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

Gene ID: 55153, updated on 3-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
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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 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)

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

  • FLJ10498, DKFZp686E22207

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables molecular_function ND
No biological Data available
more info
  
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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