Human Gene CCDC12 (uc003cqo.3)
  Description: Homo sapiens coiled-coil domain containing 12 (CCDC12), transcript variant 1, mRNA.
Transcript (Including UTRs)
   Position: hg19 chr3:46,963,220-47,023,500 Size: 60,281 Total Exon Count: 8 Strand: -
Coding Region
   Position: hg19 chr3:46,963,547-47,018,261 Size: 54,715 Coding Exon Count: 7 

Page IndexSequence and LinksPrimersCTDGene AllelesRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesmRNA DescriptionsPathways
Other NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr3:46,963,220-47,023,500)mRNA (may differ from genome)Protein (179 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsGeneNetwork
H-INVHGNCHPRDLynxMGIPubMed
UniProtKBBioGrid 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


-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           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: 34.97 RPKM in Skin - Not Sun Exposed (Suprapubic)
Total median expression: 1030.53 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 -35.30151-0.234 Picture PostScript Text
3' UTR -122.60327-0.375 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
IPR013169 - mRNA_splic_Cwf18

Pfam Domains:
PF08315 - cwf18 pre-mRNA splicing factor

ModBase Predicted Comparative 3D Structure on J3KR35
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 orthologNo orthologGenome BrowserGenome BrowserGenome BrowserNo ortholog
Gene Details  Gene DetailsGene Details 
Gene Sorter  Gene SorterGene Sorter 
  EnsemblFlyBaseWormBase 
  Protein SequenceProtein SequenceProtein Sequence 
  AlignmentAlignmentAlignment 

-  Descriptions from all associated GenBank mRNAs
  AK096749 - Homo sapiens cDNA FLJ39430 fis, clone PROST2002489.
BC020830 - Homo sapiens coiled-coil domain containing 12, mRNA (cDNA clone MGC:23918 IMAGE:4771328), complete cds.
AK098120 - Homo sapiens cDNA FLJ40801 fis, clone TRACH2008278.
JD425788 - Sequence 406812 from Patent EP1572962.
JD358425 - Sequence 339449 from Patent EP1572962.
JD385756 - Sequence 366780 from Patent EP1572962.
CU676738 - Synthetic construct Homo sapiens gateway clone IMAGE:100022042 5' read CCDC12 mRNA.
HQ447754 - Synthetic construct Homo sapiens clone IMAGE:100071085; CCSB013121_02 coiled-coil domain containing 12 (CCDC12) gene, encodes complete protein.
KJ903887 - Synthetic construct Homo sapiens clone ccsbBroadEn_13281 CCDC12 gene, encodes complete protein.
AK303160 - Homo sapiens cDNA FLJ57688 complete cds, highly similar to Coiled-coil domain-containing protein 12.
AK295532 - Homo sapiens cDNA FLJ58397 complete cds, moderately similar to Coiled-coil domain-containing protein 12.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa03040 - Spliceosome

-  Other Names for This Gene
  Alternate Gene Symbols: hCG_15433, J3KR35, J3KR35_HUMAN, NM_144716, NP_653317, uc003cqo.2
UCSC ID: uc003cqo.3
RefSeq Accession: NM_144716
Protein: J3KR35 CCDS: CCDS63612.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_144716.5
exon count: 8CDS single in 3' UTR: no RNA size: 1035
ORF size: 540CDS single in intron: no Alignment % ID: 99.90
txCdsPredict score: 1232.50frame shift in genome: no % Coverage: 98.36
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.