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LOC111718495 skeletal muscle cis-regulatory module in SETBP1 intron [ Homo sapiens (human) ]

Gene ID: 111718495, updated on 10-Oct-2023

Summary

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Gene symbol
LOC111718495
Gene description
skeletal muscle cis-regulatory module in SETBP1 intron
Gene type
biological region
Feature type(s)
regulatory: enhancer
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Summary
This genomic region, which is located in an intron of the SETBP1 (SET binding protein 1) gene on chromosome 18, represents a cis-regulatory module (CRM) that functions as an enhancer in skeletal muscle. This element was identified as a CRM by the Logistic Regression Analysis, MSCAN and ClusterBuster prediction methods. It was shown to drive selective reporter gene expression in differentiated C2C12 myotubes. [provided by RefSeq, Jan 2018]
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Genomic context

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See LOC111718495 in Genome Data Viewer
Location:
18q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 18 NC_000018.10 (44803134..44803616)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 18 NC_060942.1 (44994492..44994974)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 18 NC_000018.9 (42383099..42383581)

Chromosome 18 - NC_000018.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105372089 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9411 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9412 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9413 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13250 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13251 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13252 Neighboring gene SETBP1 divergent transcript Neighboring gene VISTA enhancer hs2335 Neighboring gene SET binding protein 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9414 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13253 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13254 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr18:42313178-42314377 Neighboring gene VISTA enhancer hs1362 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13255 Neighboring gene ReSE screen-validated silencer GRCh37_chr18:42360675-42360877 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13256 Neighboring gene VISTA enhancer hs2336 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13257 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13258 Neighboring gene Sharpr-MPRA regulatory region 15026 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr18:42523301-42523910 Neighboring gene microRNA 4319 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:42588617-42589118 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:42589119-42589618 Neighboring gene uncharacterized LOC105372091 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13259 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13260

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Bibliography

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Related articles in PubMed

  1. Validation of skeletal muscle cis-regulatory module predictions reveals nucleotide composition bias in functional enhancers. Kwon AT, et al. PLoS Comput Biol, 2011 Dec. PMID 22144875, 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 Variation Viewer (GRCh37.p13)

General gene information

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Other Names

  • SETBP1 intronic myotube-selective CRM

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.

Genomic

  1. NG_056143.1 

    Range
    101..583
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

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_000018.10 Reference GRCh38.p14 Primary Assembly

    Range
    44803134..44803616
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060942.1 Alternate T2T-CHM13v2.0

    Range
    44994492..44994974
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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