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SILC1 sciatic injury induced lincRNA upregulator of SOX11 [ Homo sapiens (human) ]

Gene ID: 150622, updated on 10-Oct-2023

Summary

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Official Symbol
SILC1provided by HGNC
Official Full Name
sciatic injury induced lincRNA upregulator of SOX11provided by HGNC
Primary source
HGNC:HGNC:26403
See related
AllianceGenome:HGNC:26403
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
LINC01105
Expression
Restricted expression toward brain (RPKM 5.8) See more
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Genomic context

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See SILC1 in Genome Data Viewer
Location:
2p25.2
Exon count:
2
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (5932687..5980218)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (5954658..6002183)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (6072819..6120350)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC112268411 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr2:5865940-5866895 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:5881029-5881529 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr2:5937560-5938759 Neighboring gene long intergenic non-protein coding RNA 1810 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:6114361-6114862 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr2:6115742-6116395 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:6120871-6121617 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr2:6135557-6136756 Neighboring gene uncharacterized LOC400940 Neighboring gene microRNA 7158 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr2:6193971-6194712 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr2:6232422-6233621 Neighboring gene NANOG hESC enhancer GRCh37_chr2:6253851-6254352 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:6289007-6289241 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15240 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr2:6378134-6379333 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:6396128-6396341 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:6423042-6423564 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr2:6431337-6432536 Neighboring gene uncharacterized LOC105373401

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. MEG3, HCN3 and linc01105 influence the proliferation and apoptosis of neuroblastoma cells via the HIF-1α and p53 pathways. Tang W, et al. Sci Rep, 2016 Nov 8. PMID 27824082, Free PMC Article
  2. Regulation of Neuroregeneration by Long Noncoding RNAs. Perry RB, et al. Mol Cell, 2018 Nov 1. PMID 30401432, Free PMC Article
  3. Co-expression Network Analysis of Human lncRNAs and Cancer Genes. Cogill SB, et al. Cancer Inform, 2014. PMID 25392693, Free PMC Article
  4. Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. Kimura K, et al. Genome Res, 2006 Jan. PMID 16344560, Free PMC Article
  5. Complete sequencing and characterization of 21,243 full-length human cDNAs. Ota T, et al. Nat Genet, 2004 Jan. PMID 14702039

See all (6) citations in PubMed

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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Markers

Other Names

  • long intergenic non-protein coding RNA 1105

Clone Names

  • MGC120893, DKFZp761K2322

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_026832.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AC073479, AC079770, DA139711

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_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    5932687..5980218
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    5954658..6002183
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_153011.2: Suppressed sequence

    Description
    NM_153011.2: This RefSeq record was removed by NCBI staff. Contact info@ncbi.nlm.nih.gov for further information.
Nucleotide Protein
Heading Accession and Version

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