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LOC108281163 PTPRC intron CAGE-defined mid-level expression enhancer [ Homo sapiens (human) ]

Gene ID: 108281163, updated on 10-Oct-2023

Summary

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Gene symbol
LOC108281163
Gene description
PTPRC intron CAGE-defined mid-level expression enhancer
Gene type
biological region
Feature type(s)
misc_feature: CAGE_cluster
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 element is located in an intron of the PTPRC (protein tyrosine phosphatase, receptor type C) gene. It was defined as a mid-level expression actively transcribed enhancer based on the presence of balanced bidirectional capped transcripts by cap analysis of gene expression (CAGE). It was validated as a functional enhancer by reporter assays in HeLa cells. [provided by RefSeq, Jul 2016]
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Genomic context

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Location:
1q31-q32
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (198681670..198682514)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (197941583..197942427)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (198650799..198651643)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124904478 Neighboring gene CRISPRi-validated cis-regulatory element chr1.10450 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr1:198637893-198639092 Neighboring gene protein tyrosine phosphatase receptor type C Neighboring gene phosphatidylethanolamine binding protein 1 pseudogene 3 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr1:198670715-198671264 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1667 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr1:198776880-198778079 Neighboring gene MIR181A1 host gene Neighboring gene microRNA 181b-1 Neighboring gene microRNA 181a-1

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. An atlas of active enhancers across human cell types and tissues. Andersson R, et al. Nature, 2014 Mar 27. PMID 24670763, 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

  • PTPRC intron mid CAGE FANTOM5 enhancer

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_051123.1 

    Range
    101..945
    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_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    198681670..198682514
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    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 ALT_REF_LOCI_1

Genomic

  1. NW_003315907.2 Reference GRCh38.p14 ALT_REF_LOCI_1

    Range
    323075..323919
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    197941583..197942427
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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