U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

LOC129936879 ATAC-STARR-seq lymphoblastoid silent region 14458 [ Homo sapiens (human) ]

Gene ID: 129936879, updated on 12-Sep-2024

Summary

Gene symbol
LOC129936879
Gene description
ATAC-STARR-seq lymphoblastoid silent region 14458
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 represents an accessible chromatin region that was validated as a silencer based on its ability to repress an origin of replication minimal core promoter by the ATAC-STARR-seq (assay for transposase-accessible chromatin with self-transcribing active regulatory region sequencing) massively parallel reporter assay (MPRA) in GM12878 lymphoblastoid cells. [provided by RefSeq, May 2023]
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

See LOC129936879 in Genome Data Viewer
Location:
chromosome: 3
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (53046292..53046401)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (53079196..53079305)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (53080308..53080417)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene STIMATE-MUSTN1 readthrough Neighboring gene STIM activating enhancer Neighboring gene microRNA 8064 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:52906559-52906829 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14454 Neighboring gene Scm like with four mbt domains 1 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_70661 Neighboring gene Sharpr-MPRA regulatory region 7399 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:53032540-53033040 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:53033923-53034166 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19949 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr3:53064883-53065417 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_70686 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14455 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14456 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:53080405-53080906 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14457 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:53080907-53081406 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19950 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:53106949-53107566 Neighboring gene SERPINE1 mRNA binding protein 1 pseudogene 3 Neighboring gene Sharpr-MPRA regulatory region 3047 Neighboring gene RFT1 homolog Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19952 Neighboring gene NANOG hESC enhancer GRCh37_chr3:53136831-53137332 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19953 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr3:53148350-53149549 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19954

Genomic regions, transcripts, and products

NCBI Reference Sequences (RefSeq)

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_169890.1 

    Range
    101..210
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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
    53046292..53046401
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    53079196..53079305
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)