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LOC121366025 Sharpr-MPRA regulatory region 12295 [ Homo sapiens (human) ]

Gene ID: 121366025, updated on 10-Oct-2023

Summary

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Gene symbol
LOC121366025
Gene description
Sharpr-MPRA regulatory region 12295
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 matched - State 5:Enh, candidate strong enhancer, open chromatin). [provided by RefSeq, May 2021]
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Genomic context

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See LOC121366025 in Genome Data Viewer
Location:
9q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (125246450..125246744)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (137444755..137445049)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (128008729..128009023)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene Rab9 effector protein with kelch motifs Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29000 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancers GRCh37_chr9:128003252-128003756 and GRCh37_chr9:128003757-128004261 Neighboring gene heat shock protein family A (Hsp70) member 5 Neighboring gene HSPA5 divergent transcript Neighboring gene ReSE screen-validated silencer GRCh37_chr9:128020420-128020678 Neighboring gene ReSE screen-validated silencer GRCh37_chr9:128024002-128024183 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:128029981-128030481 Neighboring gene ribosomal protein S10 pseudogene 17 Neighboring gene GTPase activating protein and VPS9 domains 1 Neighboring gene RNA, U6 small nuclear 1020, pseudogene

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_074375.1 

    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_000009.12 Reference GRCh38.p14 Primary Assembly

    Range
    125246450..125246744
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    137444755..137445049
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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