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

Gene ID: 7940, updated on 21-Aug-2020

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

Genomic context

See LST1 in Genome Data Viewer
Location:
6p21.33
Exon count:
6
Annotation release Status Assembly Chr Location
109.20200815 current GRCh38.p13 (GCF_000001405.39) 6 NC_000006.12 (31586185..31588909)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (31553956..31556686)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene tumor necrosis factor Neighboring gene lymphotoxin beta Neighboring gene natural cytotoxicity triggering receptor 3 Neighboring gene ubiquinol-cytochrome c reductase hinge protein pseudogene 1 Neighboring gene allograft inflammatory factor 1

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

Associated conditions

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

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • MGC119006, MGC119007

Gene Ontology Provided by GOA

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

General protein information

Preferred Names
leukocyte-specific transcript 1 protein
Names
lymphocyte antigen 117

NCBI Reference Sequences (RefSeq)

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_030378.1 RefSeqGene

    Range
    5099..7731
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001166538.1NP_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:772
    LST1; LST-1 protein
  2. NM_007161.3NP_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:28103
    LST1; LST-1 protein
  3. NM_205837.3NP_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
  4. NM_205838.3NP_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:765
    LST1; LST-1 protein
  5. NM_205839.3NP_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
    ENSP00000391929.2, ENST00000438075.6
    Conserved Domains (1) summary
    pfam05083
    Location:2896
    LST1; LST-1 protein
  6. NM_205840.2NP_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

  1. 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
  2. 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

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20200815

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000006.12 Reference GRCh38.p13 Primary Assembly

    Range
    31586185..31588909
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006715210.3XP_006715273.1  leukocyte-specific transcript 1 protein isoform X3

    See identical proteins and their annotated locations for XP_006715273.1

    UniProtKB/Swiss-Prot
    O00453
  2. XM_006715206.3XP_006715269.1  leukocyte-specific transcript 1 protein isoform X1

    See identical proteins and their annotated locations for XP_006715269.1

    UniProtKB/Swiss-Prot
    O00453
    Conserved Domains (1) summary
    pfam05083
    Location:28103
    LST1; LST-1 protein
  3. XM_006715209.3XP_006715272.1  leukocyte-specific transcript 1 protein isoform X2

    See identical proteins and their annotated locations for XP_006715272.1

    UniProtKB/Swiss-Prot
    O00453
    Conserved Domains (1) summary
    pfam05083
    Location:772
    LST1; LST-1 protein
  4. XM_011514914.2XP_011513216.1  leukocyte-specific transcript 1 protein isoform X1

    See identical proteins and their annotated locations for XP_011513216.1

    UniProtKB/Swiss-Prot
    O00453
    Conserved Domains (1) summary
    pfam05083
    Location:28103
    LST1; LST-1 protein

Reference GRCh38.p13 ALT_REF_LOCI_1

Genomic

  1. NT_167244.2 Reference GRCh38.p13 ALT_REF_LOCI_1

    Range
    2918856..2921488
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p13 ALT_REF_LOCI_2

Genomic

  1. NT_113891.3 Reference GRCh38.p13 ALT_REF_LOCI_2

    Range
    3063564..3066192
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p13 ALT_REF_LOCI_3

Genomic

  1. NT_167245.2 Reference GRCh38.p13 ALT_REF_LOCI_3

    Range
    2834012..2836646
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p13 ALT_REF_LOCI_4

Genomic

  1. NT_167246.2 Reference GRCh38.p13 ALT_REF_LOCI_4

    Range
    2891318..2893950
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p13 ALT_REF_LOCI_5

Genomic

  1. NT_167247.2 Reference GRCh38.p13 ALT_REF_LOCI_5

    Range
    2928172..2930802
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p13 ALT_REF_LOCI_6

Genomic

  1. NT_167248.2 Reference GRCh38.p13 ALT_REF_LOCI_6

    Range
    2842098..2844732
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p13 ALT_REF_LOCI_7

Genomic

  1. NT_167249.2 Reference GRCh38.p13 ALT_REF_LOCI_7

    Range
    2885558..2888190
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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