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LOC121725035 Sharpr-MPRA regulatory region 3408 [ Homo sapiens (human) ]

Gene ID: 121725035, updated on 10-Oct-2023

Summary

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Gene symbol
LOC121725035
Gene description
Sharpr-MPRA regulatory region 3408
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 non-DNase unmatched - State 23:Low, low signal proximal to active elements). [provided by RefSeq, Jun 2021]
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Genomic context

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See LOC121725035 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 (84253946..84254240)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (84094411..84094705)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (84719629..84719923)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene protein kinase cAMP-activated catalytic subunit beta Neighboring gene TXN2 pseudogene 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1247 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1016 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr1:84621187-84622386 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1017 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:84689847-84690648 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:84690649-84691448 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr1:84720292-84720890 Neighboring gene NANOG hESC enhancer GRCh37_chr1:84724969-84725470 Neighboring gene NEDD8 pseudogene 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1248 Neighboring gene small nucleolar RNA SNORA2/SNORA34 family Neighboring gene MPRA-validated peak299 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1018 Neighboring gene sterile alpha motif domain containing 13

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_075505.1 

    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_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    84253946..84254240
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    84094411..84094705
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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