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TFPT TCF3 fusion partner [ Homo sapiens (human) ]

Gene ID: 29844, updated on 2-Nov-2024

Summary

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Official Symbol
TFPTprovided by HGNC
Official Full Name
TCF3 fusion partnerprovided by HGNC
Primary source
HGNC:HGNC:13630
See related
Ensembl:ENSG00000105619 MIM:609519; AllianceGenome:HGNC:13630
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
FB1; amida; INO80F
Summary
Predicted to enable DNA binding activity. Involved in several processes, including apoptotic signaling pathway; chromatin remodeling; and regulation of nucleobase-containing compound metabolic process. Located in nucleoplasm. Part of Ino80 complex. [provided by Alliance of Genome Resources, Nov 2024]
Expression
Ubiquitous expression in brain (RPKM 11.2), prostate (RPKM 8.4) and 25 other tissues See more
Orthologs
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Genomic context

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See TFPT in Genome Data Viewer
Location:
19q13.42
Exon count:
7
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (54107020..54115657, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (57185717..57194354, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (54610327..54619037, complement)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene T cell-interacting, activating receptor on myeloid cells 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:54605952-54606928 Neighboring gene osteoclast associated Ig-like receptor Neighboring gene NADH:ubiquinone oxidoreductase subunit A3 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:54617323-54618196 Neighboring gene PRPF31 antisense RNA 1 Neighboring gene pre-mRNA processing factor 31 Neighboring gene CCR4-NOT transcription complex subunit 3 Neighboring gene uncharacterized LOC102724273

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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?
  1. TCF3/E2A is Conserved Specific Coregulators of the p21:PUMA Expression Ratio.
    Title: A genetic screen identifies TCF3/E2A and TRIAP1 as pathway-specific regulators of the cellular response to p53 activation.
  2. Characterization of the core promoters controlling the expression of PRPF31 and TFPT, a bi-directional gene-pair.
    Title: Expression of PRPF31 and TFPT: regulation in health and retinal disease.
  3. FB1 is an important binding partner and a functional regulator of U19/EAF2, EAF1, and/or ELL.
    Title: FB1, an E2A fusion partner in childhood leukemia, interacts with U19/EAF2 and inhibits its transcriptional activity.
  4. Although p53 is a main regulator of apoptosis in mammalian cells, the Tfpt induced apoptosis appears p53-independent.
    Title: Apoptosis promoted by up-regulation of TFPT (TCF3 fusion partner) appears p53 independent, cell type restricted and cell density influenced.
Submit: New GeneRIF Correction

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

EBI GWAS Catalog

Description
Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables DNA binding ISS
Inferred from Sequence or Structural Similarity
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein kinase binding IEA
Inferred from Electronic Annotation
more info
  
enables protein-containing complex binding IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
involved_in DNA recombination IEA
Inferred from Electronic Annotation
more info
  
involved_in DNA repair IEA
Inferred from Electronic Annotation
more info
  
involved_in apoptotic signaling pathway IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in apoptotic signaling pathway IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in chromatin remodeling IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in male gonad development IEA
Inferred from Electronic Annotation
more info
  
involved_in positive regulation of DNA repair ISO
Inferred from Sequence Orthology
more info
  
involved_in positive regulation of DNA-templated transcription IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in positive regulation of apoptotic process IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in positive regulation of telomere maintenance in response to DNA damage ISO
Inferred from Sequence Orthology
more info
  
involved_in regulation of DNA repair ISO
Inferred from Sequence Orthology
more info
  
involved_in regulation of DNA replication IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in regulation of DNA strand elongation IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in regulation of cell cycle IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in regulation of chromosome organization IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in regulation of embryonic development ISO
Inferred from Sequence Orthology
more info
  
involved_in telomere maintenance ISO
Inferred from Sequence Orthology
more info
  
Component Evidence Code Pubs
part_of Ino80 complex IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of Ino80 complex IDA
Inferred from Direct Assay
more info
 PubMed 
located_in actin filament IEA
Inferred from Electronic Annotation
more info
  
located_in cytoplasm ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
  
located_in nucleoplasm TAS
Traceable Author Statement
more info
  
located_in nucleus ISS
Inferred from Sequence or Structural Similarity
more info
  

General protein information

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Preferred Names
TCF3 fusion partner
Names
INO80 complex subunit F
TCF3 (E2A) fusion partner (in childhood Leukemia)
amida, partner of the E2A

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)

  1. NM_001321792.2 → NP_001308721.1  TCF3 fusion partner isoform 2

    Status: VALIDATED

    Source sequence(s)
    AC245052, BC001728
    Consensus CDS
    CCDS82396.1
    UniProtKB/Swiss-Prot
    P0C1Z6
    Related
    ENSP00000375638.1, ENST00000391758.5

  2. NM_013342.4 → NP_037474.1  TCF3 fusion partner isoform 1

    See identical proteins and their annotated locations for NP_037474.1

    Status: VALIDATED

    Source sequence(s)
    AF052052, BI820344, BQ027375
    Consensus CDS
    CCDS12878.1
    UniProtKB/Swiss-Prot
    G5E9B5, P0C1Z6
    Related
    ENSP00000375639.1, ENST00000391759.6

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

  1. NC_000019.10 Reference GRCh38.p14 Primary Assembly

    Range
    54107020..54115657 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005278261.2 → XP_005278318.1  TCF3 fusion partner isoform X1

    See identical proteins and their annotated locations for XP_005278318.1

Reference GRCh38.p14 ALT_REF_LOCI_1

Genomic

  1. NW_003571054.1 Reference GRCh38.p14 ALT_REF_LOCI_1

    Range
    81440..90150 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054329680.1 → XP_054185655.1  TCF3 fusion partner isoform X1

Reference GRCh38.p14 ALT_REF_LOCI_2

Genomic

  1. NW_003571055.2 Reference GRCh38.p14 ALT_REF_LOCI_2

    Range
    81440..90150 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054330165.1 → XP_054186140.1  TCF3 fusion partner isoform X1

Reference GRCh38.p14 ALT_REF_LOCI_3

Genomic

  1. NW_003571056.2 Reference GRCh38.p14 ALT_REF_LOCI_3

    Range
    81440..90150 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054330473.1 → XP_054186448.1  TCF3 fusion partner isoform X1

Reference GRCh38.p14 ALT_REF_LOCI_4

Genomic

  1. NW_003571057.2 Reference GRCh38.p14 ALT_REF_LOCI_4

    Range
    81440..90150 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054330726.1 → XP_054186701.1  TCF3 fusion partner isoform X1

Reference GRCh38.p14 ALT_REF_LOCI_5

Genomic

  1. NW_003571058.2 Reference GRCh38.p14 ALT_REF_LOCI_5

    Range
    81440..90150 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054330955.1 → XP_054186930.1  TCF3 fusion partner isoform X1

Reference GRCh38.p14 ALT_REF_LOCI_6

Genomic

  1. NW_003571059.2 Reference GRCh38.p14 ALT_REF_LOCI_6

    Range
    81440..90150 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054331235.1 → XP_054187210.1  TCF3 fusion partner isoform X1

Reference GRCh38.p14 ALT_REF_LOCI_7

Genomic

  1. NW_003571060.1 Reference GRCh38.p14 ALT_REF_LOCI_7

    Range
    81440..90150 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054331510.1 → XP_054187485.1  TCF3 fusion partner isoform X1

Reference GRCh38.p14 ALT_REF_LOCI_8

Genomic

  1. NW_003571061.2 Reference GRCh38.p14 ALT_REF_LOCI_8

    Range
    81440..90150 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054333545.1 → XP_054189520.1  TCF3 fusion partner isoform X1

Reference GRCh38.p14 ALT_REF_LOCI_9

Genomic

  1. NT_187693.1 Reference GRCh38.p14 ALT_REF_LOCI_9

    Range
    81440..90150 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054333646.1 → XP_054189621.1  TCF3 fusion partner isoform X1

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    57185717..57194354 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054320762.1 → XP_054176737.1  TCF3 fusion partner isoform X1

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P0C1Z6.1 GenPept UniProtKB/Swiss-Prot:P0C1Z6

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