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    TCOF1 treacle ribosome biogenesis factor 1 [ Homo sapiens (human) ]

    Gene ID: 6949, updated on 6-Jun-2017
    Official Symbol
    TCOF1provided by HGNC
    Official Full Name
    treacle ribosome biogenesis factor 1provided by HGNC
    Primary source
    HGNC:HGNC:11654
    See related
    Ensembl:ENSG00000070814 MIM:606847; Vega:OTTHUMG00000130081
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    TCS; MFD1; TCS1; treacle
    Summary
    This gene encodes a nucleolar protein with a LIS1 homology domain. The protein is involved in ribosomal DNA gene transcription through its interaction with upstream binding factor (UBF). Mutations in this gene have been associated with Treacher Collins syndrome, a disorder which includes abnormal craniofacial development. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2008]
    Orthologs
    Location:
    5q32-q33.1
    Exon count:
    29
    Annotation release Status Assembly Chr Location
    108 current GRCh38.p7 (GCF_000001405.33) 5 NC_000005.10 (150357639..150400308)
    105 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (149737202..149779871)

    Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105378225 Neighboring gene uncharacterized LOC105378226 Neighboring gene CD74 molecule Neighboring gene ribosomal protein S14

    • 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 Jun 15 11:32:44 2016

    GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

    Associated conditions

    Description Tests
    Treacher Collins syndrome 1
    MedGen: CN119605 OMIM: 154500 GeneReviews: Treacher Collins Syndrome
    Compare labs

    Copy number response

    Description
    Copy number response
    Triplosensitivity

    No evidence available (Last evaluated (2011-11-17)

    ClinGen Genome Curation Page
    Haploinsufficency

    Sufficient evidence for dosage pathogenicity (Last evaluated (2011-11-17)

    ClinGen Genome Curation PagePubMed

    Protein interactions

    Protein Gene Interaction Pubs
    Pr55(Gag) gag HIV-1 Gag interacts with TCOF1 as demonstrated by proximity dependent biotinylation proteomics PubMed

    Go to the HIV-1, Human Interaction Database

    • Ribosome biogenesis in eukaryotes, organism-specific biosystem (from KEGG)
      Ribosome biogenesis in eukaryotes, organism-specific biosystemRibosomes are the cellular factories responsible for making proteins. In eukaryotes, ribosome biogenesis involves the production and correct assembly of four rRNAs and about 80 ribosomal proteins. It...
    • Ribosome biogenesis in eukaryotes, conserved biosystem (from KEGG)
      Ribosome biogenesis in eukaryotes, conserved biosystemRibosomes are the cellular factories responsible for making proteins. In eukaryotes, ribosome biogenesis involves the production and correct assembly of four rRNAs and about 80 ribosomal proteins. It...
    Products Interactant Other Gene Complex Source Pubs Description

    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    RNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    RNA polymerase I core binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    protein heterodimerization activity IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    transporter activity TAS
    Traceable Author Statement
    more info
    PubMed 
    Process Evidence Code Pubs
    neural crest cell development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    neural crest formation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    regulation of translation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    skeletal system development TAS
    Traceable Author Statement
    more info
    PubMed 
    transport IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    cytosol IDA
    Inferred from Direct Assay
    more info
     
    fibrillar center IDA
    Inferred from Direct Assay
    more info
     
    nucleolus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    nucleus IDA
    Inferred from Direct Assay
    more info
     
    Preferred Names
    treacle protein
    Names
    Treacher Collins syndrome protein
    Treacher Collins-Franceschetti syndrome 1
    nucleolar trafficking phosphoprotein

    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.

    Genomic

    1. NG_011341.1 RefSeqGene

      Range
      5001..47670
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_000356.3NP_000347.2  treacle protein isoform b

      See identical proteins and their annotated locations for NP_000347.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks the alternate in-frame exon 7, also known as VIa, in the 5' coding region, compared to variant 4. The resulting isoform (b) lacks an internal segment but has the same N- and C-termini, compared to isoform d.
      Source sequence(s)
      AC011372, BC016144, BM664489, DC377932, U76366
      Consensus CDS
      CCDS4306.1
      UniProtKB/Swiss-Prot
      Q13428
      Related
      ENSP00000325223.6, OTTHUMP00000160560, ENST00000323668.11, OTTHUMT00000252374
      Conserved Domains (2) summary
      smart00667
      Location:637
      LisH; Lissencephaly type-1-like homology motif
      pfam03546
      Location:239827
      Treacle; Treacher Collins syndrome protein Treacle
    2. NM_001008657.2NP_001008657.1  treacle protein isoform c

      See identical proteins and their annotated locations for NP_001008657.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) uses an alternate terminal exon and lacks 10 3' exons, compared to variant 4. The resulting isoform (c) has a significantly shorter and distinct C-terminus, compared to isoform d.
      Source sequence(s)
      AC011372, AI939467, AW135418, BC011764, DC377932
      Consensus CDS
      CCDS47307.1
      UniProtKB/Swiss-Prot
      Q13428
      Related
      ENSP00000377811.3, OTTHUMP00000224043, ENST00000394269.7, OTTHUMT00000373676
      Conserved Domains (2) summary
      smart00667
      Location:637
      LisH; Lissencephaly type-1-like homology motif
      pfam03546
      Location:316904
      Treacle; Treacher Collins syndrome protein Treacle
    3. NM_001135243.1NP_001128715.1  treacle protein isoform d

      See identical proteins and their annotated locations for NP_001128715.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) represents the longest transcript and encodes the longest isoform (d).
      Source sequence(s)
      AC011372, AY460334, BC016144, BM664489, DC377932, U76366
      Consensus CDS
      CCDS54936.1
      UniProtKB/Swiss-Prot
      Q13428
      Related
      ENSP00000367028.4, ENST00000377797.7
      Conserved Domains (2) summary
      smart00667
      Location:637
      LisH; Lissencephaly type-1-like homology motif
      pfam03546
      Location:316904
      Treacle; Treacher Collins syndrome protein Treacle
    4. NM_001135244.1NP_001128716.1  treacle protein isoform e

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) lacks the alternate in-frame exon 21, also known as XIX, and uses an alternate in-frame splice site in the central coding region, compared to variant 4. The resulting isoform (e) lacks an internal segment, contains a one residue insertion, and has the same N- and C-termini, compared to isoform d.
      Source sequence(s)
      AC011372, AK303611, BC016144, BM664489, DC377932, U76366
      Consensus CDS
      CCDS47305.1
      UniProtKB/Swiss-Prot
      Q13428
      Related
      ENSP00000406888.2, OTTHUMP00000224041, ENST00000439160.6, OTTHUMT00000373674
      Conserved Domains (2) summary
      smart00667
      Location:637
      LisH; Lissencephaly type-1-like homology motif
      pfam03546
      Location:316904
      Treacle; Treacher Collins syndrome protein Treacle
    5. NM_001135245.1NP_001128717.1  treacle protein isoform f

      Status: REVIEWED

      Description
      Transcript Variant: This variant (6) lacks the alternate in-frame exon 7, also known as VIa, in the 5' coding region and uses an alternate in-frame splice site in the central coding region, compared to variant 4. The resulting isoform (f) lacks an internal segment, contains a one residue insertion, and has the same N- and C-termini, compared to isoform d.
      Source sequence(s)
      AC011372, AK299167, BC027252, BM664489, DC377932, U76366
      Consensus CDS
      CCDS47306.1
      UniProtKB/Swiss-Prot
      Q13428
      UniProtKB/TrEMBL
      B4DRA2
      Related
      ENSP00000409944.2, OTTHUMP00000224042, ENST00000445265.6, OTTHUMT00000373675
      Conserved Domains (2) summary
      smart00667
      Location:637
      LisH; Lissencephaly type-1-like homology motif
      pfam03546
      Location:239827
      Treacle; Treacher Collins syndrome protein Treacle
    6. NM_001195141.1NP_001182070.1  treacle protein isoform g

      See identical proteins and their annotated locations for NP_001182070.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (7) lacks an alternate in-frame exon in the 3' coding region, compared to variant 4. This results in a shorter protein (isoform g), compared to isoform d.
      Source sequence(s)
      AC011372, BC016144, BM664489, DC377932, U76366
      UniProtKB/Swiss-Prot
      Q13428
      Related
      ENSP00000390717.2, OTTHUMP00000231643, ENST00000427724.6, OTTHUMT00000387324
      Conserved Domains (2) summary
      smart00667
      Location:637
      LisH; Lissencephaly type-1-like homology motif
      pfam03546
      Location:316904
      Treacle; Treacher Collins syndrome protein Treacle

    RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 108 details...Open this link in a new tab

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

    Reference GRCh38.p7 Primary Assembly

    Genomic

    1. NC_000005.10 Reference GRCh38.p7 Primary Assembly

      Range
      150357639..150400308
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_005268502.3XP_005268559.1  treacle protein isoform X1

      Conserved Domains (2) summary
      smart00667
      Location:637
      LisH; Lissencephaly type-1-like homology motif
      pfam03546
      Location:316904
      Treacle; Treacher Collins syndrome protein Treacle
    2. XM_005268504.3XP_005268561.1  treacle protein isoform X3

      Conserved Domains (2) summary
      smart00667
      Location:637
      LisH; Lissencephaly type-1-like homology motif
      pfam03546
      Location:316904
      Treacle; Treacher Collins syndrome protein Treacle
    3. XM_005268506.3XP_005268563.1  treacle protein isoform X5

      UniProtKB/TrEMBL
      E7ETY2
      Related
      ENSP00000427484.1, OTTHUMP00000224077, ENST00000513346.5, OTTHUMT00000373744
      Conserved Domains (2) summary
      smart00667
      Location:637
      LisH; Lissencephaly type-1-like homology motif
      pfam03546
      Location:316904
      Treacle; Treacher Collins syndrome protein Treacle
    4. XM_017009792.1XP_016865281.1  treacle protein isoform X6

    5. XM_005268503.3XP_005268560.1  treacle protein isoform X2

      Conserved Domains (2) summary
      smart00667
      Location:637
      LisH; Lissencephaly type-1-like homology motif
      pfam03546
      Location:316904
      Treacle; Treacher Collins syndrome protein Treacle
    6. XM_005268505.3XP_005268562.1  treacle protein isoform X4

      UniProtKB/Swiss-Prot
      Q13428
      Conserved Domains (2) summary
      smart00667
      Location:637
      LisH; Lissencephaly type-1-like homology motif
      pfam03546
      Location:316904
      Treacle; Treacher Collins syndrome protein Treacle
    7. XM_011537678.2XP_011535980.1  treacle protein isoform X7

      Conserved Domains (2) summary
      smart00667
      Location:637
      LisH; Lissencephaly type-1-like homology motif
      pfam03546
      Location:388901
      Treacle; Treacher Collins syndrome protein Treacle
    8. XM_017009793.1XP_016865282.1  treacle protein isoform X9

    9. XM_017009794.1XP_016865283.1  treacle protein isoform X10

    10. XM_005268507.3XP_005268564.1  treacle protein isoform X8

      Conserved Domains (2) summary
      smart00667
      Location:637
      LisH; Lissencephaly type-1-like homology motif
      pfam03546
      Location:239827
      Treacle; Treacher Collins syndrome protein Treacle
    11. XM_005268508.3XP_005268565.1  treacle protein isoform X11

      Conserved Domains (2) summary
      smart00667
      Location:637
      LisH; Lissencephaly type-1-like homology motif
      pfam03546
      Location:316904
      Treacle; Treacher Collins syndrome protein Treacle
    12. XM_005268509.3XP_005268566.1  treacle protein isoform X12

      Conserved Domains (2) summary
      smart00667
      Location:637
      LisH; Lissencephaly type-1-like homology motif
      pfam03546
      Location:316904
      Treacle; Treacher Collins syndrome protein Treacle
    13. XM_017009795.1XP_016865284.1  treacle protein isoform X13

    RNA

    1. XR_427778.2 RNA Sequence

    2. XR_427780.2 RNA Sequence

    3. XR_427779.1 RNA Sequence

    Alternate CHM1_1.1

    Genomic

    1. NC_018916.2 Alternate CHM1_1.1

      Range
      149169776..149212290
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_001008656.2: Suppressed sequence

      Description
      NM_001008656.2: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.
    Support Center