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    TCFL5 transcription factor like 5 [ Homo sapiens (human) ]

    Gene ID: 10732, updated on 28-Oct-2024

    Summary

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    Official Symbol
    TCFL5provided by HGNC
    Official Full Name
    transcription factor like 5provided by HGNC
    Primary source
    HGNC:HGNC:11646
    See related
    Ensembl:ENSG00000101190 MIM:604745; AllianceGenome:HGNC:11646
    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
    CHA; Figlb; SOSF1; E2BP-1; bHLHe82
    Summary
    Enables DNA-binding transcription repressor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Involved in several processes, including negative regulation of transcription by RNA polymerase II; regulation of cell population proliferation; and spermatogenesis. Located in nucleus. [provided by Alliance of Genome Resources, Oct 2024]
    Expression
    Broad expression in testis (RPKM 22.8), thyroid (RPKM 7.1) and 19 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See TCFL5 in Genome Data Viewer
    Location:
    20q13.33
    Exon count:
    9
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (62841005..62861822, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (64640566..64661385, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (61472357..61493174, complement)

    Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13120 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:61435960-61436865 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13124 Neighboring gene OGFR antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13125 Neighboring gene MRG domain binding protein Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:61446582-61447268 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:61447957-61448642 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:61449331-61450016 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:61450017-61450704 Neighboring gene opioid growth factor receptor Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:61454586-61455274 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:61455275-61455962 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13126 Neighboring gene collagen type IX alpha 3 chain Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:61461792-61462748 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:61462749-61463704 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:61463705-61464661 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:61464662-61465617 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr20:61467141-61468340 Neighboring gene Sharpr-MPRA regulatory region 13411 Neighboring gene diphthamide biosynthesis 3 pseudogene 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13127 Neighboring gene uncharacterized LOC105372717 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:61492967-61493621 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:61506686-61507340 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:61507341-61507994 Neighboring gene Sharpr-MPRA regulatory region 11652 Neighboring gene MPRA-validated peak4302 silencer Neighboring gene ARF GTPase 4 pseudogene 2 Neighboring gene small nucleolar RNA, H/ACA box 117 Neighboring gene death inducer-obliterator 1

    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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    Related articles in PubMed

    1. Isoform-specific effects of transcription factor TCFL5 on the pluripotency-related genes SOX2 and KLF4 in colorectal cancer development. Galán-Martínez J, et al. Mol Oncol, 2022 May. PMID 34623757, Free PMC Article
    2. Dominant T- and B-cell epitopes in an autoantigen linked to Chagas' disease. Gironès N, et al. J Clin Invest, 2001 Apr. PMID 11306602, Free PMC Article
    3. Cloning of TCFL5 encoding a novel human basic helix-loop-helix motif protein that is specifically expressed in primary spermatocytes at the pachytene stage. Maruyama O, et al. Cytogenet Cell Genet, 1998. PMID 9763657
    4. PCR based detection of HPV 16 and 18 genotypes in normal oral mucosa of tobacco users and non-users. Pattanshetty S, et al. Biotech Histochem, 2014 Aug. PMID 24588599
    5. TCFL5 knockdown sensitizes DLBCL to doxorubicin treatment via regulation of GPX4. Lu X, et al. Cell Signal, 2023 Oct. PMID 37516394

    See all (19) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. TCFL5 knockdown sensitizes DLBCL to doxorubicin treatment via regulation of GPX4.
      Title: TCFL5 knockdown sensitizes DLBCL to doxorubicin treatment via regulation of GPX4.
    2. Isoform-specific effects of transcription factor TCFL5 on the pluripotency-related genes SOX2 and KLF4 in colorectal cancer development.
      Title: Isoform-specific effects of transcription factor TCFL5 on the pluripotency-related genes SOX2 and KLF4 in colorectal cancer development.
    3. Report differential expression of TCFL5 in normal human spermatogenesis, testicular mixed germ cell-sex cord stromal tumor, spermatocytic tumor, and seminoma.
      Title: Protein expression of the transcription factors DMRT1, TCLF5, and OCT4 in selected germ cell neoplasms of the testis.
    4. HPVs16 and 18 commonly are present in normal oral mucosa and emphasize the importance of distinguishing clinical
      Title: PCR based detection of HPV 16 and 18 genotypes in normal oral mucosa of tobacco users and non-users.
    5. A protein encoded by this locus was found to be differentially expressed in postmortem brains from patients with atypical frontotemporal lobar degeneration.
      Title: Proteomic analysis identifies dysfunction in cellular transport, energy, and protein metabolism in different brain regions of atypical frontotemporal lobar degeneration.
    6. Cha is a new bHLH transcription factor that negatively regulates upstream transcription factor-dependent transcription
      Title: Cha, a basic helix-loop-helix transcription factor involved in the regulation of upstream stimulatory factor activity.
    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

    HIV-1 interactions

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    Replication interactions

    Interaction Pubs
    Knockdown of transcription factor-like 5 (basic helix-loop-helix) (TCFL5) by siRNA inhibits HIV-1 replication in HeLa P4/R5 cells PubMed

    Go to the HIV-1, Human Interaction Database

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC46135

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables DNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables DNA-binding transcription factor activity TAS
    Traceable Author Statement
    more info
    		 PubMed 
    enables DNA-binding transcription factor activity, RNA polymerase II-specific IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables DNA-binding transcription factor activity, RNA polymerase II-specific ISA
    Inferred from Sequence Alignment
    more info
    		  
    enables DNA-binding transcription repressor activity, RNA polymerase II-specific IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    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 IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables protein dimerization activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables sequence-specific double-stranded DNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in cell differentiation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in negative regulation of transcription by RNA polymerase II IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in regulation of DNA-templated transcription IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in regulation of DNA-templated transcription IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in regulation of cell differentiation IEP
    Inferred from Expression Pattern
    more info
    		 PubMed 
    involved_in regulation of cell population proliferation IEP
    Inferred from Expression Pattern
    more info
    		 PubMed 
    involved_in spermatogenesis IEP
    Inferred from Expression Pattern
    more info
    		 PubMed 
    involved_in transcription by RNA polymerase II TAS
    Traceable Author Statement
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in chromatin ISA
    Inferred from Sequence Alignment
    more info
    		  
    located_in male germ cell nucleus IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    transcription factor-like 5 protein
    Names
    HPV-16 E2-binding protein 1
    cha transcription factor
    spermatogenesis- and oogenesis-specific bHLH-containing protein 1
    transcription factor-like 5 (basic helix-loop-helix)

    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_001301726.2 → NP_001288655.1  transcription factor-like 5 protein isoform 2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) uses an alternate in-frame splice site and contains an alternate exon in the 3' coding region, which results in the use of a distinct stop codon, compared to variant 1. The encoded isoform (2) is shorter and has a distinct C-terminus, compared to isoform 1.
      Source sequence(s)
      AL035669, BC046933, BC065520, BU632218
      UniProtKB/TrEMBL
      F8W9A4

    2. NM_006602.4 → NP_006593.2  transcription factor-like 5 protein isoform 1

      See identical proteins and their annotated locations for NP_006593.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AB012124, AL035669, BC046933, CA419503
      Consensus CDS
      CCDS13506.1
      UniProtKB/Swiss-Prot
      O94771, Q9BYW0, Q9UL49
      UniProtKB/TrEMBL
      F8W9A4
      Related
      ENSP00000334294.3, ENST00000335351.8

    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_000020.11 Reference GRCh38.p14 Primary Assembly

      Range
      62841005..62861822 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_024451813.2 → XP_024307581.1  transcription factor-like 5 protein isoform X9

    2. XM_005260185.5 → XP_005260242.1  transcription factor-like 5 protein isoform X3

      UniProtKB/TrEMBL
      F8W9A4

    3. XM_024451812.2 → XP_024307580.1  transcription factor-like 5 protein isoform X8

    4. XM_047439840.1 → XP_047295796.1  transcription factor-like 5 protein isoform X11

    5. XM_011528497.4 → XP_011526799.1  transcription factor-like 5 protein isoform X2

      UniProtKB/TrEMBL
      F8W9A4

    6. XM_024451808.2 → XP_024307576.1  transcription factor-like 5 protein isoform X1

      UniProtKB/TrEMBL
      F8W9A4
      Related
      ENSP00000217162.5, ENST00000217162.5

    7. XM_024451810.2 → XP_024307578.1  transcription factor-like 5 protein isoform X6

      UniProtKB/TrEMBL
      F8W9A4

    8. XM_047439838.1 → XP_047295794.1  transcription factor-like 5 protein isoform X5

    9. XM_024451809.2 → XP_024307577.1  transcription factor-like 5 protein isoform X4

      UniProtKB/TrEMBL
      F8W9A4

    10. XM_024451811.2 → XP_024307579.1  transcription factor-like 5 protein isoform X7

      UniProtKB/TrEMBL
      F8W9A4

    11. XM_047439839.1 → XP_047295795.1  transcription factor-like 5 protein isoform X10

    RNA

    1. XR_007067444.1 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060944.1 Alternate T2T-CHM13v2.0

      Range
      64640566..64661385 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054322861.1 → XP_054178836.1  transcription factor-like 5 protein isoform X9

    2. XM_054322855.1 → XP_054178830.1  transcription factor-like 5 protein isoform X3

    3. XM_054322860.1 → XP_054178835.1  transcription factor-like 5 protein isoform X8

    4. XM_054322864.1 → XP_054178839.1  transcription factor-like 5 protein isoform X11

    5. XM_054322854.1 → XP_054178829.1  transcription factor-like 5 protein isoform X2

    6. XM_054322853.1 → XP_054178828.1  transcription factor-like 5 protein isoform X1

    7. XM_054322858.1 → XP_054178833.1  transcription factor-like 5 protein isoform X6

    8. XM_054322857.1 → XP_054178832.1  transcription factor-like 5 protein isoform X5

    9. XM_054322856.1 → XP_054178831.1  transcription factor-like 5 protein isoform X4

    10. XM_054322859.1 → XP_054178834.1  transcription factor-like 5 protein isoform X7

    11. XM_054322862.1 → XP_054178837.1  transcription factor-like 5 protein isoform X12

    12. XM_054322863.1 → XP_054178838.1  transcription factor-like 5 protein isoform X10

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9UL49.2 GenPept UniProtKB/Swiss-Prot:Q9UL49

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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