Litaf lipopolysaccharide-induced TNF factor [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Litafprovided by RGD
Official Full Name: lipopolysaccharide-induced TNF factorprovided by RGD
Primary source: RGD:69294
See related: EnsemblRapid:ENSRNOG00000002520 AllianceGenome:RGD:69294
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as: Pig7; EET-1
Summary: Predicted to enable several functions, including DNA-binding transcription activator activity, RNA polymerase II-specific; WW domain binding activity; and zinc ion binding activity. Predicted to be involved in positive regulation of canonical NF-kappaB signal transduction; positive regulation of transcription by RNA polymerase II; and regulation of cytokine production. Predicted to act upstream of or within cellular response to lipopolysaccharide; negative regulation of non-canonical NF-kappaB signal transduction; and regulation of macrophage cytokine production. Predicted to be located in several cellular components, including Golgi apparatus; bounding membrane of organelle; and cytoplasmic side of plasma membrane. Predicted to be active in cytoplasmic side of late endosome membrane; cytoplasmic side of lysosomal membrane; and nucleus. Human ortholog(s) of this gene implicated in Charcot-Marie-Tooth disease type 1C. Orthologous to human LITAF (lipopolysaccharide induced TNF factor). [provided by Alliance of Genome Resources, Dec 2024]
Expression: Biased expression in Kidney (RPKM 164.1), Adrenal (RPKM 137.5) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 10q11

Exon count:: 6

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	10	NC_086028.1 (5163258..5199930)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	10	NC_051345.1 (4656308..4692981)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	10	NC_005109.4 (4753546..4763272)

Chromosome 10 - NC_086028.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
BioProject: PRJNA238328
Publication: PMID 24510058
Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

cerebral TNFalpha is mainly produced in glia cells and that its production is dependently regulated by each stimulant
Title: Regulation of brain cell environment on neuronal protection: role of TNFalpha in glia cells.

Submit: New GeneRIF Correction

General gene information

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Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables DNA binding	IEA Inferred from Electronic Annotation more info
enables DNA-binding transcription activator activity, RNA polymerase II-specific	ISO Inferred from Sequence Orthology more info
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	ISO Inferred from Sequence Orthology more info
enables WW domain binding	ISO Inferred from Sequence Orthology more info
enables WW domain binding	ISS Inferred from Sequence or Structural Similarity more info
enables identical protein binding	ISO Inferred from Sequence Orthology more info
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables zinc ion binding	IBA Inferred from Biological aspect of Ancestor more info
enables zinc ion binding	ISO Inferred from Sequence Orthology more info
enables zinc ion binding	ISS Inferred from Sequence or Structural Similarity more info

Process	Evidence Code	Pubs
acts_upstream_of_or_within cellular response to lipopolysaccharide	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within negative regulation of non-canonical NF-kappaB signal transduction	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of canonical NF-kappaB signal transduction	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in regulation of cytokine production	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within regulation of macrophage cytokine production	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within response to lipopolysaccharide	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
located_in Golgi apparatus	ISO Inferred from Sequence Orthology more info
located_in Golgi apparatus	ISS Inferred from Sequence or Structural Similarity more info
located_in Golgi membrane	IEA Inferred from Electronic Annotation more info
located_in cytoplasmic side of early endosome membrane	ISO Inferred from Sequence Orthology more info
located_in cytoplasmic side of early endosome membrane	ISS Inferred from Sequence or Structural Similarity more info
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	ISO Inferred from Sequence Orthology more info
located_in cytoplasmic side of late endosome membrane	ISS Inferred from Sequence or Structural Similarity more info
is_active_in cytoplasmic side of lysosomal membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in cytoplasmic side of lysosomal membrane	ISO Inferred from Sequence Orthology more info
located_in cytoplasmic side of lysosomal membrane	ISS Inferred from Sequence or Structural Similarity more info
located_in cytoplasmic side of plasma membrane	ISO Inferred from Sequence Orthology more info
located_in cytoplasmic side of plasma membrane	ISS Inferred from Sequence or Structural Similarity more info
located_in early endosome membrane	IEA Inferred from Electronic Annotation more info
located_in extracellular region	TAS Traceable Author Statement more info	PubMed
located_in intracellular membrane-bounded organelle	ISO Inferred from Sequence Orthology more info
located_in late endosome membrane	IEA Inferred from Electronic Annotation more info
located_in lysosomal membrane	IEA Inferred from Electronic Annotation more info
located_in lysosomal membrane	ISO Inferred from Sequence Orthology more info
located_in nucleoplasm	ISO Inferred from Sequence Orthology more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IEA Inferred from Electronic Annotation more info
located_in plasma membrane	IEA Inferred from Electronic Annotation more info
located_in plasma membrane	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: lipopolysaccharide-induced tumor necrosis factor-alpha factor homolog

Names: LPS-induced TN factor; LPS-induced TNF-alpha factor homolog; estrogen-enhanced transcript protein 1; estrogen-responsive uterine transcript

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.

mRNA and Protein(s)

NM_001105735.3 → NP_001099205.1 lipopolysaccharide-induced tumor necrosis factor-alpha factor homolog

See identical proteins and their annotated locations for NP_001099205.1

Status: VALIDATED

Source sequence(s)

JAXUCZ010000010

UniProtKB/Swiss-Prot

P0C0T0

UniProtKB/TrEMBL

A0A8L2Q1K5, B2RYP2

Related

ENSRNOP00000003412.3, ENSRNOT00000003412.5

Conserved Domains (1) summary

pfam10601
Location:91 → 159

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

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

Reference GRCr8

Genomic

NC_086028.1 Reference GRCr8

Range

5163258..5199930

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_063269825.1 → XP_063125895.1 lipopolysaccharide-induced tumor necrosis factor-alpha factor homolog isoform X1

UniProtKB/Swiss-Prot

P0C0T0

UniProtKB/TrEMBL

A0A8L2Q1K5, B2RYP2
XM_039086806.2 → XP_038942734.1 lipopolysaccharide-induced tumor necrosis factor-alpha factor homolog isoform X1

UniProtKB/Swiss-Prot

P0C0T0

UniProtKB/TrEMBL

A0A8L2Q1K5, B2RYP2

Conserved Domains (1) summary

pfam10601
Location:91 → 159

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