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LOC121725016 Sharpr-MPRA regulatory region 3563 [ Homo sapiens (human) ]

Gene ID: 121725016, updated on 10-Oct-2023

Summary

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Gene symbol
LOC121725016
Gene description
Sharpr-MPRA regulatory region 3563
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 sequence was predicted to be a transcriptional regulatory region based on chromatin state analysis from the ENCODE (ENCyclopedia Of DNA Elements) project. It was validated as a functional enhancer by the Sharpr-MPRA technique (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in K562 erythroleukemia cells (group: K562 Activating DNase unmatched - State 12:CtcfO, distal CTCF/candidate insulator with open chromatin). [provided by RefSeq, Jun 2021]
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Genomic context

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See LOC121725016 in Genome Data Viewer
Location:
1p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (41268217..41268511)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (41137659..41137953)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (41733889..41734183)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene Scm polycomb group protein homolog 1 Neighboring gene ribosomal protein L23a pseudogene 17 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:41622311-41622500 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 860 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 741 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 742 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 743 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:41715456-41715624 Neighboring gene SCMH1 divergent transcript Neighboring gene ribosomal protein L36a pseudogene 9 Neighboring gene uncharacterized LOC124904158 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 861 Neighboring gene uncharacterized LOC124904159 Neighboring gene Sharpr-MPRA regulatory region 968 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_8062

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Bibliography

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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)

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_075485.1 

    Range
    101..395
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    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
    41268217..41268511
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    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_009646194.1 Reference GRCh38.p14 PATCHES

    Range
    17890..18184
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    41137659..41137953
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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