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TFEB transcription factor EB [ Homo sapiens (human) ]

Gene ID: 7942, updated on 17-Jun-2019

Summary

Official Symbol
TFEBprovided by HGNC
Official Full Name
transcription factor EBprovided by HGNC
Primary source
HGNC:HGNC:11753
See related
Ensembl:ENSG00000112561 MIM:600744
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
TCFEB; BHLHE35; ALPHATFEB
Expression
Ubiquitous expression in spleen (RPKM 9.7), lymph node (RPKM 8.3) and 25 other tissues See more
Orthologs

Genomic context

See TFEB in Genome Data Viewer
Location:
6p21.1
Exon count:
17
Annotation release Status Assembly Chr Location
109.20190607 current GRCh38.p13 (GCF_000001405.39) 6 NC_000006.12 (41683978..41736223, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (41651716..41703997, complement)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene MyoD family inhibitor Neighboring gene nucleophosmin 1 pseudogene 51 Neighboring gene microRNA 10398 Neighboring gene progastricsin Neighboring gene fibroblast growth factor receptor substrate 3

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 FunctionsWhat's a GeneRIF?

Phenotypes

NHGRI GWAS Catalog

Description
Molecular genetics of adult ADHD: converging evidence from genome-wide association and extended pedigree linkage studies.
NHGRI GWA Catalog

HIV-1 interactions

Replication interactions

Interaction Pubs
HIV-1 activates (and dephosphorylates) TFEB in human macrophages at 24 hours post-treatment with purified HIV-1 virions PubMed

Protein interactions

Protein Gene Interaction Pubs
Nef nef HIV-1 Nef inhibits TFEB nuclear localization and autophagic flux; HIV-1 Nef is required for anti-autophagy during permissive (ongoing) HIV infection PubMed

Go to the HIV-1, Human Interaction Database

Pathways from BioSystems

  • Mitophagy - animal, organism-specific biosystem (from KEGG)
    Mitophagy - animal, organism-specific biosystemMitochondria act as the energy powerhouse of the cell, and are essential for eukaryotic cells to grow and function normally. However, deleterious byproducts of oxidative phosphorylation process calle...
  • Mitophagy - animal, conserved biosystem (from KEGG)
    Mitophagy - animal, conserved biosystemMitochondria act as the energy powerhouse of the cell, and are essential for eukaryotic cells to grow and function normally. However, deleterious byproducts of oxidative phosphorylation process calle...
  • PI3K-AKT-mTOR signaling pathway and therapeutic opportunities, organism-specific biosystem (from WikiPathways)
    PI3K-AKT-mTOR signaling pathway and therapeutic opportunities, organism-specific biosystemThis pathway is based on figure 1 from Merritt et al. (See Bibliography). The PI3K-AKT-mTOR signaling pathway has been shown to have a significant correlation with the development of castration-resis...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Process Evidence Code Pubs
adaptive immune response IEA
Inferred from Electronic Annotation
more info
 
autophagy IEA
Inferred from Electronic Annotation
more info
 
embryonic placenta development ISS
Inferred from Sequence or Structural Similarity
more info
 
humoral immune response ISS
Inferred from Sequence or Structural Similarity
more info
 
lysosome localization IMP
Inferred from Mutant Phenotype
more info
PubMed 
lysosome organization IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of autophagy IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of transcription, DNA-templated IDA
Inferred from Direct Assay
more info
PubMed 
regulation of transcription, DNA-templated NAS
Non-traceable Author Statement
more info
PubMed 
Component Evidence Code Pubs
cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 
nucleus NAS
Non-traceable Author Statement
more info
PubMed 

General protein information

Preferred Names
transcription factor EB
Names
T-cell transcription factor EB
class E basic helix-loop-helix protein 35

NCBI Reference Sequences (RefSeq)

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)

  1. NM_001167827.3NP_001161299.2  transcription factor EB isoform 2

    See identical proteins and their annotated locations for NP_001161299.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2, also known as TFEB-A) encodes the longest isoform (2).
    Source sequence(s)
    AJ608786, BC032448
    Consensus CDS
    CCDS64425.1
    UniProtKB/Swiss-Prot
    P19484
    UniProtKB/TrEMBL
    B0QYS6
    Related
    ENSP00000351742.2, ENST00000358871.6
    Conserved Domains (3) summary
    cd00083
    Location:247307
    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:335471
    DUF3371; Domain of unknown function (DUF3371)
    pfam15951
    Location:18175
    MITF_TFEB_C_3_N; MITF/TFEB/TFEC/TFE3 N-terminus
  2. NM_001271943.1NP_001258872.1  transcription factor EB isoform 3

    Status: VALIDATED

    Description
    Transcript Variant: This variant (5) contains an alternate 5' exon, which results in a downstream AUG start codon, and also lacks an in-frame coding exon, compared to variant 2. The resulting isoform (3) has a shorter N-terminus and lacks an internal segment, compared to isoform 2.
    Source sequence(s)
    AW294760, BC032448, CT000098
    Consensus CDS
    CCDS64424.1
    UniProtKB/Swiss-Prot
    P19484
    Related
    ENSP00000412551.1, ENST00000420312.5
    Conserved Domains (3) summary
    cd00083
    Location:148208
    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:236372
    DUF3371; Domain of unknown function (DUF3371)
    pfam15951
    Location:471
    MITF_TFEB_C_3_N; MITF/TFEB/TFEC/TFE3 N-terminus
  3. NM_001271944.2NP_001258873.1  transcription factor EB isoform 1

    See identical proteins and their annotated locations for NP_001258873.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) contains an alternate 5' exon, which results in a downstream AUG start codon, compared to variant 2. The resulting isoform (1) has a shorter N-terminus, compared to isoform 2. Variants 1, 3 and 4 encode the same isoform 1.
    Source sequence(s)
    AL365205, AW294760, BC032448
    Consensus CDS
    CCDS4858.1
    UniProtKB/Swiss-Prot
    P19484
    UniProtKB/TrEMBL
    A0A024RCY3
    Related
    ENSP00000362124.1, ENST00000373033.6
    Conserved Domains (2) summary
    cd00083
    Location:233293
    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, ...
    pfam15951
    Location:4161
    MITF_TFEB_C_3_N; MITF/TFEB/TFEC/TFE3 N-terminus
  4. NM_001271945.1NP_001258874.1  transcription factor EB isoform 1

    See identical proteins and their annotated locations for NP_001258874.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) contains an alternate 5' exon, which results in a downstream AUG start codon, compared to variant 2. The resulting isoform (1) has a shorter N-terminus, compared to isoform 2. Variants 1, 3 and 4 encode the same isoform 1.
    Source sequence(s)
    BC032448, BU527754
    Consensus CDS
    CCDS4858.1
    UniProtKB/Swiss-Prot
    P19484
    UniProtKB/TrEMBL
    A0A024RCY3
    Related
    ENSP00000384203.4, ENST00000403298.8
    Conserved Domains (2) summary
    cd00083
    Location:233293
    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, ...
    pfam15951
    Location:4161
    MITF_TFEB_C_3_N; MITF/TFEB/TFEC/TFE3 N-terminus
  5. NM_007162.2NP_009093.1  transcription factor EB isoform 1

    See identical proteins and their annotated locations for NP_009093.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) contains an alternate 5' sequence, which results in a downstream AUG start codon, compared to variant 2. The resulting isoform (1) has a shorter N-terminus, compared to isoform 2. Variants 1, 3 and 4 encode the same isoform 1.
    Source sequence(s)
    BC032448
    Consensus CDS
    CCDS4858.1
    UniProtKB/Swiss-Prot
    P19484
    UniProtKB/TrEMBL
    A0A024RCY3
    Related
    ENSP00000230323.4, ENST00000230323.8
    Conserved Domains (2) summary
    cd00083
    Location:233293
    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, ...
    pfam15951
    Location:4161
    MITF_TFEB_C_3_N; MITF/TFEB/TFEC/TFE3 N-terminus

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000006.12 Reference GRCh38.p13 Primary Assembly

    Range
    41683978..41736223 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005249411.1XP_005249468.1  transcription factor EB isoform X1

    See identical proteins and their annotated locations for XP_005249468.1

    UniProtKB/Swiss-Prot
    P19484
    UniProtKB/TrEMBL
    A0A024RCY3
    Conserved Domains (2) summary
    cd00083
    Location:233293
    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, ...
    pfam15951
    Location:4161
    MITF_TFEB_C_3_N; MITF/TFEB/TFEC/TFE3 N-terminus
  2. XM_011514915.1XP_011513217.1  transcription factor EB isoform X1

    See identical proteins and their annotated locations for XP_011513217.1

    UniProtKB/Swiss-Prot
    P19484
    UniProtKB/TrEMBL
    A0A024RCY3
    Conserved Domains (2) summary
    cd00083
    Location:233293
    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, ...
    pfam15951
    Location:4161
    MITF_TFEB_C_3_N; MITF/TFEB/TFEC/TFE3 N-terminus
  3. XM_005249412.1XP_005249469.1  transcription factor EB isoform X1

    See identical proteins and their annotated locations for XP_005249469.1

    UniProtKB/Swiss-Prot
    P19484
    UniProtKB/TrEMBL
    A0A024RCY3
    Conserved Domains (2) summary
    cd00083
    Location:233293
    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, ...
    pfam15951
    Location:4161
    MITF_TFEB_C_3_N; MITF/TFEB/TFEC/TFE3 N-terminus
  4. XM_006715212.4XP_006715275.1  transcription factor EB isoform X1

    See identical proteins and their annotated locations for XP_006715275.1

    UniProtKB/Swiss-Prot
    P19484
    UniProtKB/TrEMBL
    A0A024RCY3
    Conserved Domains (2) summary
    cd00083
    Location:233293
    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, ...
    pfam15951
    Location:4161
    MITF_TFEB_C_3_N; MITF/TFEB/TFEC/TFE3 N-terminus
  5. XM_011514916.2XP_011513218.1  transcription factor EB isoform X1

    See identical proteins and their annotated locations for XP_011513218.1

    UniProtKB/Swiss-Prot
    P19484
    UniProtKB/TrEMBL
    A0A024RCY3
    Conserved Domains (2) summary
    cd00083
    Location:233293
    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, ...
    pfam15951
    Location:4161
    MITF_TFEB_C_3_N; MITF/TFEB/TFEC/TFE3 N-terminus
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