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

    Gene ID: 9516, updated on 23-Sep-2022

    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; AllianceGenome:HGNC:16841
    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
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See LITAF in Genome Data Viewer
    Location:
    16p13.13
    Exon count:
    13
    Annotation release Status Assembly Chr Location
    110 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (11547722..11640317, complement)
    110 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (11583827..11623552, complement)
    105.20220307 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 putative uncharacterized protein LOC400499 Neighboring gene uncharacterized LOC101927131 Neighboring gene small nucleolar RNA U13 Neighboring gene Sharpr-MPRA regulatory region 8116 Neighboring gene Sharpr-MPRA regulatory region 4417 Neighboring gene uncharacterized LOC124903643 Neighboring gene Sharpr-MPRA regulatory region 8349 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 Apr 4 07:08:55 2018

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    Associated conditions

    Description Tests
    Charcot-Marie-Tooth disease type 1C
    MedGen: C0270913 OMIM: 601098 GeneReviews: Not available
    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

    EBI GWAS Catalog

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

    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

    Function Evidence Code Pubs
    enables DNA-binding transcription activator activity, RNA polymerase II-specific IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables WW domain binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables identical protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables zinc ion binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    enables zinc ion binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    Component Evidence Code Pubs
    located_in Golgi apparatus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in Golgi apparatus IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    located_in Golgi membrane IEA
    Inferred from Electronic Annotation
    more info
     
    located_in cytoplasmic side of early endosome membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    is_active_in cytoplasmic side of late endosome membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    located_in cytoplasmic side of late endosome membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    is_active_in cytoplasmic side of lysosomal membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    located_in cytoplasmic side of lysosomal membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in cytoplasmic side of plasma membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in intracellular membrane-bounded organelle IDA
    Inferred from Direct Assay
    more info
     
    located_in lysosomal membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
     
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    located_in 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)

    NEW Try the new Transcript table

    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_001136472.2NP_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, Q9C0L6
      Related
      ENSP00000483114.1, ENST00000622633.5
      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, ENST00000413364.6
      Conserved Domains (1) summary
      pfam10601
      Location:91126
      zf-LITAF-like; LITAF-like zinc ribbon domain
    3. NM_004862.4NP_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
      Consensus CDS
      CCDS32386.1
      UniProtKB/Swiss-Prot
      Q99732, Q9C0L6
      Related
      ENSP00000340118.5, ENST00000339430.9
      Conserved Domains (1) summary
      pfam10601
      Location:91157
      zf-LITAF-like; LITAF-like zinc ribbon domain

    RNA

    1. NR_024320.2 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 110 details...Open this link in a new tab

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000016.10 Reference GRCh38.p14 Primary Assembly

      Range
      11547722..11640317 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047434928.1XP_047290884.1  lipopolysaccharide-induced tumor necrosis factor-alpha factor isoform X1

    2. XM_047434929.1XP_047290885.1  lipopolysaccharide-induced tumor necrosis factor-alpha factor isoform X1

    3. XM_047434927.1XP_047290883.1  lipopolysaccharide-induced tumor necrosis factor-alpha factor isoform X1

    4. XM_011522754.4XP_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
    5. XM_047434926.1XP_047290882.1  lipopolysaccharide-induced tumor necrosis factor-alpha factor isoform X1

    6. XM_006720982.4XP_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, Q9C0L6
      Related
      ENSP00000459138.1, ENST00000570904.5
      Conserved Domains (1) summary
      pfam10601
      Location:91157
      zf-LITAF-like; LITAF-like zinc ribbon domain
    7. XM_006720984.5XP_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, Q9C0L6
      Conserved Domains (1) summary
      pfam10601
      Location:91157
      zf-LITAF-like; LITAF-like zinc ribbon domain
    8. XM_006720983.5XP_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, Q9C0L6
      Related
      ENSP00000459533.1, ENST00000571688.5
      Conserved Domains (1) summary
      pfam10601
      Location:91157
      zf-LITAF-like; LITAF-like zinc ribbon domain

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060940.1 Alternate T2T-CHM13v2.0

      Range
      11583827..11623552 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)