Tfeb transcription factor EB [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Tfebprovided by RGD
Official Full Name: transcription factor EBprovided by RGD
Primary source: RGD:1309583
See related: Ensembl:ENSRNOG00000014666 AllianceGenome:RGD:1309583
Gene type: protein coding
RefSeq status: PROVISIONAL
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as: Tcfeb
Summary: Predicted to enable several functions, including DNA-binding transcription activator activity, RNA polymerase II-specific; RNA polymerase II cis-regulatory region sequence-specific DNA binding activity; and protein heterodimerization activity. Predicted to be involved in several processes, including cellular response to amino acid starvation; defense response to Gram-negative bacterium; and lysosome localization. Predicted to act upstream of or within positive regulation of transcription, DNA-templated. Predicted to be located in cytosol; lysosomal membrane; and nucleoplasm. Predicted to be part of transcription regulator complex. Predicted to be active in nucleus. Orthologous to human TFEB (transcription factor EB). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in Muscle (RPKM 57.8), Spleen (RPKM 43.3) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 9q12

Exon count:: 13

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	9	NC_086027.1 (20696440..20752265, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	9	NC_051344.1 (13198890..13254726, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	9	NC_005108.4 (15208141..15264101, complement)

Chromosome 9 - NC_086027.1 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?

TFEB regulates cellular labile iron and prevents ferroptosis in a TfR1-dependent manner.
Title: TFEB regulates cellular labile iron and prevents ferroptosis in a TfR1-dependent manner.
Transcription factor EB (TFEB) improves ventricular remodeling after myocardial infarction by inhibiting Wnt/beta-catenin signaling pathway.
Title: Transcription factor EB (TFEB) improves ventricular remodeling after myocardial infarction by inhibiting Wnt/β-catenin signaling pathway.
Impaired TFEB activation and mitophagy as a cause of PPP3/calcineurin inhibitor-induced pancreatic beta-cell dysfunction.
Title: Impaired TFEB activation and mitophagy as a cause of PPP3/calcineurin inhibitor-induced pancreatic β-cell dysfunction.
Phosphorylation of STAT3 at Tyr705 contributes to TFEB-mediated autophagy-lysosomal pathway dysfunction and leads to ischemic injury in rats.
Title: Phosphorylation of STAT3 at Tyr705 contributes to TFEB-mediated autophagy-lysosomal pathway dysfunction and leads to ischemic injury in rats.
The inhibition of TRPML1/TFEB leads to lysosomal biogenesis disorder, contributes to developmental fluoride neurotoxicity.
Title: The inhibition of TRPML1/TFEB leads to lysosomal biogenesis disorder, contributes to developmental fluoride neurotoxicity.
TFEB-Mediated Lysosomal Restoration Alleviates High Glucose-Induced Cataracts Via Attenuating Oxidative Stress.
Title: TFEB-Mediated Lysosomal Restoration Alleviates High Glucose-Induced Cataracts Via Attenuating Oxidative Stress.
TFEB ameliorates autophagy flux disturbance induced by PBDE-47 via up-regulating autophagy-lysosome fusion.
Title: TFEB ameliorates autophagy flux disturbance induced by PBDE-47 via up-regulating autophagy-lysosome fusion.
Altered D2 receptor and transcription factor EB expression in offspring of aggressive male rats, along with having depressive and anxiety-like behaviors.
Title: Altered D2 receptor and transcription factor EB expression in offspring of aggressive male rats, along with having depressive and anxiety-like behaviors.
Positive regulation of TFEB and mitophagy by PGC-1alpha to alleviate LPS-induced acute lung injury in rats.
Title: Positive regulation of TFEB and mitophagy by PGC-1α to alleviate LPS-induced acute lung injury in rats.
TFEB Overexpression, Not mTOR Inhibition, Ameliorates RagC(S75Y) Cardiomyopathy.
Title: TFEB Overexpression, Not mTOR Inhibition, Ameliorates RagC(S75Y) Cardiomyopathy.

Submit: New GeneRIF Correction See all GeneRIFs (14)

General gene information

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Markers

REN60515 (e-PCR)
- UniSTS:385315

REN60529 (e-PCR)
- UniSTS:385329

Tcfeb (e-PCR), detects polymorphism
- UniSTS:144571

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables DNA binding	ISO Inferred from Sequence Orthology more info
enables DNA-binding transcription activator activity, RNA polymerase II-specific	ISO Inferred from Sequence Orthology more info
enables DNA-binding transcription factor activity	ISO Inferred from Sequence Orthology more info
enables DNA-binding transcription factor activity, RNA polymerase II-specific	IBA Inferred from Biological aspect of Ancestor more info
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	ISO Inferred from Sequence Orthology more info
enables enzyme binding	ISO Inferred from Sequence Orthology more info
enables protein heterodimerization activity	ISO Inferred from Sequence Orthology more info
enables sequence-specific double-stranded DNA binding	ISO Inferred from Sequence Orthology more info
enables transcription cis-regulatory region binding	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in antibacterial innate immune response	ISO Inferred from Sequence Orthology more info
involved_in cellular response to amino acid starvation	ISO Inferred from Sequence Orthology more info
involved_in cellular response to starvation	ISO Inferred from Sequence Orthology more info
involved_in defense response to Gram-negative bacterium	ISO Inferred from Sequence Orthology more info
involved_in embryonic placenta development	ISO Inferred from Sequence Orthology more info
involved_in humoral immune response	ISO Inferred from Sequence Orthology more info
involved_in lysosome localization	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within lysosome organization	ISO Inferred from Sequence Orthology more info
involved_in lysosome organization	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within positive regulation of DNA-templated transcription	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of DNA-templated transcription	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of autophagy	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
located_in cytoplasm	ISO Inferred from Sequence Orthology more info
located_in cytosol	ISO Inferred from Sequence Orthology more info
located_in lysosomal membrane	ISO Inferred from Sequence Orthology more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
is_active_in nucleus	ISO Inferred from Sequence Orthology more info
located_in nucleus	ISO Inferred from Sequence Orthology more info
part_of transcription regulator complex	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: transcription factor EB

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_001025707.1 → NP_001020878.1 transcription factor EB

See identical proteins and their annotated locations for NP_001020878.1

Status: PROVISIONAL

Source sequence(s)

BC099102

UniProtKB/TrEMBL

A6JII2, Q4KLM8

Related

ENSRNOP00000037517.6, ENSRNOT00000039102.6

Conserved Domains (3) summary

cd00083
Location:292 → 352

HLH; Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, ...

pfam11851
Location:380 → 516

DUF3371; Domain of unknown function (DUF3371)

pfam15951
Location:63 → 220

MITF_TFEB_C_3_N; MITF/TFEB/TFEC/TFE3 N-terminus

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_086027.1 Reference GRCr8

Range

20696440..20752265 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_039083486.2 → XP_038939414.1 transcription factor EB isoform X2

UniProtKB/TrEMBL

A6JII2, A6JII3

Conserved Domains (3) summary

cd18927
Location:226 → 316

bHLHzip_TFEB; basic Helix-Loop-Helix-zipper (bHLHzip) domain found in transcription factor EB (TFEB) and similar proteins

pfam11851
Location:321 → 473

DUF3371; Domain of unknown function (DUF3371)

pfam15951
Location:4 → 162

MITF_TFEB_C_3_N; MITF/TFEB/TFEC/TFE3 N-terminus
XM_006244442.4 → XP_006244504.1 transcription factor EB isoform X2

See identical proteins and their annotated locations for XP_006244504.1

UniProtKB/TrEMBL

A6JII2, A6JII3

Conserved Domains (3) summary

cd18927
Location:226 → 316

bHLHzip_TFEB; basic Helix-Loop-Helix-zipper (bHLHzip) domain found in transcription factor EB (TFEB) and similar proteins

pfam11851
Location:321 → 473

DUF3371; Domain of unknown function (DUF3371)

pfam15951
Location:4 → 162

MITF_TFEB_C_3_N; MITF/TFEB/TFEC/TFE3 N-terminus
XM_039083488.2 → XP_038939416.1 transcription factor EB isoform X2

UniProtKB/TrEMBL

A6JII2, A6JII3

Conserved Domains (3) summary

cd18927
Location:226 → 316

bHLHzip_TFEB; basic Helix-Loop-Helix-zipper (bHLHzip) domain found in transcription factor EB (TFEB) and similar proteins

pfam11851
Location:321 → 473

DUF3371; Domain of unknown function (DUF3371)

pfam15951
Location:4 → 162

MITF_TFEB_C_3_N; MITF/TFEB/TFEC/TFE3 N-terminus
XM_006244446.5 → XP_006244508.1 transcription factor EB isoform X2

See identical proteins and their annotated locations for XP_006244508.1

UniProtKB/TrEMBL

A6JII2, A6JII3

Conserved Domains (3) summary

cd18927
Location:226 → 316

bHLHzip_TFEB; basic Helix-Loop-Helix-zipper (bHLHzip) domain found in transcription factor EB (TFEB) and similar proteins

pfam11851
Location:321 → 473

DUF3371; Domain of unknown function (DUF3371)

pfam15951
Location:4 → 162

MITF_TFEB_C_3_N; MITF/TFEB/TFEC/TFE3 N-terminus
XM_063267087.1 → XP_063123157.1 transcription factor EB isoform X1