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

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: mouse all
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Genomic context

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_000016.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues 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?

Circ_0030042 inhibits trophoblast cell growth, invasion and epithelial-mesenchymal transition process in preeclampsia via miR-942-5p/LITAF.
Title: Circ_0030042 inhibits trophoblast cell growth, invasion and epithelial-mesenchymal transition process in preeclampsia via miR-942-5p/LITAF.
Identification and clinical characterization of Charcot-Marie-Tooth disease type 1C patients with LITAF p.G112S mutation.
Title: Identification and clinical characterization of Charcot-Marie-Tooth disease type 1C patients with LITAF p.G112S mutation.
SIMPLE Is an Endosomal Regulator That Protects Against NAFLD by Targeting the Lysosomal Degradation of EGFR.
Title: SIMPLE Is an Endosomal Regulator That Protects Against NAFLD by Targeting the Lysosomal Degradation of EGFR.
Atypical presentation of Charcot-Marie-Tooth disease type 1C with a new mutation: a case report.
Title: Atypical presentation of Charcot-Marie-Tooth disease type 1C with a new mutation: a case report.
Involvement of the MicroRNA-1-LITAF Axis in Gastric Cancer Cell Growth and Invasion.
Title: Involvement of the MicroRNA-1-LITAF Axis in Gastric Cancer Cell Growth and Invasion.
The authors show that WDR86-AS1, miR-10b-3p, and LITAF are involved in preeclampsia pathogenesis.
Title: A potential regulatory network among WDR86-AS1, miR-10b-3p, and LITAF is possibly involved in preeclampsia pathogenesis.
LITAF expression is decreased in glioma tissues and might enhance radiosensitivity of glioma cells via upregulation of the FoxO1 pathway.
Title: LITAF Enhances Radiosensitivity of Human Glioma Cells via the FoxO1 Pathway.
miR-106a was significantly elevated in high-grade human prostate tumors relative to intermediate- and low-grade specimens. An inverse correlation was seen with its target, LITAF. Furthermore, high miR-106a and low LITAF expression predict for biochemical recurrence at 5 years after radical prostatectomy.
Title: miRNA-106a and prostate cancer radioresistance: a novel role for LITAF in ATM regulation.
results indicate that SIMPLE may regulate protein trafficking physiologically by localizing to the TGN and/or REs by binding PI4P.
Title: SIMPLE binds specifically to PI4P through SIMPLE-like domain and participates in protein trafficking in the trans-Golgi network and/or recycling endosomes.
our findings provide a novel apoptotic regulatory pathway in which LITAF, as a transcription factor, inhibits the expression of BCL6, which leads to activation of the intrinsic mitochondrial pathway and tumor apoptosis.
Title: The feedback loop of LITAF and BCL6 is involved in regulating apoptosis in B cell non-Hodgkin's-lymphoma.

Submit: New GeneRIF Correction See all GeneRIFs (45)

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

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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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

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH70306 (e-PCR)
- UniSTS:19202

D16S519 (e-PCR), detects polymorphism
- UniSTS:14156

D16S2671 (e-PCR)
- UniSTS:152420

D16S3304 (e-PCR)
- UniSTS:23420

D16S764 (e-PCR), detects polymorphism
- UniSTS:80782

NoName (e-PCR)
- UniSTS:482965

G62064 (e-PCR)
- UniSTS:139179

SHGC-61147 (e-PCR)
- UniSTS:21213

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

Process	Evidence Code	Pubs
involved_in cellular response to lipopolysaccharide	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of non-canonical NF-kappaB signal transduction	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of canonical NF-kappaB signal transduction	HMP more info	PubMed
involved_in positive regulation of transcription by RNA polymerase II	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of cytokine production	IBA Inferred from Biological aspect of Ancestor more info
involved_in regulation of macrophage cytokine production	IEA Inferred from Electronic Annotation more info

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

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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)

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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_009008.1 RefSeqGene

Range

4485..44229

Download

GenBank, FASTA, Sequence Viewer (Graphics), LRG_253

mRNA and Protein(s)

NM_001136472.2 → NP_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:91 → 157

zf-LITAF-like; LITAF-like zinc ribbon domain
NM_001136473.1 → NP_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:91 → 126

zf-LITAF-like; LITAF-like zinc ribbon domain
NM_004862.4 → NP_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:91 → 157

zf-LITAF-like; LITAF-like zinc ribbon domain

RNA

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

NC_000016.10 Reference GRCh38.p14 Primary Assembly

Range

11547722..11640317 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_047434928.1 → XP_047290884.1 lipopolysaccharide-induced tumor necrosis factor-alpha factor isoform X1
XM_047434929.1 → XP_047290885.1 lipopolysaccharide-induced tumor necrosis factor-alpha factor isoform X1
XM_047434927.1 → XP_047290883.1 lipopolysaccharide-induced tumor necrosis factor-alpha factor isoform X1
XM_011522754.4 → XP_011521056.1 lipopolysaccharide-induced tumor necrosis factor-alpha factor isoform X1

UniProtKB/TrEMBL

I3L3U8

Conserved Domains (1) summary

pfam10601
Location:121 → 189

zf-LITAF-like; LITAF-like zinc ribbon domain
XM_047434926.1 → XP_047290882.1 lipopolysaccharide-induced tumor necrosis factor-alpha factor isoform X1
XM_006720982.4 → XP_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:91 → 157

zf-LITAF-like; LITAF-like zinc ribbon domain
XM_006720984.5 → XP_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:91 → 157

zf-LITAF-like; LITAF-like zinc ribbon domain
XM_006720983.5 → XP_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:91 → 157

zf-LITAF-like; LITAF-like zinc ribbon domain

Alternate T2T-CHM13v2.0

Genomic

NC_060940.1 Alternate T2T-CHM13v2.0

Range

11583827..11676644 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054314440.1 → XP_054170415.1 lipopolysaccharide-induced tumor necrosis factor-alpha factor isoform X1
XM_054314441.1 → XP_054170416.1 lipopolysaccharide-induced tumor necrosis factor-alpha factor isoform X1
XM_054314439.1 → XP_054170414.1 lipopolysaccharide-induced tumor necrosis factor-alpha factor isoform X1
XM_054314442.1 → XP_054170417.1 lipopolysaccharide-induced tumor necrosis factor-alpha factor isoform X2
XM_054314443.1 → XP_054170418.1 lipopolysaccharide-induced tumor necrosis factor-alpha factor isoform X2
XM_054314444.1 → XP_054170419.1 lipopolysaccharide-induced tumor necrosis factor-alpha factor isoform X2