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LOC121848005 Sharpr-MPRA regulatory region 669 [ Homo sapiens (human) ]

Gene ID: 121848005, updated on 10-Oct-2023

Summary

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Gene symbol
LOC121848005
Gene description
Sharpr-MPRA regulatory region 669
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 8:EnhW, candidate weak enhancer and open chromatin). [provided by RefSeq, Jul 2021]
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Genomic context

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Location:
17p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (3737795..3738089)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (3626379..3626673)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (3641089..3641383)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene P2RX5-TAX1BP3 readthrough (NMD candidate) Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:3591902-3592810 Neighboring gene purinergic receptor P2X 5 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11512 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11513 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:3598520-3599036 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11514 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8018 Neighboring gene MPRA-validated peak2690 silencer Neighboring gene MPRA-validated peak2691 silencer Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:3627127-3627882 Neighboring gene integrin subunit alpha E Neighboring gene histone H3 associated protein kinase Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:3658435-3659138 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11515 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11516 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11517 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:3697478-3698200 Neighboring gene nonconserved acetylation island sequence 85 enhancer Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:3701060-3701958 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11520 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11521 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:3716184-3716689 Neighboring gene nuclear cap binding subunit 3 Neighboring gene ReSE screen-validated silencer GRCh37_chr17:3735506-3735685 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8020 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8021 Neighboring gene uncharacterized LOC124903897

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_076025.1 

    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_000017.11 Reference GRCh38.p14 Primary Assembly

    Range
    3737795..3738089
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    3626379..3626673
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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