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

Gene ID: 6949, updated on 5-Sep-2021

Summary

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
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]
Expression
Ubiquitous expression in lymph node (RPKM 7.8), appendix (RPKM 6.8) and 25 other tissues See more
Orthologs
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Try the new Transcript table

Genomic context

See TCOF1 in Genome Data Viewer
Location:
5q32-q33.1
Exon count:
29
Annotation release Status Assembly Chr Location
109.20210514 current GRCh38.p13 (GCF_000001405.39) 5 NC_000005.10 (150357697..150400306)
105.20201022 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (149737260..149779856)

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

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 Functions

What's a GeneRIF?

Phenotypes

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
Haploinsufficency

Sufficient evidence for dosage pathogenicity (Last evaluated 2021-04-28)

ClinGen Genome Curation PagePubMed
Triplosensitivity

No evidence available (Last evaluated 2021-04-28)

ClinGen Genome Curation Page

HIV-1 interactions

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

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables RNA binding HDA PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables protein heterodimerization activity IPI
Inferred from Physical Interaction
more info
PubMed 
enables protein-macromolecule adaptor activity IDA
Inferred from Direct Assay
more info
PubMed 
enables scaffold protein binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
enables scaffold protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables transporter activity TAS
Traceable Author Statement
more info
PubMed 
Process Evidence Code Pubs
involved_in neural crest cell development IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in neural crest formation IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in nucleolar large rRNA transcription by RNA polymerase I IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in regulation of translation IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in skeletal system development TAS
Traceable Author Statement
more info
PubMed 
Component Evidence Code Pubs
located_in cytosol IDA
Inferred from Direct Assay
more info
 
located_in fibrillar center IDA
Inferred from Direct Assay
more info
 
is_active_in nucleolus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
located_in nucleolus IDA
Inferred from Direct Assay
more info
PubMed 
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
 

General protein information

Preferred Names
treacle protein
Names
Treacher Collins syndrome protein
Treacher Collins-Franceschetti syndrome 1
nucleolar trafficking phosphoprotein

NCBI Reference Sequences (RefSeq)

NEW Try the new Transcript table

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
    5059..47655
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_000356.4NP_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)
    BC016144, BM664489, U76366
    Consensus CDS
    CCDS4306.1
    UniProtKB/Swiss-Prot
    Q13428
    Related
    ENSP00000325223.6, ENST00000323668.11
    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_001008657.3NP_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
    Consensus CDS
    CCDS47307.1
    UniProtKB/Swiss-Prot
    Q13428
    Related
    ENSP00000377811.3, ENST00000394269.7
    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_001135243.2NP_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, 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_001135244.2NP_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, U76366
    Consensus CDS
    CCDS47305.1
    UniProtKB/Swiss-Prot
    Q13428
    Related
    ENSP00000406888.2, ENST00000439160.6
    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_001135245.2NP_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, U76366
    Consensus CDS
    CCDS47306.1
    UniProtKB/Swiss-Prot
    Q13428
    UniProtKB/TrEMBL
    B4DRA2
    Related
    ENSP00000409944.2, ENST00000445265.6
    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_001195141.2NP_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, U76366
    UniProtKB/Swiss-Prot
    Q13428
    Related
    ENSP00000390717.3, ENST00000427724.7
    Conserved Domains (2) summary
    smart00667
    Location:637
    LisH; Lissencephaly type-1-like homology motif
    pfam03546
    Location:316904
    Treacle; Treacher Collins syndrome protein Treacle
  7. NM_001371623.1NP_001358552.1  treacle protein isoform h

    Status: REVIEWED

    Source sequence(s)
    AC011372
    Related
    ENSP00000493815.1, ENST00000643257.2
    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 Updated Annotation Release 109.20210514

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000005.10 Reference GRCh38.p13 Primary Assembly

    Range
    150357697..150400306
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005268502.4XP_005268559.1  treacle protein isoform X1

    Related
    ENSP00000501343.1, ENST00000674413.1
    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_005268504.4XP_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_005268506.4XP_005268563.1  treacle protein isoform X5

    UniProtKB/TrEMBL
    E7ETY2
    Related
    ENSP00000427484.1, ENST00000513346.5
    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_017009792.2XP_016865281.1  treacle protein isoform X6

  5. XM_005268503.4XP_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_011537678.3XP_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
  7. XM_017009793.2XP_016865282.1  treacle protein isoform X9

  8. XM_017009794.2XP_016865283.1  treacle protein isoform X10

  9. XM_005268507.4XP_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
  10. XM_005268508.4XP_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
  11. XM_005268509.4XP_005268566.1  treacle protein isoform X12

    Related
    ENSP00000422567.2, ENST00000513538.2
    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_017009795.2XP_016865284.1  treacle protein isoform X13

RNA

  1. XR_427780.3 RNA Sequence

  2. XR_427778.3 RNA Sequence

  3. XR_427779.2 RNA Sequence

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.
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