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    TFCP2L1 transcription factor CP2 like 1 [ Homo sapiens (human) ]

    Gene ID: 29842, updated on 2-Nov-2024

    Summary

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    Official Symbol
    TFCP2L1provided by HGNC
    Official Full Name
    transcription factor CP2 like 1provided by HGNC
    Primary source
    HGNC:HGNC:17925
    See related
    Ensembl:ENSG00000115112 MIM:609785; AllianceGenome:HGNC:17925
    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
    LBP9; CRTR1; LBP-9
    Summary
    Enables RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Involved in regulation of transcription by RNA polymerase II. Predicted to be located in chromatin. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Biased expression in kidney (RPKM 25.1), salivary gland (RPKM 23.9) and 10 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See TFCP2L1 in Genome Data Viewer
    Location:
    2q14.2
    Exon count:
    19
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (121216587..121285202, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (121651879..121720501, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (121974163..122042778, complement)

    Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105373587 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:121828403-121828966 Neighboring gene VISTA enhancer hs522 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:121889594-121890232 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:121890689-121891190 Neighboring gene uncharacterized LOC105373588 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:121954553-121955451 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:121957297-121957798 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:121957799-121958298 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:121972077-121972577 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:121974845-121975346 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:122003829-122004330 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11920 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:122091915-122092848 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:122094177-122094762 Neighboring gene ribosomal protein S17 pseudogene 7 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:122109698-122109870 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16463 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:122140378-122140878 Neighboring gene cytoplasmic linker associated protein 1 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr2:122187059-122188258 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:122205649-122205872 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16464 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11922 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16465 Neighboring gene CLASP1 antisense RNA 1 Neighboring gene RNA, U4atac small nuclear

    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. [Functional state of the stomach in patients with diffuse toxic goiter and hypothyroidism]. Mukhamadieva GA. Vrach Delo, 1975 Jun. PMID 1173954
    2. Tfcp2l1 safeguards the maintenance of human embryonic stem cell self-renewal. Sun H, et al. J Cell Physiol, 2018 Sep. PMID 29323720
    3. The Transcription Factor TFCP2L1 is Associated with Myelination via miR708-5p Regulation in the Peripheral Nerve System. Sohn EJ, et al. Neurochem Res, 2022 Feb. PMID 34581937
    4. The transcription factor TFCP2L1 induces expression of distinct target genes and promotes self-renewal of mouse and human embryonic stem cells. Wang X, et al. J Biol Chem, 2019 Apr 12. PMID 30782842, Free PMC Article
    5. Phosphorylation of TFCP2L1 by CDK1 is required for stem cell pluripotency and bladder carcinogenesis. Heo J, et al. EMBO Mol Med, 2020 Jan 9. PMID 31709755, Free PMC Article

    See all (30) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. SMARCB1 regulates a TFCP2L1-MYC transcriptional switch promoting renal medullary carcinoma transformation and ferroptosis resistance.
      Title: SMARCB1 regulates a TFCP2L1-MYC transcriptional switch promoting renal medullary carcinoma transformation and ferroptosis resistance.
    2. The Transcription Factor TFCP2L1 is Associated with Myelination via miR708-5p Regulation in the Peripheral Nerve System.
      Title: The Transcription Factor TFCP2L1 is Associated with Myelination via miR708-5p Regulation in the Peripheral Nerve System.
    3. The transcription factor Tfcp2l1 promotes primordial germ cell-like cell specification of pluripotent stem cells.
      Title: The transcription factor Tfcp2l1 promotes primordial germ cell-like cell specification of pluripotent stem cells.
    4. Divergent roles for KLF4 and TFCP2L1 in naive ground state pluripotency and human primordial germ cell development.
      Title: Divergent roles for KLF4 and TFCP2L1 in naive ground state pluripotency and human primordial germ cell development.
    5. Phosphorylation of TFCP2L1 by CDK1 is required for stem cell pluripotency and bladder carcinogenesis.
      Title: Phosphorylation of TFCP2L1 by CDK1 is required for stem cell pluripotency and bladder carcinogenesis.
    6. These findings indicate that TFCP2L1 functions differently in naive and primed pluripotency, insights that may help elucidate the different states of pluripotency.
      Title: The transcription factor TFCP2L1 induces expression of distinct target genes and promotes self-renewal of mouse and human embryonic stem cells.
    7. these findings reveal the unique and crucial role of Tfcp2l1 in the determination of human embryonic stem cell fate.
      Title: Tfcp2l1 safeguards the maintenance of human embryonic stem cell self-renewal.
    8. Studies reveal that TFCP2, TFCP2L1, UBP1 belong to a transcription factors subfamily and involved in various aspects of cancer types and development as either proto-oncogenes or tumor suppressors. They can directly interact with each other; TFCP2, TFCP2L1 and UBP1 can form heteromeric DNA-binding complexes. In addition, TFCP2L1 can modulate the activity of TFCP2 and UBP1. [review]
      Title: TFCP2/TFCP2L1/UBP1 transcription factors in cancer.
    9. Study show that CRTR-1 is generally an activator of transcription and that it modulates the activity of other family members, CP2, NF2d9 and altNF2d9, in a cell specific manner.
      Title: Modulation of CP2 family transcriptional activity by CRTR-1 and sumoylation.
    10. LBP-1b and LBP-9 both stimulate LBP-32/MGR promoter activity.
      Title: LBP-1b, LBP-9, and LBP-32/MGR detected in syncytiotrophoblasts from first-trimester human placental tissue and their transcriptional regulation.
    Submit: New GeneRIF Correction See all GeneRIFs (11)

    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
    Identification of a susceptibility locus in STAT4 for Behçet's disease in Han Chinese in a genome-wide association study.
    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

    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 transcription activator 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 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 sequence-specific double-stranded DNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in cell morphogenesis IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in cytoplasm organization IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in determination of adult lifespan IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in epithelial cell maturation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in negative regulation of transcription by RNA polymerase II IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in positive regulation of growth IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in positive regulation of transcription by RNA polymerase II IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in regulation of transcription by RNA polymerase II IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in salivary gland development IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in chromatin ISA
    Inferred from Sequence Alignment
    more info
    		  
    located_in cytoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    transcription factor CP2-like protein 1
    Names
    CP2-related transcriptional repressor 1
    CRTR-1
    transcription factor LBP-9

    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_014553.3 → NP_055368.1  transcription factor CP2-like protein 1

      See identical proteins and their annotated locations for NP_055368.1

      Status: VALIDATED

      Source sequence(s)
      AC013399, AC079988, BC064698, BM055156
      Consensus CDS
      CCDS2134.1
      UniProtKB/Swiss-Prot
      Q4ZG43, Q9NZI6
      Related
      ENSP00000263707.5, ENST00000263707.6
      Conserved Domains (2) summary
      cd09590
      Location:310 → 376
      SAM_LBP9; SAM domain of LBP9 transcriptional factors
      pfam04516
      Location:34 → 237
      CP2; CP2 transcription factor

    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_000002.12 Reference GRCh38.p14 Primary Assembly

      Range
      121216587..121285202 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017003902.2 → XP_016859391.1  transcription factor CP2-like protein 1 isoform X1

    2. XM_047444020.1 → XP_047299976.1  transcription factor CP2-like protein 1 isoform X5

    3. XM_047444021.1 → XP_047299977.1  transcription factor CP2-like protein 1 isoform X5

    4. XM_017003903.1 → XP_016859392.1  transcription factor CP2-like protein 1 isoform X2

    5. XM_017003905.2 → XP_016859394.1  transcription factor CP2-like protein 1 isoform X4

      UniProtKB/TrEMBL
      Q5JV87

    6. XM_017003904.2 → XP_016859393.1  transcription factor CP2-like protein 1 isoform X3

      UniProtKB/TrEMBL
      Q5JV87
      Conserved Domains (1) summary
      pfam04516
      Location:34 → 237
      CP2; CP2 transcription factor

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060926.1 Alternate T2T-CHM13v2.0

      Range
      121651879..121720501 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054341547.1 → XP_054197522.1  transcription factor CP2-like protein 1 isoform X1

    2. XM_054341551.1 → XP_054197526.1  transcription factor CP2-like protein 1 isoform X5

    3. XM_054341552.1 → XP_054197527.1  transcription factor CP2-like protein 1 isoform X5

    4. XM_054341548.1 → XP_054197523.1  transcription factor CP2-like protein 1 isoform X2

    5. XM_054341550.1 → XP_054197525.1  transcription factor CP2-like protein 1 isoform X4

    6. XM_054341549.1 → XP_054197524.1  transcription factor CP2-like protein 1 isoform X3

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9NZI6.1 GenPept UniProtKB/Swiss-Prot:Q9NZI6

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