610

    2. NR_138093.2 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC007610

    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_000016.10 Reference GRCh38.p14 Primary Assembly

      Range
      50065970..50107272
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060940.1 Alternate T2T-CHM13v2.0

      Range
      55863712..55905022
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_017939.1: Suppressed sequence

      Description
      NM_017939.1: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q7Z4Q2.2 GenPept UniProtKB/Swiss-Prot:Q7Z4Q2

    Gene LinkOut

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

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