Human Gene LITAF (ENST00000622633.5) from GENCODE V44
  Description: Homo sapiens lipopolysaccharide induced TNF factor (LITAF), transcript variant 2, mRNA. (from RefSeq NM_001136472)
RefSeq Summary (NM_001136472): 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].
Gencode Transcript: ENST00000622633.5
Gencode Gene: ENSG00000189067.14
Transcript (Including UTRs)
   Position: hg38 chr16:11,547,722-11,586,919 Size: 39,198 Total Exon Count: 4 Strand: -
Coding Region
   Position: hg38 chr16:11,549,637-11,556,730 Size: 7,094 Coding Exon Count: 3 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsOther NamesGeneReviewsMethods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr16:11,547,722-11,586,919)mRNA (may differ from genome)Protein (161 aa)
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HGNCHPRDMalacardsMGIneXtProtOMIM
PubMedUniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: LITAF_HUMAN
DESCRIPTION: RecName: Full=Lipopolysaccharide-induced tumor necrosis factor-alpha factor; Short=LPS-induced TNF-alpha factor; AltName: Full=Small integral membrane protein of lysosome/late endosome; AltName: Full=p53-induced gene 7 protein;
FUNCTION: Probable role in regulating transcription of specific genes. May regulate through NFKB1 the expression of the CCL2/MCP-1 chemokine. May play a role in tumor necrosis factor alpha (TNF- alpha) gene expression.
SUBUNIT: Interacts with NEDD4 (By similarity). Interacts with WWOX. Isoform 2 may interact with STAT6.
INTERACTION: P46934:NEDD4; NbExp=4; IntAct=EBI-725647, EBI-726944; Q99816:TSG101; NbExp=3; IntAct=EBI-725647, EBI-346882;
SUBCELLULAR LOCATION: Lysosome membrane; Peripheral membrane protein; Cytoplasmic side. Note=Associated with membranes of lysosomes.
TISSUE SPECIFICITY: Ubiquitously and abundantly expressed. Expressed predominantly in the placenta, peripheral blood leukocytes, lymph nodes and spleen.
INDUCTION: By bacterial lipopolysaccharides (LPS) or p53/TP53. In monocytes by the Bacillus Calmette-Guerin (BCG).
DOMAIN: The WW-binding motif mediates interaction with WWOX and, probably NEDD4.
DISEASE: Defects in LITAF are the cause of Charcot-Marie-Tooth disease type 1C (CMT1C) [MIM:601098]. CMT1C is a form of Charcot- Marie-Tooth disease, the most common inherited disorder of the peripheral nervous system. Charcot-Marie-Tooth disease is classified in two main groups on the basis of electrophysiologic properties and histopathology: primary peripheral demyelinating neuropathy or CMT1, and primary peripheral axonal neuropathy or CMT2. Neuropathies of the CMT1 group are characterized by severely reduced nerve conduction velocities (less than 38 m/sec), segmental demyelination and remyelination with onion bulb formations on nerve biopsy, slowly progressive distal muscle atrophy and weakness, absent deep tendon reflexes, and hollow feet.
DISEASE: Note=Defects in LITAF may be involved in extramammary Paget disease (EMPD) carcinogenesis. EMPD is a cancerous disease representing about 8% of all malignant skin cancers; it usually appears in the anogenital area and can be fatal by metastasizing to internal organs when left untreated for a long time. The clinical features are usually those of eczematous eruptions with weeping and crust formation.
WEB RESOURCE: Name=Inherited peripheral neuropathies mutation db; URL="http://www.molgen.ua.ac.be/CMTMutations/";
WEB RESOURCE: Name=GeneReviews; URL="http://www.ncbi.nlm.nih.gov/sites/GeneTests/lab/gene/LITAF";

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  MalaCards Disease Associations
  MalaCards Gene Search: LITAF
Diseases sorted by gene-association score: charcot-marie-tooth disease, type 1c* (1688), tooth disease (18), charcot-marie-tooth disease (16), peroneal neuropathy (11), hereditary neuropathy with liability to pressure palsy (11), charcot-marie-tooth disease, type 1e (8), sensory peripheral neuropathy (6), neuropathy, recurrent, with pressure palsies (5), dejerine-sottas disease (4), neuropathy, congenital hypomyelinating (1)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 206.16 RPKM in Whole Blood
Total median expression: 1426.54 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -13.8039-0.354 Picture PostScript Text
3' UTR -561.501915-0.293 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR006629 - LITAF

Pfam Domains:
PF10601 - LITAF-like zinc ribbon domain

ModBase Predicted Comparative 3D Structure on Q99732
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-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
Genome BrowserGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
MGIRGD    
Protein SequenceProtein Sequence    
AlignmentAlignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000978 RNA polymerase II core promoter proximal region sequence-specific DNA binding
GO:0001077 transcriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding
GO:0003677 DNA binding
GO:0005515 protein binding
GO:0008270 zinc ion binding
GO:0046872 metal ion binding
GO:0050699 WW domain binding

Biological Process:
GO:0001817 regulation of cytokine production
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0006357 regulation of transcription from RNA polymerase II promoter
GO:0006366 transcription from RNA polymerase II promoter
GO:0007568 aging
GO:0032496 response to lipopolysaccharide
GO:0043123 positive regulation of I-kappaB kinase/NF-kappaB signaling
GO:0045944 positive regulation of transcription from RNA polymerase II promoter
GO:0071222 cellular response to lipopolysaccharide
GO:1901223 negative regulation of NIK/NF-kappaB signaling

Cellular Component:
GO:0000139 Golgi membrane
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005737 cytoplasm
GO:0005764 lysosome
GO:0005765 lysosomal membrane
GO:0005768 endosome
GO:0005794 Golgi apparatus
GO:0005829 cytosol
GO:0005886 plasma membrane
GO:0009898 cytoplasmic side of plasma membrane
GO:0010008 endosome membrane
GO:0016020 membrane
GO:0031901 early endosome membrane
GO:0031902 late endosome membrane
GO:0043231 intracellular membrane-bounded organelle
GO:0098559 cytoplasmic side of early endosome membrane
GO:0098560 cytoplasmic side of late endosome membrane
GO:0098574 cytoplasmic side of lysosomal membrane


-  Descriptions from all associated GenBank mRNAs
  BC065293 - Homo sapiens lipopolysaccharide-induced TNF factor, mRNA (cDNA clone IMAGE:6060454).
AK095955 - Homo sapiens cDNA FLJ38636 fis, clone HHDPC2003049, highly similar to LIPOPOLYSACCHARIDE-INDUCED TUMOR NECROSIS FACTOR-ALPHA FACTOR.
AB034747 - Homo sapiens SIMPLE mRNA for small integral membrane protein of lysosome/late endosome, complete cds.
BX537543 - Homo sapiens mRNA; cDNA DKFZp686E23192 (from clone DKFZp686E23192).
JD033992 - Sequence 15016 from Patent EP1572962.
JD025573 - Sequence 6597 from Patent EP1572962.
BC046154 - Homo sapiens lipopolysaccharide-induced TNF factor, mRNA (cDNA clone MGC:57684 IMAGE:6191106), complete cds.
U77396 - Homo sapiens LPS-Induced TNF-Alpha Factor (LITAF) mRNA, complete cds.
BC039840 - Homo sapiens lipopolysaccharide-induced TNF factor, mRNA (cDNA clone MGC:48840 IMAGE:6054811), complete cds.
BC016491 - Homo sapiens lipopolysaccharide-induced TNF factor, mRNA (cDNA clone MGC:18008 IMAGE:3923016), complete cds.
BC008309 - Homo sapiens lipopolysaccharide-induced TNF factor, mRNA (cDNA clone MGC:15262 IMAGE:3610914), complete cds.
BC000053 - Homo sapiens lipopolysaccharide-induced TNF factor, mRNA (cDNA clone MGC:2056 IMAGE:3506981), complete cds.
AF010312 - Homo sapiens Pig7 (PIG7) mRNA, complete cds.
AK130788 - Homo sapiens cDNA FLJ27278 fis, clone TMS01178.
JD273001 - Sequence 254025 from Patent EP1572962.
JD075107 - Sequence 56131 from Patent EP1572962.
JD416203 - Sequence 397227 from Patent EP1572962.
JD397720 - Sequence 378744 from Patent EP1572962.
JD476937 - Sequence 457961 from Patent EP1572962.
JD560775 - Sequence 541799 from Patent EP1572962.
JD256633 - Sequence 237657 from Patent EP1572962.
JD476938 - Sequence 457962 from Patent EP1572962.
JD255784 - Sequence 236808 from Patent EP1572962.
JD342478 - Sequence 323502 from Patent EP1572962.
JD466858 - Sequence 447882 from Patent EP1572962.
JD090925 - Sequence 71949 from Patent EP1572962.
JD240689 - Sequence 221713 from Patent EP1572962.
JD089088 - Sequence 70112 from Patent EP1572962.
JD064520 - Sequence 45544 from Patent EP1572962.
JD303484 - Sequence 284508 from Patent EP1572962.
JD333233 - Sequence 314257 from Patent EP1572962.
JD298452 - Sequence 279476 from Patent EP1572962.
JD136597 - Sequence 117621 from Patent EP1572962.
JD393678 - Sequence 374702 from Patent EP1572962.
JD302686 - Sequence 283710 from Patent EP1572962.
JD503141 - Sequence 484165 from Patent EP1572962.
JD137548 - Sequence 118572 from Patent EP1572962.
BC096063 - Homo sapiens lipopolysaccharide-induced TNF factor, mRNA (cDNA clone MGC:116698 IMAGE:40000241), complete cds.
BC096064 - Homo sapiens lipopolysaccharide-induced TNF factor, mRNA (cDNA clone IMAGE:40000243).
BC096066 - Homo sapiens lipopolysaccharide-induced TNF factor, mRNA (cDNA clone MGC:116701 IMAGE:40000247), complete cds.
BC101401 - Homo sapiens lipopolysaccharide-induced TNF factor, mRNA (cDNA clone MGC:125275 IMAGE:40000249), complete cds.
BC101969 - Homo sapiens lipopolysaccharide-induced TNF factor, mRNA (cDNA clone MGC:125276 IMAGE:40000250), complete cds.
BC101402 - Homo sapiens lipopolysaccharide-induced TNF factor, mRNA (cDNA clone MGC:125274 IMAGE:40000248), complete cds.
BC096065 - Homo sapiens lipopolysaccharide-induced TNF factor, mRNA (cDNA clone MGC:116700 IMAGE:40000246), complete cds.
JD175069 - Sequence 156093 from Patent EP1572962.
AK314519 - Homo sapiens cDNA, FLJ95338.
JD025660 - Sequence 6684 from Patent EP1572962.
JD028407 - Sequence 9431 from Patent EP1572962.
EU446689 - Synthetic construct Homo sapiens clone IMAGE:100069980; IMAGE:100011898; FLH257127.01L lipopolysaccharide-induced TNF factor (LITAF) gene, encodes complete protein.
EU831762 - Synthetic construct Homo sapiens clone HAIB:100066791; DKFZo008B0621 lipopolysaccharide-induced TNF factor protein (LITAF) gene, encodes complete protein.
EU831840 - Synthetic construct Homo sapiens clone HAIB:100066869; DKFZo004B0622 lipopolysaccharide-induced TNF factor protein (LITAF) gene, encodes complete protein.
KJ892787 - Synthetic construct Homo sapiens clone ccsbBroadEn_02181 LITAF gene, encodes complete protein.
KR711514 - Synthetic construct Homo sapiens clone CCSBHm_00025124 LITAF (LITAF) mRNA, encodes complete protein.
KR711515 - Synthetic construct Homo sapiens clone CCSBHm_00025125 LITAF (LITAF) mRNA, encodes complete protein.
KR711516 - Synthetic construct Homo sapiens clone CCSBHm_00025126 LITAF (LITAF) mRNA, encodes complete protein.
KR711517 - Synthetic construct Homo sapiens clone CCSBHm_00025131 LITAF (LITAF) mRNA, encodes complete protein.
KR712203 - Synthetic construct Homo sapiens clone CCSBHm_00900154 LITAF (LITAF) mRNA, encodes complete protein.
BC107713 - Homo sapiens cDNA clone IMAGE:6709204, with apparent retained intron.

-  Other Names for This Gene
  Alternate Gene Symbols: D3DUG1, ENST00000622633.1, ENST00000622633.2, ENST00000622633.3, ENST00000622633.4, LITAF_HUMAN, NM_001136472, PIG7, Q05DW0, Q99732, Q9C0L6, SIMPLE, uc002dbb.1, uc002dbb.2, uc002dbb.3, uc002dbb.4, uc002dbb.5
UCSC ID: ENST00000622633.5
RefSeq Accession: NM_001136472
Protein: Q99732 (aka LITAF_HUMAN)

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene LITAF:
cmt (Charcot-Marie-Tooth Hereditary Neuropathy Overview)

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.