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SCIRT stem cell inhibitory RNA transcript [ Homo sapiens (human) ]

Gene ID: 101929705, updated on 10-Oct-2023

Summary

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Official Symbol
SCIRTprovided by HGNC
Official Full Name
stem cell inhibitory RNA transcriptprovided by HGNC
Primary source
HGNC:HGNC:55341
See related
Ensembl:ENSG00000237686 AllianceGenome:HGNC:55341
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
DATOC-1
Expression
Biased expression in thyroid (RPKM 1.7), lung (RPKM 1.0) and 10 other tissues See more
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Genomic context

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Location:
6p21.1
Exon count:
6
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (43995723..44074652, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (43827435..43908109, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (43963460..44042389, complement)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene RNA polymerase I and III subunit C Neighboring gene uncharacterized LOC105375070 Neighboring gene uncharacterized LOC105375068 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:43845203-43845710 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:43845711-43846218 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24621 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:43854868-43855768 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:43857224-43858185 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:43878694-43879258 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:43879259-43879821 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:43880895-43881684 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24622 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:43893291-43894024 Neighboring gene long intergenic non-protein coding RNA 1512 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:43911713-43912238 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:43918399-43919384 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:43932755-43933254 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24623 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:43952691-43953286 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:43957693-43958202 Neighboring gene uncharacterized LOC124901321 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:43961654-43962154 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24624 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17244 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:43972319-43972950 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr6:43977969-43979168 Neighboring gene long intergenic non-protein coding RNA 3040 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:44007317-44008074 Neighboring gene Sharpr-MPRA regulatory region 2143 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:44009776-44010524 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24625 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:44019358-44019952 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:44022316-44022816 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24626 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17245 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:44030458-44031420 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24627 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24628 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17247 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17248 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24629 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24630 Neighboring gene Sharpr-MPRA regulatory region 9341 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_91788 Neighboring gene Sharpr-MPRA regulatory region 15428 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:44069931-44070480 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:44070481-44071029 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_91802 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_91811 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:44075151-44075650 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_91827 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_91835 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_91840 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17250 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17251 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17252 Neighboring gene ribosomal protein L29 pseudogene 16 Neighboring gene mitochondrial ribosomal protein L14 Neighboring gene transmembrane protein 63B

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. Long Noncoding RNA SCIRT Promotes HUVEC Angiogenesis via Stabilizing VEGFA mRNA Induced by Hypoxia. Gao L, et al. Oxid Med Cell Longev, 2022. PMID 35698607, Free PMC Article
  2. Long noncoding RNA DATOC-1 that associate with DICER promotes development in epithelial ovarian cancer by upregulating miR-7 expression. Qin W, et al. Transl Cancer Res, 2021 May. PMID 35116553, Free PMC Article
  3. SCIRT lncRNA Restrains Tumorigenesis by Opposing Transcriptional Programs of Tumor-Initiating Cells. Zagorac S, et al. Cancer Res, 2021 Feb 1. PMID 33172932
  4. LncRNA SCIRT is downregulated in atherosclerosis and suppresses the proliferation of human aortic smooth muscle cells (HAOSMCs) by sponging miR-146a in cytoplasm. Gao W, et al. J Cardiothorac Surg, 2021 Nov 6. PMID 34742341, Free PMC Article
  5. LncRNA SCIRT absorbs miR-221 to advance the expression of lncRNA GAS5 in oral squamous cell carcinoma to inhibit cancer cell apoptosis. Yang L, et al. J Oral Pathol Med, 2022 Mar. PMID 34547134

See all (6) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Long Noncoding RNA SCIRT Promotes HUVEC Angiogenesis via Stabilizing VEGFA mRNA Induced by Hypoxia.
    Title: Long Noncoding RNA SCIRT Promotes HUVEC Angiogenesis via Stabilizing VEGFA mRNA Induced by Hypoxia.
  2. LncRNA SCIRT absorbs miR-221 to advance the expression of lncRNA GAS5 in oral squamous cell carcinoma to inhibit cancer cell apoptosis.
    Title: LncRNA SCIRT absorbs miR-221 to advance the expression of lncRNA GAS5 in oral squamous cell carcinoma to inhibit cancer cell apoptosis.
  3. LncRNA SCIRT is downregulated in atherosclerosis and suppresses the proliferation of human aortic smooth muscle cells (HAOSMCs) by sponging miR-146a in cytoplasm.
    Title: LncRNA SCIRT is downregulated in atherosclerosis and suppresses the proliferation of human aortic smooth muscle cells (HAOSMCs) by sponging miR-146a in cytoplasm.
Submit: New GeneRIF Correction

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

  • DICER Associated Transcript 1 in Ovarian Cancer

Clone Names

  • AL109615.3

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_125864.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1, also known as SCIRT) represents the longer transcript.
    Source sequence(s)
    AK024736, AL109615
    Related
    ENST00000422059.5

  2. NR_125865.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) lacks two exons and contains an alternate 5' terminal exon, resulting in a shorter transcript, compared to variant 1.
    Source sequence(s)
    AK024736, AL109615, DA621605, DB025548

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_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    43995723..44074652 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    43827435..43908109 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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