Human Gene CDYL (uc003mwj.3) Description and Page Index
  Description: Homo sapiens chromodomain protein, Y-like (CDYL), transcript variant 1, mRNA.
RefSeq Summary (NM_004824): Chromodomain Y is a primate-specific Y-chromosomal gene family expressed exclusively in the testis and implicated in infertility. Although the Y-linked genes are testis-specific, this autosomal gene is ubiquitously expressed. The Y-linked genes arose by retrotransposition of an mRNA from this gene, followed by amplification of the retroposed gene. Proteins encoded by this gene superfamily possess a chromodomain, a motif implicated in chromatin binding and gene suppression, and a catalytic domain believed to be involved in histone acetylation. Multiple proteins are encoded by transcript variants of this gene. [provided by RefSeq, Jul 2008].
Transcript (Including UTRs)
   Position: hg19 chr6:4,776,680-4,955,778 Size: 179,099 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 LinksGenetic AssociationsCTDGene AllelesRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesmRNA DescriptionsOther Names
Model InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr6:4,776,680-4,955,778)mRNA (may differ from genome)Protein (544 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMGI
OMIMPubMedStanford SOURCETreefamUniProtKB

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): CDYL
CDC HuGE Published Literature: CDYL
Positive Disease Associations: Ocular Physiological Phenomena , Potassium , Pulmonary Disease, Chronic Obstructive
Related Studies:
  1. Ocular Physiological Phenomena
    Sudha Seshadri et al. BMC medical genetics 2007, Genetic correlates of brain aging on MRI and cognitive test measures: a genome-wide association and linkage analysis in the Framingham Study., BMC medical genetics. [PubMed 17903297]
    Our results suggest that genes associated with clinical neurological disease also have detectable effects on subclinical phenotypes. These hypothesis generating data illustrate the use of an unbiased approach to discover novel pathways that may be involved in brain aging, and could be used to replicate observations made in other studies.
  2. Potassium
    , , . [PubMed 0]
  3. Potassium
    , , . [PubMed 0]
           more ... click here to view the complete list

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
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-  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 -177.10338-0.524 Picture PostScript Text
3' UTR -402.801488-0.271 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
  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

ModBase Predicted Comparative 3D Structure on Q9Y232-2
FrontTopSide
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 orthologGenome BrowserGenome BrowserNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGDEnsembl   
 Protein SequenceProtein Sequence   
 AlignmentAlignment   

-  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: CDYL1, NM_004824, NP_001137443, Q9Y232-2
UCSC ID: uc003mwj.3
RefSeq Accession: NM_004824
Protein: Q9Y232-2, splice isoform of Q9Y232 CCDS: CCDS4491.2

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_004824.3
exon count: 7CDS single in 3' UTR: no RNA size: 3477
ORF size: 1635CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 3410.00frame shift in genome: no % Coverage: 99.54
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
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