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LOC114004408 Sharpr-MPRA regulatory region 3634 [ Homo sapiens (human) ]

Gene ID: 114004408, updated on 10-Oct-2023

Summary

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Gene symbol
LOC114004408
Gene description
Sharpr-MPRA regulatory region 3634
Gene type
biological region
Feature type(s)
regulatory: silencer
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 repressive element by the Sharpr-MPRA technique (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in HepG2 liver carcinoma cells (group: HepG2 Repressive DNase matched - State 12:CtcfO, distal CTCF/candidate insulator with open chromatin), with weaker repression in K562 erythroleukemia cells (group: K562 Repressive non-DNase unmatched - State 25:Art, potential CNV or repetitive artifacts). [provided by RefSeq, Jan 2019]
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Genomic context

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See LOC114004408 in Genome Data Viewer
Location:
7p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (44477350..44477644)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (44637087..44637381)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (44516949..44517243)

Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene calcium/calmodulin dependent protein kinase II beta Neighboring gene uncharacterized LOC124901621 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25939 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:44389311-44389811 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25940 Neighboring gene NudC domain containing 3 Neighboring gene ribosomal protein L32 pseudogene 18 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18144 Neighboring gene ReSE screen-validated silencer GRCh37_chr7:44532074-44532200 Neighboring gene RNA, U6 small nuclear 1097, pseudogene Neighboring gene ribosomal protein L36a pseudogene 27

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. Toward a complete human genome sequence. Sanger Center, et al. Genome Res, 1998 Nov. PMID 9847074
  2. Genome-scale high-resolution mapping of activating and repressive nucleotides in regulatory regions. Ernst J, et al. Nat Biotechnol, 2016 Nov. PMID 27701403, 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)

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_063908.1 

    Range
    101..395
    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_000007.14 Reference GRCh38.p14 Primary Assembly

    Range
    44477350..44477644
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060931.1 Alternate T2T-CHM13v2.0

    Range
    44637087..44637381
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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