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LOC129929509 ATAC-STARR-seq lymphoblastoid active region 253 [ Homo sapiens (human) ]

Gene ID: 129929509, updated on 12-Sep-2024

Summary

Gene symbol
LOC129929509
Gene description
ATAC-STARR-seq lymphoblastoid active region 253
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 represents an accessible chromatin region that was validated as an enhancer based on its ability to activate 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]
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Genomic context

See LOC129929509 in Genome Data Viewer
Location:
chromosome: 1
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (15949235..15949404)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (15390515..15390684)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (16275730..16275899)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:16161483-16162468 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 248 Neighboring gene Sharpr-MPRA regulatory region 11658 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 314 Neighboring gene SPEN antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 315 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 249 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:16173332-16173844 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:16173845-16174356 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 317 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:16175780-16176374 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 250 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:16191755-16192255 Neighboring gene spen family transcriptional repressor Neighboring gene NFE2L2 motif-containing MPRA enhancer 216 Neighboring gene MPRA-validated peak83 silencer Neighboring gene small nucleolar RNA U13 Neighboring gene MPRA-validated peak84 silencer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:16261375-16261876 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr1:16268619-16269818 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 252 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:16276391-16277178 Neighboring gene uncharacterized LOC124903855 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 254 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr1:16278891-16280090 Neighboring gene zinc finger and BTB domain containing 17 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr1:16287659-16288532 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 255 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 256 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 257 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 318 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 319 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:16302461-16302960 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:16320391-16321231 Neighboring gene TBC1 domain family member 3 pseudogene 6

Genomic regions, transcripts, and products

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_162566.1 

    Range
    101..270
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    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_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    15949235..15949404
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    15390515..15390684
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)