LOC110806262 solute carrier family 6 member 4 gene promoter [Homo sapiens (human)] - Gene

Summary

Gene symbol: LOC110806262
Gene description: solute carrier family 6 member 4 gene promoter
Gene type: biological region
Feature type(s): misc_feature: nucleotide_motif, sequence_alteration
mobile_element
protein_bind
regulatory: TATA_box, promoter, silencer, transcriptional_cis_regulatory_region
repeat_region
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 the 5' regulatory region of the solute carrier family 6 member 4 (SLC6A4) gene on chromosome 17. It includes the gene promoter and a polymorphic region known as 5-HTTLPR, which is located approximately 1 kb upstream of the major transcription start site. The polymorphic region is composed of 16 tandemly-repeated units in the long (L) allele, where each repeat unit is 20-23 bps in length. Deletion of repeat units 6-8 results in a short (S) allele. Single nucleotide polymorphisms, including rs25531 and rs25532, have also been identified in this region. The 5-HTTLPR region has both positive- and negative-acting cis-regulatory components in SLC6A4 promoter activity assays, and the L and S alleles also display allele-dependent promoter activity. Due to the role of the SLC6A4 gene in serotonin reuptake, a large number of studies have associated the 5-HTTLPR, rs25531 and rs25532 polymorphisms with a variety of mood, behavioral and stress-related psychopathologies. However, these associations are complex and may be population-dependent, and/or related to epigenetic processes or other known polymorphisms, including the STin2 variable number tandem repeat (VNTR) that overlaps an enhancer element in an SLC6A4 intron. This genomic sequence also includes an accessible chromatin region used in a lentiviral ReSE (repressive ability of silencer elements) screen that assays for cell survival based on transcriptional repression of an apoptosis-inducing fusion protein. That subregion was identified as a functional silencer in phorbol 12-myristate 13-acetate-treated (for megakaryocytic differentiation) K562 erythroleukemia cells. [provided by RefSeq, Apr 2023]
Orthologs: mouse all
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Genomic context

Location:: 17q11.2

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	17	NC_000017.11 (30235481..30237521)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	17	NC_060941.1 (31180015..31182055)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	17	NC_000017.10 (28562499..28564539)

Chromosome 17 - NC_000017.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

The role of 5-HTTLPR in autism spectrum disorder: New evidence and a meta-analysis of this polymorphism in Latin American population with psychiatric disorders.
Title: The role of 5-HTTLPR in autism spectrum disorder: New evidence and a meta-analysis of this polymorphism in Latin American population with psychiatric disorders.

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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

See Variation Viewer (GRCh37.p13)

General gene information

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Other Names

5-HTT promoter
5-HTTLPR promoter polymorphism region
ReSE screen-validated silencer GRCh37_chr17:28562949-28563131
SLC6A4 promoter
serotonin transporter gene promoter

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.