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Cph Chronophage [ Drosophila melanogaster (fruit fly) ]

Gene ID: 31660, updated on 4-Jan-2025

Summary

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Official Symbol
Cphprovided by FlyBase
Official Full Name
Chronophageprovided by FlyBase
Primary source
FLYBASE:FBgn0029939
Locus tag
Dmel_CG9650
See related
AllianceGenome:FB:FBgn0029939
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Drosophila melanogaster
Lineage
Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Diptera; Brachycera; Muscomorpha; Ephydroidea; Drosophilidae; Drosophila; Sophophora
Also known as
Bcl11; CG9650; cph; Dmel\CG9650
Summary
Enables RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Involved in negative regulation of peptide hormone secretion; neuroblast fate specification; and positive regulation of gene expression. Located in cytosol. Is expressed in several structures, including central brain; head epidermis primordium; proventriculus; sensory nervous system primordium; and ventral nerve cord. Used to study neurodegenerative disease; specific developmental disorder; and type 2 diabetes mellitus. Human ortholog(s) of this gene implicated in autism spectrum disorder; beta thalassemia; immunodeficiency 49; schizophrenia; and sickle cell anemia. Orthologous to human BCL11A (BCL11 transcription factor A) and BCL11B (BCL11 transcription factor B). [provided by Alliance of Genome Resources, Jan 2025]
Orthologs
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Genomic context

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See Cph in Genome Data Viewer
Location:
6F10-7A5; 1-20 cM
Exon count:
8
Annotation release Status Assembly Chr Location
Release 6.54 current Release 6 plus ISO1 MT (GCF_000001215.4) X NC_004354.4 (7137723..7241932)
Release 5.57 previous assembly Release 5 (GCF_000001215.2) X NC_004354.3 (7031756..7135965)

Chromosome X - NC_004354.4Genomic Context describing neighboring genes Neighboring gene long non-coding RNA:CR45532 Neighboring gene long non-coding RNA:CR46245 Neighboring gene long non-coding RNA:CR32730 Neighboring gene long non-coding RNA:CR44357 Neighboring gene uncharacterized protein Neighboring gene uncharacterized protein Neighboring gene uncharacterized protein

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Bibliography

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Related articles in PubMed

  1. Knockdown of Chronophage in the nervous system mimics features of neurodevelopmental disorders caused by BCL11A/B variants. Yamaguchi M, et al. Exp Cell Res, 2023 Dec 15. PMID 37926342
  2. Role of the BCL11A/B Homologue Chronophage (Cph) in Locomotor Behaviour of Drosophila melanogaster. Murthy S, et al. Neuroscience, 2024 Jul 23. PMID 38763224
  3. Repeat length and RNA expression level are not primary determinants in CUG expansion toxicity in Drosophila models. Le Mée G, et al. PLoS One, 2008 Jan 23. PMID 18213375, Free PMC Article
  4. The Drosophila homologue of CTIP1 (Bcl11a) and CTIP2 (Bcl11b) regulates neural stem cell temporal patterning. Fox PM, et al. Development, 2022 Sep 1. PMID 36069896, Free PMC Article
  5. Beadex, the Drosophila LIM only protein, is required for the growth of the larval neuromuscular junction. Chitre K, et al. J Neurophysiol, 2024 Aug 1. PMID 38838299

See all (74) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Role of the BCL11A/B Homologue Chronophage (Cph) in Locomotor Behaviour of Drosophila melanogaster.
    Title: Role of the BCL11A/B Homologue Chronophage (Cph) in Locomotor Behaviour of Drosophila melanogaster.
  2. Knockdown of Chronophage in the nervous system mimics features of neurodevelopmental disorders caused by BCL11A/B variants.
    Title: Knockdown of Chronophage in the nervous system mimics features of neurodevelopmental disorders caused by BCL11A/B variants.
Submit: New GeneRIF Correction

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Homology

Gene Ontology Provided by FlyBase

Function Evidence Code Pubs
enables DNA-binding transcription factor activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables DNA-binding transcription factor binding ISS
Inferred from Sequence or Structural Similarity
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 
Process Evidence Code Pubs
involved_in negative regulation of peptide hormone secretion IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in neuroblast fate specification IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in positive regulation of gene expression IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
  
Component Evidence Code Pubs
located_in cytosol HDA PubMed 
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in nucleus ISS
Inferred from Sequence or Structural Similarity
more info
 PubMed 

General protein information

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Preferred Names
chronophage
Names
CG9650-PG
CG9650-PI
CG9650-PJ
CG9650-PK
CG9650-PL
Cph-PG
Cph-PI
Cph-PJ
Cph-PK
Cph-PL

NCBI Reference Sequences (RefSeq)

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Genome Annotation

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

Reference assembly

Genomic

  1. NC_004354.4 Reference assembly

    Range
    7137723..7241932
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001103429.5 → NP_001096899.2  chronophage, isoform G [Drosophila melanogaster]

    See identical proteins and their annotated locations for NP_001096899.2

    Status: REVIEWED

    UniProtKB/TrEMBL
    A8JV12, C7LA65
    Conserved Domains (3) summary
    sd00017
    Location:1026 → 1046
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:713 → 735
    zf-C2H2; Zinc finger, C2H2 type
    pfam13465
    Location:1038 → 1063
    zf-H2C2_2; Zinc-finger double domain

  2. NM_132157.2 → NP_572385.2  chronophage, isoform J [Drosophila melanogaster]

    See identical proteins and their annotated locations for NP_572385.2

    Status: REVIEWED

    UniProtKB/TrEMBL
    A0A023GPJ3, C7LA65
    Conserved Domains (3) summary
    sd00017
    Location:957 → 977
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:644 → 666
    zf-C2H2; Zinc finger, C2H2 type
    pfam13465
    Location:969 → 994
    zf-H2C2_2; Zinc-finger double domain

  3. NM_167121.3 → NP_727173.2  chronophage, isoform I [Drosophila melanogaster]

    See identical proteins and their annotated locations for NP_727173.2

    Status: REVIEWED

    UniProtKB/TrEMBL
    C7LA65, R9PY46
    Conserved Domains (3) summary
    sd00017
    Location:1024 → 1044
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:711 → 733
    zf-C2H2; Zinc finger, C2H2 type
    pfam13465
    Location:1036 → 1061
    zf-H2C2_2; Zinc-finger double domain

  4. NM_001370055.1 → NP_001356899.1  chronophage, isoform K [Drosophila melanogaster]

    Status: REVIEWED

    UniProtKB/TrEMBL
    A0A499JF18, C7LA65
    Conserved Domains (3) summary
    sd00017
    Location:1030 → 1050
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:717 → 739
    zf-C2H2; Zinc finger, C2H2 type
    pfam13465
    Location:1042 → 1067
    zf-H2C2_2; Zinc-finger double domain

  5. NM_001103430.4 → NP_001096900.3  chronophage, isoform L [Drosophila melanogaster]

    Status: REVIEWED

    UniProtKB/TrEMBL
    A8JV11, C7LA65
    Conserved Domains (3) summary
    sd00017
    Location:1030 → 1050
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:717 → 739
    zf-C2H2; Zinc finger, C2H2 type
    pfam13465
    Location:1042 → 1067
    zf-H2C2_2; Zinc-finger double domain
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
A0A023GPJ3 A0A023GPJ3
A0A499JF18 A0A499JF18
A8JV11 A8JV11
A8JV12 A8JV12
R9PY46 R9PY46

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