U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

LOC123038179 Sharpr-MPRA regulatory region 2951 [ Homo sapiens (human) ]

Gene ID: 123038179, updated on 10-Oct-2023

Summary

Go to the top of the page Help
Gene symbol
LOC123038179
Gene description
Sharpr-MPRA regulatory region 2951
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 23:Low, low signal proximal to active elements). [provided by RefSeq, Oct 2021]
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

Go to the top of the page Help
Location:
3q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (129546606..129546900)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (132291033..132291327)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (129265449..129265743)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20514 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20515 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20516 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20517 Neighboring gene Sharpr-MPRA regulatory region 8693 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:129168229-129168945 Neighboring gene intraflagellar transport 122 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:129200162-129201039 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:129208521-129208729 Neighboring gene Sharpr-MPRA regulatory region 10640 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr3:129213542-129214741 Neighboring gene MPRA-validated peak4826 silencer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:129247433-129248158 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:129248159-129248884 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:129253999-129254668 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:129261557-129262058 Neighboring gene rhodopsin enhancer region Neighboring gene rhodopsin Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:129277154-129278043 Neighboring gene H1.8 linker histone Neighboring gene plexin D1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:129291899-129292624 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:129295530-129296256 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:129315061-129315792 Neighboring gene RNA, 7SL, cytoplasmic 752, pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:129321778-129322770 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:129323763-129324755 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14726 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:129325748-129326740 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:129326741-129327731 Neighboring gene uncharacterized LOC124909431 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:129330613-129331535 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:129331536-129332457 Neighboring gene Sharpr-MPRA regulatory region 12201

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to nucleotide: Graphics FASTA GenBank

Bibliography

Go to the top of the pageHelp

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

Go to the top of the page Help

Review eQTL and phenotype association data in this region using PheGenI

Variation

Go to the top of the page Help

See variants in ClinVar

See Variation Viewer (GRCh37.p13)

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

NEW Try the new Transcript table

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_077310.1 

    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_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    129546606..129546900
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    132291033..132291327
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

Molecular Biology Databases