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LOC121009635 Sharpr-MPRA regulatory region 11586 [ Homo sapiens (human) ]

Gene ID: 121009635, updated on 10-Oct-2023

Summary

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Gene symbol
LOC121009635
Gene description
Sharpr-MPRA regulatory region 11586
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 5:Enh, candidate strong enhancer, open chromatin). [provided by RefSeq, Mar 2021]
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Genomic context

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Location:
2q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (240579212..240579506)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (241073237..241073531)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (241518629..241518923)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene glypican 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:241397321-241397972 Neighboring gene GPC1 antisense RNA 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:241397973-241398622 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:241398623-241399273 Neighboring gene microRNA 149 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:241417613-241418122 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:241418123-241418632 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:241418633-241419142 Neighboring gene ankyrin repeat and MYND domain containing 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:241439369-241439869 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:241443459-241443959 Neighboring gene Sharpr-MPRA regulatory region 11390 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17396 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:241467695-241468196 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12512 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:241494599-241495099 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17397 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12513 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12514 Neighboring gene conserved acetylation island sequence C08 enhancer Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12515 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17398 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17399 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17400 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17401 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12516 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12517 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12519 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12518 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:241508348-241508986 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:241508987-241509625 Neighboring gene dual specificity phosphatase 28 Neighboring gene arginyl aminopeptidase like 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17403 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17404 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17405 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17406 Neighboring gene Sharpr-MPRA regulatory region 5965 Neighboring gene CAPN10 divergent transcript Neighboring gene calpain 10

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_074032.1 

    Range
    101..395
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    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_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    240579212..240579506
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    241073237..241073531
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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