Human Gene CCDC54 (uc003dwi.1)
  Description: Homo sapiens coiled-coil domain containing 54 (CCDC54), mRNA.
Transcript (Including UTRs)
   Position: hg19 chr3:107,096,188-107,097,481 Size: 1,294 Total Exon Count: 1 Strand: +
Coding Region
   Position: hg19 chr3:107,096,435-107,097,421 Size: 987 Coding Exon Count: 1 

Page IndexSequence and LinksPrimersGenetic AssociationsGene AllelesRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesmRNA DescriptionsOther Names
Model InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr3:107,096,188-107,097,481)mRNA (may differ from genome)Protein (328 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsGeneNetwork
H-INVHGNCHPRDLynxMGIneXtProt
PubMedTreefamUniProtKBBioGrid CRISPR DB

-  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


-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): CCDC54
CDC HuGE Published Literature: CCDC54
Positive Disease Associations: Alcoholism , Memory , Schizophrenia , Triglycerides
Related Studies:
  1. Alcoholism
    , , . [PubMed 0]
  2. Alcoholism
    , , . [PubMed 0]
  3. Memory
    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.
           more ... click here to view the complete list

+  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: 126.88 RPKM in Testis
Total median expression: 129.72 RPKM



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

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -49.41247-0.200 Picture PostScript Text
3' UTR -7.8060-0.130 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
  ModBase Predicted Comparative 3D Structure on Q8NEL0
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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 Details     
Gene Sorter     
      
      
      

-  Descriptions from all associated GenBank mRNAs
  AK058091 - Homo sapiens cDNA FLJ25362 fis, clone TST01724.
HM005346 - Homo sapiens clone HTL-T-33 testicular tissue protein Li 33 mRNA, complete cds.
JD512954 - Sequence 493978 from Patent EP1572962.
JD524243 - Sequence 505267 from Patent EP1572962.
BC030780 - Homo sapiens coiled-coil domain containing 54, mRNA (cDNA clone MGC:26586 IMAGE:4824584), complete cds.
AF367469 - Homo sapiens testes development-related NYD-SP17 mRNA, complete cds.
JD288753 - Sequence 269777 from Patent EP1572962.
CU689006 - Synthetic construct Homo sapiens gateway clone IMAGE:100018112 5' read CCDC54 mRNA.
DQ893985 - Synthetic construct Homo sapiens clone IMAGE:100008445; FLH166286.01L; RZPDo839E1285D coiled-coil domain containing 54 (CCDC54) gene, encodes complete protein.
KJ899825 - Synthetic construct Homo sapiens clone ccsbBroadEn_09219 CCDC54 gene, encodes complete protein.
DQ890829 - Synthetic construct clone IMAGE:100003459; FLH166290.01X; RZPDo839E1286D coiled-coil domain containing 54 (CCDC54) gene, encodes complete protein.
DQ890830 - Synthetic construct Homo sapiens clone IMAGE:100003460; FLH263541.01X; RZPDo839F0286D coiled-coil domain containing 54 (CCDC54) gene, encodes complete protein.

-  Other Names for This Gene
  Alternate Gene Symbols: CCD54_HUMAN, NM_032600, NP_115989, Q8NEL0, Q96A43
UCSC ID: uc003dwi.1
RefSeq Accession: NM_032600
Protein: Q8NEL0 (aka CCD54_HUMAN)
CCDS: CCDS2949.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_032600.2
exon count: 1CDS single in 3' UTR: no RNA size: 1294
ORF size: 987CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 2082.00frame shift in genome: no % Coverage: 100.00
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
  Click here for details on how this gene model was made and data restrictions if any.