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LOC123956284 Sharpr-MPRA regulatory region 8416 [ Homo sapiens (human) ]

Gene ID: 123956284, updated on 10-Oct-2023

Summary

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Gene symbol
LOC123956284
Gene description
Sharpr-MPRA regulatory region 8416
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 K562 erythroleukemia cells (group: K562 Repressive non-DNase unmatched - State 14:Gen5', transcription transition, highly expressed genes towards 5' end). [provided by RefSeq, Jan 2022]
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Genomic context

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Location:
7q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (158815078..158815372)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (160039012..160039306)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (158607769..158608063)

Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene non-SMC condensin II complex subunit G2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:158455355-158455856 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:158455857-158456356 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr7:158456637-158457836 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:158496256-158496834 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18866 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18867 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18868 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr7:158526538-158527737 Neighboring gene ribosomal protein L21 pseudogene 76 Neighboring gene extended synaptotagmin 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:158589571-158590070 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:158593246-158593746 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:158593747-158594247 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:158596845-158597436 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:158604138-158604712 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26931 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26932 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18870 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18869 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18871 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18872 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18873 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26933 Neighboring gene uncharacterized LOC124901796 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18874 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:158650125-158650666 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:158654251-158654750 Neighboring gene dynein 2 intermediate chain 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:158670703-158671380 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:158671381-158672057 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr7:158702850-158704049 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:158735855-158736701 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:158749944-158750515 Neighboring gene uncharacterized LOC124901794

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. 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_078475.1 

    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
    158815078..158815372
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060931.1 Alternate T2T-CHM13v2.0

    Range
    160039012..160039306
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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