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LITAF lipopolysaccharide induced TNF factor [ Homo sapiens (human) ]

Gene ID: 9516, updated on 12-Aug-2018

Summary

Official Symbol
LITAFprovided by HGNC
Official Full Name
lipopolysaccharide induced TNF factorprovided by HGNC
Primary source
HGNC:HGNC:16841
See related
Ensembl:ENSG00000189067 MIM:603795; Vega:OTTHUMG00000177415
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
PIG7; SIMPLE; TP53I7
Summary
Lipopolysaccharide is a potent stimulator of monocytes and macrophages, causing secretion of tumor necrosis factor-alpha (TNF-alpha) and other inflammatory mediators. This gene encodes lipopolysaccharide-induced TNF-alpha factor, which is a DNA-binding protein and can mediate the TNF-alpha expression by direct binding to the promoter region of the TNF-alpha gene. The transcription of this gene is induced by tumor suppressor p53 and has been implicated in the p53-induced apoptotic pathway. Mutations in this gene cause Charcot-Marie-Tooth disease type 1C (CMT1C) and may be involved in the carcinogenesis of extramammary Paget's disease (EMPD). Multiple alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Dec 2014]
Expression
Ubiquitous expression in appendix (RPKM 52.8), thyroid (RPKM 42.1) and 25 other tissues See more
Orthologs

Genomic context

See LITAF in Genome Data Viewer
Location:
16p13.13
Exon count:
15
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 16 NC_000016.10 (11547722..11636377, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (11641578..11681322, complement)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105371082 Neighboring gene mitochondrial ribosomal protein L18 pseudogene Neighboring gene vitellogenin Neighboring gene uncharacterized LOC101927131 Neighboring gene uncharacterized LOC107984880 Neighboring gene nonconserved acetylation island sequence 94 enhancer Neighboring gene thioredoxin domain containing 11 Neighboring gene stannin

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 Jun 15 11:32:44 2016

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
Charcot-Marie-Tooth disease, type 1C Compare labs

Copy number response

Description
Copy number response
Haploinsufficency

No evidence available (Last evaluated (2016-10-21)

ClinGen Genome Curation Page
Triplosensitivity

No evidence available (Last evaluated (2016-10-21)

ClinGen Genome Curation Page

NHGRI GWAS Catalog

Description
Common variants at ten loci influence QT interval duration in the QTGEN Study.
NHGRI GWA Catalog
Common variants at ten loci modulate the QT interval duration in the QTSCD Study.
NHGRI GWA Catalog
Genetic association study of QT interval highlights role for calcium signaling pathways in myocardial repolarization.
NHGRI GWA Catalog
Genome-wide association study of coronary heart disease and its risk factors in 8,090 African Americans: the NHLBI CARe Project.
NHGRI GWA Catalog
Genome-wide association study of peripheral neuropathy with D-drug-containing regimens in AIDS Clinical Trials Group protocol 384.
NHGRI GWA Catalog
Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease.
NHGRI GWA Catalog
Impact of ancestry and common genetic variants on QT interval in African Americans.
NHGRI GWA Catalog

HIV-1 interactions

Protein interactions

Protein Gene Interaction Pubs
Vif vif HIV-1 Vif upregulates the expression of lipopolysaccharide-induced TNF factor (LITAF) in Vif-expression T cells PubMed

Go to the HIV-1, Human Interaction Database

Pathways from BioSystems

  • Lysosome, organism-specific biosystem (from KEGG)
    Lysosome, organism-specific biosystemLysosomes are membrane-delimited organelles in animal cells serving as the cell's main digestive compartment to which all sorts of macromolecules are delivered for degradation. They contain more than...
  • Lysosome, conserved biosystem (from KEGG)
    Lysosome, conserved biosystemLysosomes are membrane-delimited organelles in animal cells serving as the cell's main digestive compartment to which all sorts of macromolecules are delivered for degradation. They contain more than...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ38636, MGC116698, MGC116700, MGC116701, MGC125274, MGC125275, MGC125276

Gene Ontology Provided by GOA

Process Evidence Code Pubs
aging IEA
Inferred from Electronic Annotation
more info
 
cellular response to lipopolysaccharide IEA
Inferred from Electronic Annotation
more info
 
negative regulation of NIK/NF-kappaB signaling IEA
Inferred from Electronic Annotation
more info
 
positive regulation of I-kappaB kinase/NF-kappaB signaling HMP PubMed 
positive regulation of transcription by RNA polymerase II IMP
Inferred from Mutant Phenotype
more info
PubMed 
regulation of cytokine production IEA
Inferred from Electronic Annotation
more info
 
regulation of transcription by RNA polymerase II TAS
Traceable Author Statement
more info
PubMed 
transcription by RNA polymerase II IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
Golgi apparatus IDA
Inferred from Direct Assay
more info
PubMed 
Golgi apparatus IMP
Inferred from Mutant Phenotype
more info
PubMed 
Golgi membrane IEA
Inferred from Electronic Annotation
more info
 
cytoplasmic side of early endosome membrane IDA
Inferred from Direct Assay
more info
PubMed 
cytoplasmic side of late endosome membrane IDA
Inferred from Direct Assay
more info
PubMed 
cytoplasmic side of lysosomal membrane IDA
Inferred from Direct Assay
more info
PubMed 
cytoplasmic side of plasma membrane IDA
Inferred from Direct Assay
more info
PubMed 
cytosol IDA
Inferred from Direct Assay
more info
 
intracellular membrane-bounded organelle IDA
Inferred from Direct Assay
more info
 
lysosomal membrane IDA
Inferred from Direct Assay
more info
PubMed 
nucleoplasm IDA
Inferred from Direct Assay
more info
 
plasma membrane IMP
Inferred from Mutant Phenotype
more info
PubMed 

General protein information

Preferred Names
lipopolysaccharide-induced tumor necrosis factor-alpha factor
Names
LPS-induced TNF-alpha factor
lipopolysaccharide-induced TNF-alpha factor
p53-induced gene 7 protein
small integral membrane protein of lysosome/late endosome
tumor protein p53 inducible protein 7

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_009008.1 RefSeqGene

    Range
    4485..44229
    Download
    GenBank, FASTA, Sequence Viewer (Graphics), LRG_253

mRNA and Protein(s)

  1. NM_001136472.1NP_001129944.1  lipopolysaccharide-induced tumor necrosis factor-alpha factor isoform 1

    See identical proteins and their annotated locations for NP_001129944.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) has an alternate 5' UTR exon, as compared to variant 1. Variants 1 and 2 encode the same isoform 1.
    Source sequence(s)
    AA625937, AB034747, AK314519
    Consensus CDS
    CCDS32386.1
    UniProtKB/Swiss-Prot
    Q99732
    Related
    ENSP00000483114.1, ENST00000622633.4
    Conserved Domains (1) summary
    pfam10601
    Location:91157
    zf-LITAF-like; LITAF-like zinc ribbon domain
  2. NM_001136473.1NP_001129945.1  lipopolysaccharide-induced tumor necrosis factor-alpha factor isoform 2

    See identical proteins and their annotated locations for NP_001129945.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) has an alternate 5' UTR exon and an additional exon in the 3' region, as compared to variant 1. The resulting isoform (2) has a different and shorter C-terminus, as compared to isoform 1.
    Source sequence(s)
    AA625937, AB034747, AK095955
    Consensus CDS
    CCDS45411.1
    UniProtKB/Swiss-Prot
    Q99732
    Related
    ENSP00000397958.2, OTTHUMP00000256597, ENST00000413364.6, OTTHUMT00000436818
    Conserved Domains (1) summary
    pfam10601
    Location:91126
    zf-LITAF-like; LITAF-like zinc ribbon domain
  3. NM_004862.3NP_004853.2  lipopolysaccharide-induced tumor necrosis factor-alpha factor isoform 1

    See identical proteins and their annotated locations for NP_004853.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longer isoform (1).
    Source sequence(s)
    AA625937, AB034747, BC101402, DA955452
    Consensus CDS
    CCDS32386.1
    UniProtKB/Swiss-Prot
    Q99732
    Related
    ENSP00000340118.5, OTTHUMP00000256598, ENST00000339430.9, OTTHUMT00000436819
    Conserved Domains (1) summary
    pfam10601
    Location:91157
    zf-LITAF-like; LITAF-like zinc ribbon domain

RNA

  1. NR_024320.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) has an alternate 5' exon, as compared to variant 1. The alternate 5' exon includes an upstream AUG codon, which results in an upstream ORF, and the transcript is a nonsense-mediated mRNA decay (NMD) candidate. Therefore, this variant is unlikely to make a functional protein.
    Source sequence(s)
    AA625937, AB034747, BI858484, BX537543

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000016.10 Reference GRCh38.p12 Primary Assembly

    Range
    11547722..11636377 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011522754.3XP_011521056.1  lipopolysaccharide-induced tumor necrosis factor-alpha factor isoform X1

    Conserved Domains (1) summary
    pfam10601
    Location:121189
    zf-LITAF-like; LITAF-like zinc ribbon domain
  2. XM_017023896.1XP_016879385.1  lipopolysaccharide-induced tumor necrosis factor-alpha factor isoform X2

    UniProtKB/Swiss-Prot
    Q99732
    Related
    ENSP00000461667.1, OTTHUMP00000256603, ENST00000576036.5, OTTHUMT00000436826
    Conserved Domains (1) summary
    pfam10601
    Location:91157
    zf-LITAF-like; LITAF-like zinc ribbon domain
  3. XM_006720982.3XP_006721045.1  lipopolysaccharide-induced tumor necrosis factor-alpha factor isoform X2

    See identical proteins and their annotated locations for XP_006721045.1

    UniProtKB/Swiss-Prot
    Q99732
    Related
    ENSP00000459138.1, OTTHUMP00000256599, ENST00000570904.5
    Conserved Domains (1) summary
    pfam10601
    Location:91157
    zf-LITAF-like; LITAF-like zinc ribbon domain
  4. XM_006720985.3XP_006721048.1  lipopolysaccharide-induced tumor necrosis factor-alpha factor isoform X2

    See identical proteins and their annotated locations for XP_006721048.1

    UniProtKB/Swiss-Prot
    Q99732
    Related
    ENSP00000458871.1, OTTHUMP00000256606, ENST00000570798.5, OTTHUMT00000436829
    Conserved Domains (1) summary
    pfam10601
    Location:91157
    zf-LITAF-like; LITAF-like zinc ribbon domain
  5. XM_006720984.4XP_006721047.1  lipopolysaccharide-induced tumor necrosis factor-alpha factor isoform X2

    See identical proteins and their annotated locations for XP_006721047.1

    UniProtKB/Swiss-Prot
    Q99732
    Related
    ENSP00000461813.1, OTTHUMP00000256604, ENST00000574763.5
    Conserved Domains (1) summary
    pfam10601
    Location:91157
    zf-LITAF-like; LITAF-like zinc ribbon domain
  6. XM_006720983.4XP_006721046.1  lipopolysaccharide-induced tumor necrosis factor-alpha factor isoform X2

    See identical proteins and their annotated locations for XP_006721046.1

    UniProtKB/Swiss-Prot
    Q99732
    Conserved Domains (1) summary
    pfam10601
    Location:91157
    zf-LITAF-like; LITAF-like zinc ribbon domain
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