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LOC108254664 SCARA5 intron CAGE-defined high expression enhancer [ Homo sapiens (human) ]

Gene ID: 108254664, updated on 10-Oct-2023

Summary

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Gene symbol
LOC108254664
Gene description
SCARA5 intron CAGE-defined high expression enhancer
Gene type
biological region
Feature type(s)
misc_feature: CAGE_cluster
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 region is located in an intron of the SCARA5 (scavenger receptor class A member 5) gene. It was defined as a high expression actively transcribed enhancer based on the presence of balanced bidirectional capped transcripts by cap analysis of gene expression (CAGE). It was validated as a functional enhancer by reporter assays in both HeLa and HepG2 cells. [provided by RefSeq, Jun 2016]
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Genomic context

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See LOC108254664 in Genome Data Viewer
Location:
8p21.1
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 8 NC_000008.11 (27872519..27873047)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 8 NC_060932.1 (28149848..28150376)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 8 NC_000008.10 (27730036..27730564)

Chromosome 8 - NC_000008.11Genomic Context describing neighboring genes Neighboring gene establishment of sister chromatid cohesion N-acetyltransferase 2 Neighboring gene MPRA-validated peak6971 silencer Neighboring gene PDZ binding kinase Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27157 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27158 Neighboring gene TAF9 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 32kDa pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:27735141-27735642 Neighboring gene scavenger receptor class A member 5 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:27750341-27750927 Neighboring gene VISTA enhancer hs1741 Neighboring gene microRNA 4287 Neighboring gene uncharacterized LOC105379342

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. An atlas of active enhancers across human cell types and tissues. Andersson R, et al. Nature, 2014 Mar 27. PMID 24670763, 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

See Variation Viewer (GRCh37.p13)

General gene information

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Other Names

  • SCARA5 intron high CAGE FANTOM5 enhancer

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_051010.1 

    Range
    101..629
    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_000008.11 Reference GRCh38.p14 Primary Assembly

    Range
    27872519..27873047
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060932.1 Alternate T2T-CHM13v2.0

    Range
    28149848..28150376
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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