LOC108348027 RN7SL499P-PTMA intergenic region enhancers [Homo sapiens (human)] - Gene

Summary

Gene symbol: LOC108348027
Gene description: RN7SL499P-PTMA intergenic region enhancers
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 is located between the RN7SL499P (RNA, 7SL, cytoplasmic 499, pseudogene) and PTMA (prothymosin, alpha) loci. Tissue-specific transcribed enhancers were defined within this region based on the co-occurrence of H3K4me1, H3K27ac and DNase hypersensitive epigenetic marks with the presence of balanced bidirectional capped transcripts by cap analysis of gene expression (CAGE) in blood cells. Different subregions were validated as functional enhancers by reporter assays in DAUDI B cells or THP-1 monocytes, or by reporter assays in transgenic mice. Three subregions marked by the H3K27ac and/or H3K4me1 histone modifications were shown to be active enhancers by ChIP-STARR-seq in human embryonic stem cells. Another subregion was validated as a functional enhancer by Sharpr-MPRA (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in both HepG2 liver carcinoma cells (group: HepG2 Activating non-DNase unmatched - State 10:DNaseD, primarily Duke DNase, candidate regulatory elements in more likely repressive locations) and K562 erythroleukemia cells (group: K562 Activating DNase matched - State 5:Enh, candidate strong enhancer, open chromatin). A different subregion also displayed enhancer activity by Sharpr-MPRA in K562 cells (group: K562 Activating DNase unmatched - State 1:Tss, active promoter, TSS/CpG island region). This locus also includes eight accessible chromatin subregions, five of which were validated as enhancers and three as silencers, based on their ability to activate or 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) MPRA in GM12878 lymphoblastoid cells. [provided by RefSeq, May 2023]
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Genomic context

Location:: 2q37.1

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	2	NC_000002.12 (231662318..231673568)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	2	NC_060926.1 (232146862..232158111)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	2	NC_000002.11 (232527029..232537959)

Chromosome 2 - NC_000002.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

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Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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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

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General gene information

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Other Names

ATAC-STARR-seq lymphoblastoid active region 17301
ATAC-STARR-seq lymphoblastoid active region 17302
ATAC-STARR-seq lymphoblastoid active region 17303
ATAC-STARR-seq lymphoblastoid active region 17304
ATAC-STARR-seq lymphoblastoid active region 17305
ATAC-STARR-seq lymphoblastoid silent region 12436
ATAC-STARR-seq lymphoblastoid silent region 12437
ATAC-STARR-seq lymphoblastoid silent region 12438
H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:232531157-232531692
H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:232537557-232538279
H3K4me1 hESC enhancer GRCh37_chr2:232533305-232533841
RN7SL499P-PTMA intergenic CAGE-defined blood enhancers
RN7SL499P-PTMA interval FANTOM5 blood enhancers
Sharpr-MPRA regulatory region 12409
Sharpr-MPRA regulatory region 815
VISTA enhancer hs1886

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.