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SCAT1 S-phase cancer associated transcript 1 [ Homo sapiens (human) ]

Gene ID: 101928710, updated on 10-Oct-2023

Summary

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Official Symbol
SCAT1provided by HGNC
Official Full Name
S-phase cancer associated transcript 1provided by HGNC
Primary source
HGNC:HGNC:52930
See related
Ensembl:ENSG00000267123 AllianceGenome:HGNC:52930
Gene type
ncRNA
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
LINC02081; XLOC_012582
Expression
Low expression observed in reference dataset See more
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Genomic context

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See SCAT1 in Genome Data Viewer
Location:
17q25.3
Exon count:
5
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (78617384..78632057, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (79511858..79526994, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (76613466..76628139, complement)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene dynein axonemal heavy chain 17 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr17:76528450-76529649 Neighboring gene uncharacterized LOC124904065 Neighboring gene RNA, 7SL, cytoplasmic 454, pseudogene Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr17:76554009-76555208 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:76576879-76577380 Neighboring gene ReSE screen-validated silencer GRCh37_chr17:76583208-76583369 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:76584370-76584882 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:76584883-76585395 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:76614363-76614864 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:76614865-76615364 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:76618411-76619402 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:76622057-76622556 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:76627973-76628474 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:76641825-76642326 Neighboring gene uncharacterized LOC124904066 Neighboring gene MPRA-validated peak3019 silencer Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:76662364-76662975 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:76662976-76663586 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:76663587-76664197 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:76664198-76664807 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:76671141-76672019 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:76672283-76672784 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:76672785-76673284 Neighboring gene cytohesin 1 Neighboring gene RNA, U6 small nuclear 638, pseudogene

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. Deregulated lncRNAs in B Cells from Patients with Active Tuberculosis. Fu Y, et al. PLoS One, 2017. PMID 28125665, Free PMC Article
  2. PAN-cancer analysis of S-phase enriched lncRNAs identifies oncogenic drivers and biomarkers. Ali MM, et al. Nat Commun, 2018 Feb 28. PMID 29491376, Free PMC Article
  3. Identification of a RNA-Seq Based 8-Long Non-Coding RNA Signature Predicting Survival in Esophageal Cancer. Fan Q, et al. Med Sci Monit, 2016 Dec 28. PMID 28028307, Free PMC Article

GeneRIFs: Gene References Into Functions

Phenotypes

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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)

Genotypes

General gene information

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Other Names

  • long intergenic non-protein coding RNA 2081

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.

RNA

  1. NR_110848.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longer transcript.
    Source sequence(s)
    AC099804, KF456332
    Related
    ENST00000586185.2

  2. NR_110849.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) uses alternate splice sites at the 5' and 3' terminal exons and at an internal exon, resulting in a shorter transcript, compared to variant 1.
    Source sequence(s)
    AC099804, KF456332
    Related
    ENST00000591384.7

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000017.11 Reference GRCh38.p14 Primary Assembly

    Range
    78617384..78632057 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    79511858..79526994 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

Gene LinkOut

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