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LOC128854706 KLF9-II enhancer [ Homo sapiens (human) ]

Gene ID: 128854706, updated on 10-Oct-2023

Summary

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Gene symbol
LOC128854706
Gene description
KLF9-II enhancer
Gene type
biological region
Feature type(s)
regulatory: enhancer, 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 region was identified as a DNase I hypersensitive site (DHS) in erythroid cells. It was validated as an enhancer that can activate the KLF9 (KLF transcription factor 9) promoter by reporter assays in K562 erythroleukemia cells. This locus also includes an accessible chromatin subregion 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]
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Genomic context

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Location:
chromosome: 9
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (70398162..70398464)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (82564988..82565290)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene MAM domain containing 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28449 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19938 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28450 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:72888582-72889082 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:72889083-72889583 Neighboring gene SMC5 divergent transcript Neighboring gene RPL24 pseudogene 8 Neighboring gene uncharacterized LOC124900273 Neighboring gene ReSE screen-validated silencer GRCh37_chr9:73027338-73027530 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28451 Neighboring gene structural maintenance of chromosomes 5 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:73028054-73028907 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:73033721-73034442 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19943 Neighboring gene Sharpr-MPRA regulatory region 12362 Neighboring gene uncharacterized LOC105376079 Neighboring gene KLF9-I enhancer Neighboring gene KLF9 divergent transcript Neighboring gene MPRA-validated peak7263 silencer Neighboring gene KLF transcription factor 9 Neighboring gene RNA, 7SL, cytoplasmic 726, pseudogene Neighboring gene transient receptor potential cation channel subfamily M member 3

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. Comprehensive characterization of erythroid-specific enhancers in the genomic regions of human Krüppel-like factors. Xiong Q, et al. BMC Genomics, 2013 Aug 28. PMID 23985037, Free PMC Article
  2. ATAC-STARR-seq reveals transcription factor-bound activators and silencers across the chromatin accessible human genome. Hansen TJ, et al. Genome Res, 2022 Jul 20. PMID 35858748, 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

General gene information

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Other Names

  • ATAC-STARR-seq lymphoblastoid silent region 19939

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_149960.1 

    Range
    101..403
    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_000009.12 Reference GRCh38.p14 Primary Assembly

    Range
    70398162..70398464
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    82564988..82565290
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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