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

Gene ID: 9516, updated on 27-Nov-2024

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
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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
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (11547722..11640317, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (11583827..11676644, complement)
RS_2024_09 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 H3K4me1 hESC enhancer GRCh37_chr16:11480804-11481686 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:11483724-11484478 Neighboring gene putative uncharacterized protein LOC400499 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:11507777-11508748 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10444 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:11550335-11550854 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:11550855-11551372 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10445 Neighboring gene uncharacterized LOC101927131 Neighboring gene uncharacterized LOC124903807 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:11564147-11564648 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:11588027-11589023 Neighboring gene Sharpr-MPRA regulatory region 8116 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:11592015-11592563 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:11595297-11596228 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:11610059-11610587 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:11612139-11612638 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:11620432-11621366 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:11621367-11622300 Neighboring gene OCT4-H3K4me1 hESC enhancer GRCh37_chr16:11637410-11638225 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:11654074-11654928 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:11656029-11656658 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:11657289-11657918 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:11657919-11658546 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:11665841-11666778 Neighboring gene Sharpr-MPRA regulatory region 2706 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10450 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7204 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7205 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:11688769-11689642 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:11689643-11690514 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:11697089-11697681 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:11699131-11699630 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10451 Neighboring gene Sharpr-MPRA regulatory region 4417 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:11708187-11708794 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:11708795-11709402 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:11715855-11716623 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:11720940-11721474 Neighboring gene uncharacterized LOC124903643 Neighboring gene Sharpr-MPRA regulatory region 8349 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:11735633-11736296 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7206 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10455 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:11766535-11767354 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

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
 
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
 
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
 
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
 
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
    D3DUG1, G5E9K0, Q05DW0, Q99732, Q9C0L6
    UniProtKB/TrEMBL
    I3L3U8
    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/TrEMBL
    I3L1P1
    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
    D3DUG1, G5E9K0, Q05DW0, Q99732, Q9C0L6
    UniProtKB/TrEMBL
    I3L3U8
    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: GCF_000001405.40-RS_2024_08

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

    UniProtKB/TrEMBL
    I3L3U8
    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
    D3DUG1, G5E9K0, Q05DW0, Q99732, Q9C0L6
    UniProtKB/TrEMBL
    I3L3U8
    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
    D3DUG1, G5E9K0, Q05DW0, Q99732, Q9C0L6
    UniProtKB/TrEMBL
    I3L3U8
    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
    D3DUG1, G5E9K0, Q05DW0, Q99732, Q9C0L6
    UniProtKB/TrEMBL
    I3L3U8
    Related
    ENSP00000459533.1, ENST00000571688.6
    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..11676644 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054314440.1XP_054170415.1  lipopolysaccharide-induced tumor necrosis factor-alpha factor isoform X1

  2. XM_054314441.1XP_054170416.1  lipopolysaccharide-induced tumor necrosis factor-alpha factor isoform X1

  3. XM_054314439.1XP_054170414.1  lipopolysaccharide-induced tumor necrosis factor-alpha factor isoform X1

  4. XM_054314442.1XP_054170417.1  lipopolysaccharide-induced tumor necrosis factor-alpha factor isoform X2

  5. XM_054314443.1XP_054170418.1  lipopolysaccharide-induced tumor necrosis factor-alpha factor isoform X2

  6. XM_054314444.1XP_054170419.1  lipopolysaccharide-induced tumor necrosis factor-alpha factor isoform X2