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    SDAD1 SDA1 domain containing 1 [ Homo sapiens (human) ]

    Gene ID: 55153, updated on 27-Nov-2024

    Summary

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    Official Symbol
    SDAD1provided by HGNC
    Official Full Name
    SDA1 domain containing 1provided by HGNC
    Primary source
    HGNC:HGNC:25537
    See related
    Ensembl:ENSG00000198301 AllianceGenome:HGNC:25537
    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
    Sda1
    Summary
    Predicted to be involved in ribosomal large subunit biogenesis and ribosomal large subunit export from nucleus. Predicted to act upstream of or within cellular response to leukemia inhibitory factor. Located in nucleolus and nucleoplasm. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Ubiquitous expression in testis (RPKM 19.5), thyroid (RPKM 18.4) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See SDAD1 in Genome Data Viewer
    Location:
    4q21.1
    Exon count:
    22
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (75949915..75990945, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (79290380..79331462, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (76871068..76912098, complement)

    Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105377285 Neighboring gene protein phosphatase with EF-hand domain 2 Neighboring gene Sharpr-MPRA regulatory region 11706 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr4:76829825-76830747 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr4:76830748-76831669 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21623 Neighboring gene N-acylethanolamine acid amidase Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15483 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15484 Neighboring gene SDAD1 antisense RNA 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:76932273-76932917 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21624 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21625 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:76938237-76938736 Neighboring gene C-X-C motif chemokine ligand 9 Neighboring gene ADP-ribosyltransferase 3 (inactive) Neighboring gene C-X-C motif chemokine ligand 10

    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. miR-378 suppresses the proliferation, migration and invasion of colon cancer cells by inhibiting SDAD1. Zeng M, et al. Cell Mol Biol Lett, 2017. PMID 28725241, Free PMC Article
    2. Visualizing the nucleoplasmic maturation of human pre-60S ribosomal particles. Zhang Y, et al. Cell Res, 2023 Nov. PMID 37491604, Free PMC Article
    3. Expression and localization studies of hSDA, the human ortholog of the yeast SDA1 gene. Babbio F, et al. Cell Cycle, 2004 Apr. PMID 14976432
    4. Identification and characterization of RNA sequences to which human PUMILIO-2 (PUM2) and deleted in Azoospermia-like (DAZL) bind. Fox M, et al. Genomics, 2005 Jan. PMID 15607425
    5. TMEM79/MATTRIN defines a pathway for Frizzled regulation and is required for Xenopus embryogenesis. Chen M, et al. Elife, 2020 Sep 14. PMID 32924931, Free PMC Article

    See all (85) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. miR-378 inhibits the proliferation, migration and invasion of colon cancer cells by targeting SDAD1.
      Title: miR-378 suppresses the proliferation, migration and invasion of colon cancer cells by inhibiting SDAD1.
    2. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
      Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
    3. PUM2 and DAZL, are capable of binding the same mRNA sequences in the 3'UTR of human SDAD1 mRNA.
      Title: Identification and characterization of RNA sequences to which human PUMILIO-2 (PUM2) and deleted in Azoospermia-like (DAZL) bind.
    4. hSDA is the human ortholog of the yeast SDA1 gene
      Title: Expression and localization studies of hSDA, the human ortholog of the yeast SDA1 gene.
    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

    EBI GWAS Catalog

    Description
    Joint influence of small-effect genetic variants on human longevity.
    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

    • FLJ10498, DKFZp686E22207

    Gene Ontology Provided by GOA

    Process Evidence Code Pubs
    involved_in protein transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in ribosomal large subunit biogenesis IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in ribosomal large subunit biogenesis ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in ribosomal large subunit export from nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    is_active_in nucleolus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleolus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		  

    General protein information

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    Preferred Names
    protein SDA1 homolog
    Names
    SDA1 domain-containing protein 1
    nucleolar protein 130

    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_001288983.2 → NP_001275912.1  protein SDA1 homolog isoform 2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks an alternate in-frame exon in the 5' coding region, compared to variant 1. It encodes isoform 2, which is shorter than isoform 1.
      Source sequence(s)
      AK024031, AK300074, BU619826, CR749574, DB047277
      Consensus CDS
      CCDS75147.1
      UniProtKB/TrEMBL
      B4DT66, E7EW05
      Related
      ENSP00000379061.4, ENST00000395711.8
      Conserved Domains (2) summary
      pfam05285
      Location:372 → 647
      SDA1; SDA1
      pfam08158
      Location:62 → 100
      NUC130_3NT; NUC130/3NT domain

    2. NM_001288984.2 → NP_001275913.1  protein SDA1 homolog isoform 3

      See identical proteins and their annotated locations for NP_001275913.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR, lacks a portion of the 5' coding region and initiates translation at a downstream start codon, compared to variant 1. It encodes isoform 3, which is shorter at the N-terminus, compared to isoform 1.
      Source sequence(s)
      AK024031, AK300074, BJ989617, BU619826, CR749574, DB047277
      UniProtKB/TrEMBL
      B4DT66
      Conserved Domains (1) summary
      pfam05285
      Location:312 → 587
      SDA1; SDA1

    3. NM_018115.4 → NP_060585.2  protein SDA1 homolog isoform 1

      See identical proteins and their annotated locations for NP_060585.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (1).
      Source sequence(s)
      AK001360, BC048351, BJ989617, BU619826
      Consensus CDS
      CCDS3573.2
      UniProtKB/Swiss-Prot
      Q32Q11, Q68D52, Q7Z5U4, Q9H831, Q9H9P6, Q9NVU7
      UniProtKB/TrEMBL
      B4DT66
      Related
      ENSP00000348596.5, ENST00000356260.10
      Conserved Domains (2) summary
      pfam05285
      Location:409 → 684
      SDA1; SDA1
      pfam08158
      Location:62 → 111
      NUC130_3NT; NUC130/3NT 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_000004.12 Reference GRCh38.p14 Primary Assembly

      Range
      75949915..75990945 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_005263102.5 → XP_005263159.1  protein SDA1 homolog isoform X1

      UniProtKB/TrEMBL
      B4DT66
      Conserved Domains (2) summary
      pfam05285
      Location:384 → 659
      SDA1; SDA1
      pfam08158
      Location:37 → 86
      NUC130_3NT; NUC130/3NT domain

    2. XM_047415888.1 → XP_047271844.1  protein SDA1 homolog isoform X2

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060928.1 Alternate T2T-CHM13v2.0

      Range
      79290380..79331462 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054350368.1 → XP_054206343.1  protein SDA1 homolog isoform X1

    2. XM_054350369.1 → XP_054206344.1  protein SDA1 homolog isoform X2

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9NVU7.3 GenPept UniProtKB/Swiss-Prot:Q9NVU7

    Gene LinkOut

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

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