LST1 leukocyte specific transcript 1 [Homo sapiens (human)] - Gene

Summary

Official Symbol: LST1provided by HGNC
Official Full Name: leukocyte specific transcript 1provided by HGNC
Primary source: HGNC:HGNC:14189
See related: Ensembl:ENSG00000204482 MIM:109170
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: B144; LST-1; D6S49E
Summary: The protein encoded by this gene is a membrane protein that can inhibit the proliferation of lymphocytes. Expression of this gene is enhanced by lipopolysaccharide, interferon-gamma, and bacteria. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2011]
Expression: Biased expression in bone marrow (RPKM 68.1), spleen (RPKM 43.9) and 13 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 6p21.33

Exon count:: 6

Annotation release	Status	Assembly	Chr	Location
109.20210514	current	GRCh38.p13 (GCF_000001405.39)	6	NC_000006.12 (31586185..31588909)
105.20201022	previous assembly	GRCh37.p13 (GCF_000001405.25)	6	NC_000006.11 (31554054..31556686)

Chromosome 6 - NC_000006.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

the present review describes LST1 promotor, gene organization, splice variants and expression in human tissues, cell lines and cancer with the focus on LST1 expression in inflammation, autoimmune diseases and cancer
Title: LST1: A multifunctional gene encoded in the MHC class III region.
Increased expression of LST1 in GC-responders before therapy warrants further investigation into their role as potential predictors for the response to GC, and in the inflammatory process of rheumatoid arthritis.
Title: Expression of ERAP2 and LST1 is increased before start of therapy in rheumatoid arthritis patients with good clinical response to glucocorticoids.
Data indicate that the MHC class III gene LST1 5' untranslated regions (5'-UTR) contains several upstream open reading frames (uORFs).
Title: An upstream open reading frame regulates LST1 expression during monocyte differentiation.
Psoriasis was associated with promoter variant, rs9267502 of LST1.Promoter activity was examined and it was larger than that of the other genetic variants, most probably due to changes in binding affinity to transcription factors.
Title: Identification of functional haplotypes in the promoter region of the LST1 gene.
This is the first report demonstrating regulated LST1 expression in human intestinal epithelial and microvascular endothelial cells and in inflamed colonic tissue from IBD patients.
Title: Regulated expression of leukocyte-specific transcript (LST) 1 in human intestinal inflammation.
induces the formation of functional nanotubes
Title: LST1 promotes the assembly of a molecular machinery responsible for tunneling nanotube formation.
LST1 is expressed specifically in leukocytes of the myeloid lineage, where it localizes to the tetraspanin-enriched microdomains andit binds SHP-1 and SHP-2 phosphatases.
Title: LST1/A is a myeloid leukocyte-specific transmembrane adaptor protein recruiting protein tyrosine phosphatases SHP-1 and SHP-2 to the plasma membrane.
Study found association between extended LTA, TNF, LST1 and HLA gene haplotypes and rubella vaccine-induced immunity.
Title: Extended LTA, TNF, LST1 and HLA gene haplotypes and their association with rubella vaccine-induced immunity.
Observational study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
Title: Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study.
Observational study of genotype prevalence. (HuGE Navigator)
Title: Genetic variation in metabolizing enzyme and transporter genes: comprehensive assessment in 3 major East Asian subpopulations with comparison to Caucasians and Africans.

Submit: New GeneRIF Correction See all GeneRIFs (16)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Genome-wide meta-analysis increases to 71 the number of confirmed Crohn's disease susceptibility loci. GeneReviews: Not available

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH76316 (e-PCR)
- UniSTS:92938

NoName (e-PCR)
- UniSTS:481830

NoName (e-PCR)
- UniSTS:482887

TNFd (e-PCR)
- UniSTS:256848

TNFd (e-PCR)
- UniSTS:256849

TNFe (e-PCR)
- UniSTS:515954

RH76281 (e-PCR)
- UniSTS:86153

D6S2790 (e-PCR)
- UniSTS:464287

D6S2789 (e-PCR)
- UniSTS:464288

SHGC-63639 (e-PCR)
- UniSTS:58789

STS-U00921 (e-PCR)
- UniSTS:45518

Homology

Orthologs from Annotation Pipeline: 162 organisms have orthologs with human gene LST1
Orthologs

Gene Ontology Provided by GOA

Process	Evidence Code	Pubs
involved_in anatomical structure morphogenesis	NAS Non-traceable Author Statement more info	PubMed
involved_in cell morphogenesis	IEA Inferred from Electronic Annotation more info
involved_in dendrite development	IBA Inferred from Biological aspect of Ancestor more info	PubMed
involved_in dendrite development	IDA Inferred from Direct Assay more info	PubMed
involved_in immune response	NAS Non-traceable Author Statement more info	PubMed
involved_in negative regulation of lymphocyte proliferation	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of cell shape	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
located_in Golgi apparatus	NAS Non-traceable Author Statement more info	PubMed
located_in Golgi membrane	IEA Inferred from Electronic Annotation more info
located_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
is_active_in integral component of membrane	IBA Inferred from Biological aspect of Ancestor more info	PubMed
located_in integral component of membrane	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: leukocyte-specific transcript 1 protein

Names: lymphocyte antigen 117

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

NG_030378.1 RefSeqGene

Range

5099..7731

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001166538.1 → NP_001160010.1 leukocyte-specific transcript 1 protein isoform 6

See identical proteins and their annotated locations for NP_001160010.1

Status: REVIEWED

Description

Transcript Variant: This variant (6) lacks an alternate in-frame exon in the 5' coding region, compared to variant 1, resulting in an isoform (6) that is shorter than isoform 1. The 5' UTR of this variant is incomplete because the transcripts supporting this CDS exon combination lack a complete 5' UTR, and alternative splicing choices exist further upstream.

Source sequence(s)

AI091696, Y18486

Consensus CDS

CCDS54987.1

UniProtKB/Swiss-Prot

O00453

Related

ENSP00000365254.3, ENST00000376086.7

Conserved Domains (1) summary

pfam05083
Location:7 → 72

LST1; LST-1 protein
NM_007161.3 → NP_009092.3 leukocyte-specific transcript 1 protein isoform 1

See identical proteins and their annotated locations for NP_009092.3

Status: REVIEWED

Description

Transcript Variant: This variant (1) encodes the longest isoform (1). The 5' UTR of this variant is incomplete because the transcripts supporting this CDS exon combination lack a complete 5' UTR, and alternative splicing choices exist further upstream.

Source sequence(s)

AI091696, AL662801, AV715235, AY852266

Consensus CDS

CCDS54984.1

UniProtKB/Swiss-Prot

O00453

Related

ENSP00000365261.2, ENST00000376093.6

Conserved Domains (1) summary

pfam05083
Location:28 → 103

LST1; LST-1 protein
NM_205837.3 → NP_995309.2 leukocyte-specific transcript 1 protein isoform 2

Status: REVIEWED

Description

Transcript Variant: This variant (2) includes an additional exon in the 5' UTR and lacks an internal exon that causes a frameshift in the 3' coding region, compared to variant 1. The encoded isoform (2) has a distinct C-terminus and is shorter than isoform 1.

Source sequence(s)

AF000424, AI091696

Consensus CDS

CCDS54985.1

UniProtKB/Swiss-Prot

O00453

Related

ENSP00000339201.4, ENST00000339530.8
NM_205838.3 → NP_995310.2 leukocyte-specific transcript 1 protein isoform 3

See identical proteins and their annotated locations for NP_995310.2

Status: REVIEWED

Description

Transcript Variant: This variant (3) includes an additional exon in the 5' UTR, lacks an alternate in-frame exon in the 5' coding region, and uses an alternate in-frame splice site in the 3' coding region, compared to variant 1. The encoded isoform (3) is shorter than isoform 1.

Source sequence(s)

AI091696, AV715235

Consensus CDS

CCDS4705.2

UniProtKB/Swiss-Prot

O00453

Related

ENSP00000405900.2, ENST00000418507.6

Conserved Domains (1) summary

pfam05083
Location:7 → 65

LST1; LST-1 protein
NM_205839.3 → NP_995311.2 leukocyte-specific transcript 1 protein isoform 4

See identical proteins and their annotated locations for NP_995311.2

Status: REVIEWED

Description

Transcript Variant: This variant (4) includes an additional exon in the 5' UTR and uses an alternate in-frame splice site in the 3' coding region, compared to variant 1. The encoded isoform (4) is shorter than isoform 1.

Source sequence(s)

AF000425, AI091696, AL662801

Consensus CDS

CCDS43450.2

UniProtKB/Swiss-Prot

O00453

UniProtKB/TrEMBL

A0A024RCT6

Related

ENSP00000391929.3, ENST00000438075.7

Conserved Domains (1) summary

pfam05083
Location:28 → 96

LST1; LST-1 protein
NM_205840.2 → NP_995312.2 leukocyte-specific transcript 1 protein isoform 5

See identical proteins and their annotated locations for NP_995312.2

Status: REVIEWED

Description

Transcript Variant: This variant (5) lacks an alternate exon in the central coding region and uses an alternate splice site that causes a frameshift in the 3' coding region, compared to variant 1. The encoded isoform (5) has a distinct C-terminus and is shorter than isoform 1. The 5' UTR of this variant is incomplete because the transcripts supporting this CDS exon combination lack a complete 5' UTR, and alternative splicing choices exist further upstream.

Source sequence(s)

AI091696, Y18487

Consensus CDS

CCDS54986.1

UniProtKB/Swiss-Prot

O00453

Related

ENSP00000303649.7, ENST00000303757.12

RNA

NR_029461.2 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (7) includes an additional 5' exon, lacks two alternate internal exons, and uses an alternate splice site in the 3' terminal exon, compared to variant 1. This variant is represented as non-coding due to uncertainty about its protein-coding capacity; only a very short protein would result from translation initiation at the supported start codon, as used by variant 1.

Source sequence(s)

AI091696, AJ705986

Related

ENST00000376099.5
NR_029462.2 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (8) includes an additional 5' exon, lacks two alternate internal exons, and uses an alternate splice site in the 3' terminal exon, compared to variant 1. This variant is represented as non-coding due to uncertainty about its protein-coding capacity; only a very short protein would result from translation initiation at the supported start codon, as used by variant 1.

Source sequence(s)

AI091696, AV711621

Related

ENST00000376096.5