Human Gene CDYL (ENST00000397588.8_4) from GENCODE V47lift37
  Description: chromodomain Y like, transcript variant 1 (from RefSeq NM_004824.4)
Gencode Transcript: ENST00000397588.8_4
Gencode Gene: ENSG00000153046.18_13
Transcript (Including UTRs)
   Position: hg19 chr6:4,776,638-4,955,778 Size: 179,141 Total Exon Count: 7 Strand: +
Coding Region
   Position: hg19 chr6:4,777,018-4,954,290 Size: 177,273 Coding Exon Count: 7 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr6:4,776,638-4,955,778)mRNA (may differ from genome)Protein (544 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
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HGNCMGIOMIMPubMedUniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: CDYL1_HUMAN
DESCRIPTION: RecName: Full=Chromodomain Y-like protein; Short=CDY-like; EC=2.3.1.48;
FUNCTION: Acts as repressor of transcription (By similarity). Has histone acetyltransferase activity, with a preference for histone H4.
CATALYTIC ACTIVITY: Acetyl-CoA + [histone] = CoA + acetyl- [histone].
SUBUNIT: Interacts with HDAC1 and HDAC2 via its C-terminal acetyl- CoA-binding domain (By similarity).
SUBCELLULAR LOCATION: Nucleus (By similarity).
TISSUE SPECIFICITY: Ubiquitous. Expressed at moderate levels in all tissues examined.
MISCELLANEOUS: Interaction with HDAC1 or HDAC2 prevents Coenzyme A binding (By similarity).
SIMILARITY: Contains 1 chromo domain.
SEQUENCE CAUTION: Sequence=CAB43304.1; Type=Miscellaneous discrepancy;

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 10.53 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 269.48 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -192.30380-0.506 Picture PostScript Text
3' UTR -388.701488-0.261 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR023780 - Chromo_domain
IPR000953 - Chromo_domain/shadow
IPR016197 - Chromodomain-like
IPR023779 - Chromodomain_CS
IPR001753 - Crotonase_core

Pfam Domains:
PF00378 - Enoyl-CoA hydratase/isomerase
PF00385 - Chromo (CHRromatin Organisation MOdifier) domain
PF16113 - Enoyl-CoA hydratase/isomerase

SCOP Domains:
54160 - Chromo domain-like
52096 - ClpP/crotonase

Protein Data Bank (PDB) 3-D Structure
MuPIT help
2DNT - NMR MuPIT 2GTR - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on Q9Y232
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The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003682 chromatin binding
GO:0003714 transcription corepressor activity
GO:0003824 catalytic activity
GO:0005515 protein binding
GO:0016829 lyase activity
GO:0030674 protein binding, bridging
GO:0035064 methylated histone binding

Biological Process:
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0007283 spermatogenesis
GO:0007286 spermatid development
GO:0008152 metabolic process
GO:0030154 cell differentiation
GO:0060816 random inactivation of X chromosome
GO:1903507 negative regulation of nucleic acid-templated transcription

Cellular Component:
GO:0005634 nucleus
GO:0005694 chromosome
GO:0016607 nuclear speck


-  Descriptions from all associated GenBank mRNAs
  AF081258 - Homo sapiens testis-specific chromodomain Y-like protein (CDYL) mRNA, alternatively processed, complete cds.
AF081259 - Homo sapiens testis-specific chromodomain Y-like protein (CDYL) mRNA, alternatively processed, complete cds.
AK291601 - Homo sapiens cDNA FLJ77415 complete cds, highly similar to Homo sapiens chromodomain protein, Y-like (CDYL), transcript variant 2, mRNA.
BC108725 - Homo sapiens chromodomain protein, Y-like, mRNA (cDNA clone MGC:131936 IMAGE:6140263), complete cds.
BC119682 - Homo sapiens chromodomain protein, Y-like, mRNA (cDNA clone MGC:149568 IMAGE:40116323), complete cds.
AK296985 - Homo sapiens cDNA FLJ57292 complete cds, highly similar to Chromodomain Y-like protein.
JD128670 - Sequence 109694 from Patent EP1572962.
BC043397 - Homo sapiens chromodomain protein, Y-like, mRNA (cDNA clone IMAGE:6013496), partial cds.
DQ582320 - Homo sapiens piRNA piR-32432, complete sequence.
BC061516 - Homo sapiens chromodomain protein, Y-like, mRNA (cDNA clone IMAGE:6503066), partial cds.
KJ901973 - Synthetic construct Homo sapiens clone ccsbBroadEn_11367 CDYL gene, encodes complete protein.
DQ601484 - Homo sapiens piRNA piR-39550, complete sequence.
AL050164 - Homo sapiens mRNA; cDNA DKFZp586C1622 (from clone DKFZp586C1622); partial cds.
DQ570637 - Homo sapiens piRNA piR-30749, complete sequence.
DQ570638 - Homo sapiens piRNA piR-30750, complete sequence.
JD535160 - Sequence 516184 from Patent EP1572962.
JD099230 - Sequence 80254 from Patent EP1572962.
JD482204 - Sequence 463228 from Patent EP1572962.
DQ570329 - Homo sapiens piRNA piR-30441, complete sequence.
JD087824 - Sequence 68848 from Patent EP1572962.
JD097991 - Sequence 79015 from Patent EP1572962.
JD491309 - Sequence 472333 from Patent EP1572962.
JD533335 - Sequence 514359 from Patent EP1572962.
JD298303 - Sequence 279327 from Patent EP1572962.
JD062756 - Sequence 43780 from Patent EP1572962.
JD037291 - Sequence 18315 from Patent EP1572962.
JD072980 - Sequence 54004 from Patent EP1572962.
JD339756 - Sequence 320780 from Patent EP1572962.
JD354824 - Sequence 335848 from Patent EP1572962.
JD053284 - Sequence 34308 from Patent EP1572962.
JD550074 - Sequence 531098 from Patent EP1572962.
JD206605 - Sequence 187629 from Patent EP1572962.
JD357075 - Sequence 338099 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: A8K6D6, B4DLG4, CDYL , CDYL1 , CDYL_HUMAN, ENST00000397588.1, ENST00000397588.2, ENST00000397588.3, ENST00000397588.4, ENST00000397588.5, ENST00000397588.6, ENST00000397588.7, NM_004824, Q0VDG7, Q32NC5, Q5VX99, Q6P7T5, Q9BWZ2, Q9Y232, Q9Y424, uc318zdd.1, uc318zdd.2
UCSC ID: ENST00000397588.8_4
RefSeq Accession: NM_004824.4
Protein: Q9Y232 (aka CDYL1_HUMAN or CDYL_HUMAN)

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.