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Cdyl chromodomain Y-like [ Rattus norvegicus (Norway rat) ]

Gene ID: 361237, updated on 27-Nov-2024

Summary

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Official Symbol
Cdylprovided by RGD
Official Full Name
chromodomain Y-likeprovided by RGD
Primary source
RGD:1549745
See related
EnsemblRapid:ENSRNOG00000032215 AllianceGenome:RGD:1549745
Gene type
protein coding
RefSeq status
PROVISIONAL
Organism
Rattus norvegicus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Summary
Predicted to enable several functions, including crotonyl-CoA hydratase activity; identical protein binding activity; and transcription corepressor activity. Predicted to be involved in negative regulation of peptidyl-lysine crotonylation; random inactivation of X chromosome; and spermatid development. Predicted to be located in chromosome; cytoplasm; and nuclear speck. Predicted to be active in nucleus. Orthologous to human CDYL (chromodomain Y like). [provided by Alliance of Genome Resources, Nov 2024]
Expression
Biased expression in Testes (RPKM 156.4), Spleen (RPKM 105.6) and 9 other tissues See more
Orthologs
human mouse all
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Genomic context

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See Cdyl in Genome Data Viewer
Location:
17p12
Exon count:
14
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCr8 (GCF_036323735.1) 17 NC_086035.1 (29188697..29409805, complement)
RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 17 NC_051352.1 (28982009..29204345, complement)
106 previous assembly Rnor_6.0 (GCF_000001895.5) 17 NC_005116.4 (29672925..29895416, complement)

Chromosome 17 - NC_086035.1Genomic Context describing neighboring genes Neighboring gene protein phosphatase 1, regulatory subunit 3G Neighboring gene ribonuclease P/MRP subunit p40 Neighboring gene uncharacterized LOC120097861 Neighboring gene ribosomal protein S7, pseudogene 16 Neighboring gene small nucleolar RNA SNORA17

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
  • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
  • BioProject: PRJNA238328
  • Publication: PMID 24510058
  • Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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Related articles in PubMed

  1. CDYL suppresses epileptogenesis in mice through repression of axonal Nav1.6 sodium channel expression. Liu Y, et al. Nat Commun, 2017 Aug 25. PMID 28842554, Free PMC Article
  2. Tubulin acetylation: A novel functional avenue for CDYL in sperm. Parab S, et al. Cytoskeleton (Hoboken), 2017 Sep. PMID 28681565
  3. Ubiquitin ligase TRIM32 promotes dendrite arborization by mediating degradation of the epigenetic factor CDYL. Liu L, et al. FASEB J, 2022 Jan. PMID 34888944
  4. Chromodomain Protein CDYL Acts as a Crotonyl-CoA Hydratase to Regulate Histone Crotonylation and Spermatogenesis. Liu S, et al. Mol Cell, 2017 Sep 7. PMID 28803779
  5. Cdyl, a new partner of the inactive X chromosome and potential reader of H3K27me3 and H3K9me2. Escamilla-Del-Arenal M, et al. Mol Cell Biol, 2013 Dec. PMID 24144980, Free PMC Article

See all (11) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Ubiquitin ligase TRIM32 promotes dendrite arborization by mediating degradation of the epigenetic factor CDYL.
    Title: Ubiquitin ligase TRIM32 promotes dendrite arborization by mediating degradation of the epigenetic factor CDYL.
  2. studies convincingly demonstrate the ability of CDYL to moonlight as a tubulin acetyltransferase.
    Title: Tubulin acetylation: A novel functional avenue for CDYL in sperm.
  3. The epigenetic factor CDYL regulates the gene expression of the voltage gated sodium channel, Nav1.6, which contributes to seizures in a rat model of epilepsy.
    Title: CDYL suppresses epileptogenesis in mice through repression of axonal Nav1.6 sodium channel expression.
Submit: New GeneRIF Correction

General gene information

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Markers

Homology

Gene Ontology Provided by RGD

Function Evidence Code Pubs
enables acyltransferase activity IEA
Inferred from Electronic Annotation
more info
  
enables chromatin binding IEA
Inferred from Electronic Annotation
more info
  
enables chromatin binding ISO
Inferred from Sequence Orthology
more info
  
enables chromatin binding ISS
Inferred from Sequence or Structural Similarity
more info
  
enables crotonyl-CoA hydratase activity IEA
Inferred from Electronic Annotation
more info
  
enables crotonyl-CoA hydratase activity ISO
Inferred from Sequence Orthology
more info
  
enables crotonyl-CoA hydratase activity ISS
Inferred from Sequence or Structural Similarity
more info
  
enables identical protein binding ISO
Inferred from Sequence Orthology
more info
  
enables methylated histone binding IEA
Inferred from Electronic Annotation
more info
  
NOT enables methylated histone binding ISO
Inferred from Sequence Orthology
more info
  
enables methylated histone binding ISO
Inferred from Sequence Orthology
more info
  
enables methylated histone binding ISS
Inferred from Sequence or Structural Similarity
more info
  
enables protein-macromolecule adaptor activity ISO
Inferred from Sequence Orthology
more info
  
enables transcription corepressor activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables transcription corepressor activity IEA
Inferred from Electronic Annotation
more info
  
enables transcription corepressor activity ISO
Inferred from Sequence Orthology
more info
  
enables transcription corepressor activity ISS
Inferred from Sequence or Structural Similarity
more info
  
Process Evidence Code Pubs
involved_in negative regulation of DNA-templated transcription IEA
Inferred from Electronic Annotation
more info
  
involved_in negative regulation of peptidyl-lysine crotonylation IEA
Inferred from Electronic Annotation
more info
  
involved_in negative regulation of peptidyl-lysine crotonylation ISO
Inferred from Sequence Orthology
more info
  
involved_in negative regulation of peptidyl-lysine crotonylation ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in random inactivation of X chromosome IEA
Inferred from Electronic Annotation
more info
  
involved_in random inactivation of X chromosome ISO
Inferred from Sequence Orthology
more info
  
involved_in random inactivation of X chromosome ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in spermatid development IEA
Inferred from Electronic Annotation
more info
  
involved_in spermatid development ISO
Inferred from Sequence Orthology
more info
  
involved_in spermatid development ISS
Inferred from Sequence or Structural Similarity
more info
  
Component Evidence Code Pubs
located_in chromosome IEA
Inferred from Electronic Annotation
more info
  
located_in chromosome ISO
Inferred from Sequence Orthology
more info
  
located_in chromosome ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in cytoplasm IEA
Inferred from Electronic Annotation
more info
  
located_in cytoplasm ISO
Inferred from Sequence Orthology
more info
  
located_in cytoplasm ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in nuclear speck IEA
Inferred from Electronic Annotation
more info
  
located_in nuclear speck ISO
Inferred from Sequence Orthology
more info
  
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in nucleus IEA
Inferred from Electronic Annotation
more info
  
located_in nucleus ISO
Inferred from Sequence Orthology
more info
  
located_in nucleus ISS
Inferred from Sequence or Structural Similarity
more info
  

General protein information

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Preferred Names
chromodomain Y-like protein
Names
CDY-like
chromodomain protein, Y chromosome-like
chromodomain protein, Y-like
crotonyl-CoA hydratase
putative tubulin acetyltransferase Cdyl
NP_001014167.1
XP_006253901.1
XP_006253902.1
XP_017456089.1
XP_017456090.1
XP_038951807.1
XP_038951808.1
XP_038951809.1
XP_038951810.1
XP_063132650.1
XP_063132651.1
XP_063132652.1
XP_063132653.1

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_001014145.1 → NP_001014167.1  chromodomain Y-like protein

    See identical proteins and their annotated locations for NP_001014167.1

    Status: PROVISIONAL

    Source sequence(s)
    BC079003
    UniProtKB/Swiss-Prot
    Q6AYK9
    UniProtKB/TrEMBL
    A0A8I6A2N0, A6J7E0
    Related
    ENSRNOP00000106192.1, ENSRNOT00000170256.1
    Conserved Domains (2) summary
    cd06558
    Location:335 → 531
    crotonase-like; Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase. ...
    cd18634
    Location:56 → 105
    CD_CDY; chromodomain of the Chromodomain Y-like protein family

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

Reference GRCr8

Genomic

  1. NC_086035.1 Reference GRCr8

    Range
    29188697..29409805 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_063276581.1 → XP_063132651.1  chromodomain Y-like protein isoform X8

  2. XM_039095879.2 → XP_038951807.1  chromodomain Y-like protein isoform X3

    UniProtKB/TrEMBL
    A0A8I6A2N0
    Conserved Domains (2) summary
    cd06558
    Location:338 → 534
    crotonase-like; Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase. ...
    cd18634
    Location:30 → 80
    CD_CDY; chromodomain of the Chromodomain Y-like protein family

  3. XM_017600600.2 → XP_017456089.1  chromodomain Y-like protein isoform X1

    UniProtKB/TrEMBL
    A0A8I6A2N0, A0A8L2QNJ4
    Related
    ENSRNOP00000048651.4, ENSRNOT00000048757.5

  4. XM_039095881.2 → XP_038951809.1  chromodomain Y-like protein isoform X9

    UniProtKB/TrEMBL
    A0A8I6G6F9
    Conserved Domains (2) summary
    cd06558
    Location:287 → 483
    crotonase-like; Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase. ...
    cd18634
    Location:6 → 57
    CD_CDY; chromodomain of the Chromodomain Y-like protein family

  5. XM_063276580.1 → XP_063132650.1  chromodomain Y-like protein isoform X7

    UniProtKB/TrEMBL
    A0A8I6G3K3
    Related
    ENSRNOP00000095115.2, ENSRNOT00000100703.2

  6. XM_039095882.2 → XP_038951810.1  chromodomain Y-like protein isoform X12

    Conserved Domains (1) summary
    cd06558
    Location:55 → 251
    crotonase-like; Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase. ...

  7. XM_006253839.5 → XP_006253901.1  chromodomain Y-like protein isoform X5

    UniProtKB/TrEMBL
    A0A8I6G6F9
    Related
    ENSRNOP00000080331.2, ENSRNOT00000119808.2
    Conserved Domains (2) summary
    cd06558
    Location:315 → 511
    crotonase-like; Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase. ...
    smart00298
    Location:7 → 60
    CHROMO; Chromatin organization modifier domain

  8. XM_017600601.3 → XP_017456090.1  chromodomain Y-like protein isoform X2

    UniProtKB/TrEMBL
    A0A8I6G6F9

  9. XM_039095880.2 → XP_038951808.1  chromodomain Y-like protein isoform X4

    UniProtKB/TrEMBL
    A0A8I6G6F9
    Conserved Domains (2) summary
    cd06558
    Location:335 → 531
    crotonase-like; Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase. ...
    cd18634
    Location:28 → 77
    CD_CDY; chromodomain of the Chromodomain Y-like protein family

  10. XM_063276582.1 → XP_063132652.1  chromodomain Y-like protein isoform X10

    UniProtKB/TrEMBL
    A0A8I5ZLF2
    Related
    ENSRNOP00000078650.2, ENSRNOT00000106207.2

  11. XM_006253840.5 → XP_006253902.1  chromodomain Y-like protein isoform X6

    UniProtKB/TrEMBL
    A0A8I6G6F9
    Conserved Domains (2) summary
    cd06558
    Location:314 → 510
    crotonase-like; Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase. ...
    smart00298
    Location:7 → 59
    CHROMO; Chromatin organization modifier domain

  12. XM_063276583.1 → XP_063132653.1  chromodomain Y-like protein isoform X11

Nucleotide Protein Strain
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q6AYK9.1 GenPept UniProtKB/Swiss-Prot:Q6AYK9

Gene LinkOut

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