Human Gene C22orf39 (uc002zpk.2)
  Description: Homo sapiens chromosome 22 open reading frame 39 (C22orf39), transcript variant 1, mRNA.
Transcript (Including UTRs)
   Position: hg19 chr22:19,430,673-19,435,755 Size: 5,083 Total Exon Count: 3 Strand: -
Coding Region
   Position: hg19 chr22:19,431,788-19,435,322 Size: 3,535 Coding Exon Count: 3 

Page IndexSequence and LinksUniProtKB CommentsPrimersGene 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 (chr22:19,430,673-19,435,755)mRNA (may differ from genome)Protein (142 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMGI
PubMedTreefamUniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: J3KNP9_HUMAN
DESCRIPTION: SubName: Full=UPF0545 protein C22orf39;
CAUTION: The sequence shown here is derived from an Ensembl automatic analysis pipeline and should be considered as preliminary data.

-  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


+  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: 26.86 RPKM in Muscle - Skeletal
Total median expression: 559.07 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 -172.20433-0.398 Picture PostScript Text
3' UTR -390.401115-0.350 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:
PF11326 - Protein of unknown function (DUF3128)

ModBase Predicted Comparative 3D Structure on J3KNP9
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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 orthologGenome BrowserGenome BrowserNo orthologNo ortholog
Gene Details  Gene Details  
Gene Sorter  Gene Sorter  
  EnsemblFlyBase  
  Protein SequenceProtein Sequence  
  AlignmentAlignment  

-  Descriptions from all associated GenBank mRNAs
  AK289809 - Homo sapiens cDNA FLJ78369 complete cds, highly similar to H.sapiens HIRA mRNA.
AK299950 - Homo sapiens cDNA FLJ58422 complete cds, highly similar to HIRA protein.
AK308642 - Homo sapiens cDNA, FLJ98683.
BC030758 - Homo sapiens hypothetical protein LOC128977, mRNA (cDNA clone IMAGE:4797610).
AK095271 - Homo sapiens cDNA FLJ37952 fis, clone CTONG2009258.
BX648073 - Homo sapiens mRNA; cDNA DKFZp686I08210 (from clone DKFZp686I08210).
BC062599 - Homo sapiens chromosome 22 open reading frame 39, mRNA (cDNA clone MGC:74441 IMAGE:5248209), complete cds.
BC046204 - Homo sapiens chromosome 22 open reading frame 39, mRNA (cDNA clone IMAGE:6161377), with apparent retained intron.
JD412961 - Sequence 393985 from Patent EP1572962.
AK290073 - Homo sapiens cDNA FLJ78353 complete cds.
CR456339 - Homo sapiens Em:AC000068.3 full length open reading frame (ORF) cDNA clone (cDNA clone C22ORF:pGEM.Em:AC000068.3).
CU013050 - Homo sapiens Em:AC000068.C22.3, mRNA (cDNA clone IMAGE:100000308), complete cds, with stop codon, in Gateway system.
CU013338 - Homo sapiens Em:AC000068.C22.3, mRNA (cDNA clone IMAGE:100000212), complete cds, without stop codon, in Gateway system.
KJ903746 - Synthetic construct Homo sapiens clone ccsbBroadEn_13140 C22orf39 gene, encodes complete protein.
JD417064 - Sequence 398088 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: J3KNP9, J3KNP9_HUMAN, NM_173793, NP_776154
UCSC ID: uc002zpk.2
RefSeq Accession: NM_173793
Protein: J3KNP9 CCDS: CCDS33599.2

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_173793.4
exon count: 3CDS single in 3' UTR: no RNA size: 1988
ORF size: 429CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 556.50frame shift in genome: no % Coverage: 99.45
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.