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

Summary

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

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_086035.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
studies convincingly demonstrate the ability of CDYL to moonlight as a tubulin acetyltransferase.
Title: Tubulin acetylation: A novel functional avenue for CDYL in sperm.
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

AU048359 (e-PCR)
- UniSTS:109613

D17Got39 (e-PCR)
- UniSTS:115566

D17Rat67 (e-PCR)
- UniSTS:118444

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

EC 2.3.1.48

XP_006253901.1

EC 2.3.1.48

XP_006253902.1

EC 2.3.1.48

XP_017456089.1

EC 2.3.1.48

XP_017456090.1

EC 2.3.1.48

XP_038951807.1

EC 2.3.1.48

XP_038951808.1

EC 2.3.1.48

XP_038951809.1

EC 2.3.1.48

XP_038951810.1

EC 2.3.1.48

XP_063132650.1

EC 2.3.1.48

XP_063132651.1

EC 2.3.1.48

XP_063132652.1

EC 2.3.1.48

XP_063132653.1

EC 2.3.1.48

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)

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

NC_086035.1 Reference GRCr8

Range

29188697..29409805 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_063276581.1 → XP_063132651.1 chromodomain Y-like protein isoform X8
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
XM_017600600.2 → XP_017456089.1 chromodomain Y-like protein isoform X1

UniProtKB/TrEMBL

A0A8I6A2N0, A0A8L2QNJ4

Related

ENSRNOP00000048651.4, ENSRNOT00000048757.5
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
XM_063276580.1 → XP_063132650.1 chromodomain Y-like protein isoform X7

UniProtKB/TrEMBL

A0A8I6G3K3

Related

ENSRNOP00000095115.2, ENSRNOT00000100703.2
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. ...
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
XM_017600601.3 → XP_017456090.1 chromodomain Y-like protein isoform X2

UniProtKB/TrEMBL

A0A8I6G6F9
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
XM_063276582.1 → XP_063132652.1 chromodomain Y-like protein isoform X10

UniProtKB/TrEMBL

A0A8I5ZLF2

Related

ENSRNOP00000078650.2, ENSRNOT00000106207.2
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
XM_063276583.1 → XP_063132653.1 chromodomain Y-like protein isoform X11