Human Gene C15orf39 (ENST00000360639.6) from GENCODE V44
  Description: Event=Alternative splicing; Named isoforms=3; Name=1; IsoId=Q6ZRI6-1; Sequence=Displayed; Name=2; IsoId=Q6ZRI6-2; Sequence=VSP_019540, VSP_019541; Note=No experimental confirmation available; Name=3; IsoId=Q6ZRI6-3; Sequence=VSP_019538, VSP_019539; (from UniProt Q6ZRI6)
Gencode Transcript: ENST00000360639.6
Gencode Gene: ENSG00000167173.19
Transcript (Including UTRs)
   Position: hg38 chr15:75,198,892-75,212,169 Size: 13,278 Total Exon Count: 3 Strand: +
Coding Region
   Position: hg38 chr15:75,206,049-75,211,116 Size: 5,068 Coding Exon Count: 2 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
Other NamesMethods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr15:75,198,892-75,212,169)mRNA (may differ from genome)Protein (1047 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblExonPrimerGencodeGeneCardsHGNC
HPRDLynxMGIneXtProtPubMedUniProtKB

-  Comments and Description Text from UniProtKB
  ID: CO039_HUMAN
DESCRIPTION: RecName: Full=Uncharacterized protein C15orf39;
SEQUENCE CAUTION: Sequence=AAQ06680.1; Type=Frameshift; Positions=267; Sequence=CAB55985.3; Type=Erroneous initiation; Note=Translation N-terminally shortened; Sequence=CAD39045.1; Type=Frameshift; Positions=900;

-  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

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 49.98 RPKM in Testis
Total median expression: 384.47 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 -91.60320-0.286 Picture PostScript Text
3' UTR -439.801053-0.418 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 Q6ZRI6
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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
Genome BrowserGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
MGIRGD    
Protein SequenceProtein Sequence    
AlignmentAlignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Cellular Component:
GO:0005829 cytosol


-  Descriptions from all associated GenBank mRNAs
  AK128205 - Homo sapiens cDNA FLJ46337 fis, clone TESTI4046245.
LF208512 - JP 2014500723-A/16015: Polycomb-Associated Non-Coding RNAs.
MA444089 - JP 2018138019-A/16015: Polycomb-Associated Non-Coding RNAs.
AK125111 - Homo sapiens cDNA FLJ43121 fis, clone CTONG3003652.
BC110367 - Homo sapiens chromosome 15 open reading frame 39, mRNA (cDNA clone MGC:117209 IMAGE:5494248), complete cds.
AF495726 - Homo sapiens FP6578 mRNA, complete cds.
BC011379 - Homo sapiens chromosome 15 open reading frame 39, mRNA (cDNA clone MGC:9854 IMAGE:3866082), complete cds.
AK125604 - Homo sapiens cDNA FLJ43616 fis, clone SPLEN2016554.
AK304663 - Homo sapiens cDNA FLJ55915 complete cds.
AK123746 - Homo sapiens cDNA FLJ41752 fis, clone HSYRA2008376.
LF377205 - JP 2014500723-A/184708: Polycomb-Associated Non-Coding RNAs.
MA612782 - JP 2018138019-A/184708: Polycomb-Associated Non-Coding RNAs.
LF377204 - JP 2014500723-A/184707: Polycomb-Associated Non-Coding RNAs.
MA612781 - JP 2018138019-A/184707: Polycomb-Associated Non-Coding RNAs.
BC006207 - Homo sapiens chromosome 15 open reading frame 39, mRNA (cDNA clone IMAGE:3544897).
LF377203 - JP 2014500723-A/184706: Polycomb-Associated Non-Coding RNAs.
MA612780 - JP 2018138019-A/184706: Polycomb-Associated Non-Coding RNAs.
AK056589 - Homo sapiens cDNA FLJ32027 fis, clone NTONG1000246, weakly similar to CYCLIN-DEPENDENT KINASE INHIBITOR 1C.
LF377202 - JP 2014500723-A/184705: Polycomb-Associated Non-Coding RNAs.
MA612779 - JP 2018138019-A/184705: Polycomb-Associated Non-Coding RNAs.
BC109195 - Homo sapiens chromosome 15 open reading frame 39, mRNA (cDNA clone IMAGE:40005208), partial cds.
LF377201 - JP 2014500723-A/184704: Polycomb-Associated Non-Coding RNAs.
MA612778 - JP 2018138019-A/184704: Polycomb-Associated Non-Coding RNAs.
AL360143 - Homo sapiens mRNA full length insert cDNA clone EUROIMAGE 2260343.
BC000540 - Homo sapiens chromosome 15 open reading frame 39, mRNA (cDNA clone IMAGE:3163610).
AL834382 - Homo sapiens mRNA; cDNA DKFZp762M1316 (from clone DKFZp762M1316).
JD121373 - Sequence 102397 from Patent EP1572962.
JD370358 - Sequence 351382 from Patent EP1572962.
JD540532 - Sequence 521556 from Patent EP1572962.
JD183092 - Sequence 164116 from Patent EP1572962.
DQ591707 - Homo sapiens piRNA piR-58819, complete sequence.
JD369619 - Sequence 350643 from Patent EP1572962.
JD118968 - Sequence 99992 from Patent EP1572962.
JD063688 - Sequence 44712 from Patent EP1572962.
JD135234 - Sequence 116258 from Patent EP1572962.
AK057025 - Homo sapiens cDNA FLJ32463 fis, clone SKNMC1000240, weakly similar to CYCLIN-DEPENDENT KINASE INHIBITOR 1C.
JD098404 - Sequence 79428 from Patent EP1572962.
JD371697 - Sequence 352721 from Patent EP1572962.
JD535408 - Sequence 516432 from Patent EP1572962.
JD050526 - Sequence 31550 from Patent EP1572962.
JD246123 - Sequence 227147 from Patent EP1572962.
JD514234 - Sequence 495258 from Patent EP1572962.
JD142892 - Sequence 123916 from Patent EP1572962.
JD467346 - Sequence 448370 from Patent EP1572962.
JD460213 - Sequence 441237 from Patent EP1572962.
JD464607 - Sequence 445631 from Patent EP1572962.
JD395186 - Sequence 376210 from Patent EP1572962.
JD117856 - Sequence 98880 from Patent EP1572962.
JD371454 - Sequence 352478 from Patent EP1572962.
JD075799 - Sequence 56823 from Patent EP1572962.
JD143220 - Sequence 124244 from Patent EP1572962.
BC069049 - Homo sapiens cDNA clone IMAGE:3537570, partial cds.
JD197205 - Sequence 178229 from Patent EP1572962.
JD281844 - Sequence 262868 from Patent EP1572962.
JD386318 - Sequence 367342 from Patent EP1572962.
AL109730 - Homo sapiens mRNA full length insert cDNA clone EUROIMAGE 68600.
JD115953 - Sequence 96977 from Patent EP1572962.
JD141097 - Sequence 122121 from Patent EP1572962.
BC001762 - Homo sapiens chromosome 15 open reading frame 39, mRNA (cDNA clone IMAGE:3542822), complete cds.
BC051235 - Homo sapiens chromosome 15 open reading frame 39, mRNA (cDNA clone IMAGE:3621245), complete cds.
AF063593 - Homo sapiens brain my035 protein mRNA, complete cds.
BC011905 - Homo sapiens chromosome 15 open reading frame 39, mRNA (cDNA clone IMAGE:4121832), complete cds.
JD025863 - Sequence 6887 from Patent EP1572962.
JD034298 - Sequence 15322 from Patent EP1572962.
AL117540 - Homo sapiens mRNA; cDNA DKFZp434H132 (from clone DKFZp434H132).
KJ906257 - Synthetic construct Homo sapiens clone ccsbBroadEn_15927 C15orf39 gene, encodes complete protein.
CR533482 - Homo sapiens full open reading frame cDNA clone RZPDo834C0917D for gene DKFZP434H132, DKFZP434H132 protein; complete cds, incl. stopcodon.
JD019457 - Sequence 481 from Patent EP1572962.
JD492283 - Sequence 473307 from Patent EP1572962.
JD033147 - Sequence 14171 from Patent EP1572962.
JD325588 - Sequence 306612 from Patent EP1572962.
JD122863 - Sequence 103887 from Patent EP1572962.
AF143881 - Homo sapiens clone IMAGE:121159 mRNA sequence.
JD021028 - Sequence 2052 from Patent EP1572962.
JD034696 - Sequence 15720 from Patent EP1572962.
JD257851 - Sequence 238875 from Patent EP1572962.
JD434608 - Sequence 415632 from Patent EP1572962.
JD469769 - Sequence 450793 from Patent EP1572962.
JD192219 - Sequence 173243 from Patent EP1572962.
JD126428 - Sequence 107452 from Patent EP1572962.
JD158045 - Sequence 139069 from Patent EP1572962.
JD159607 - Sequence 140631 from Patent EP1572962.
JD337111 - Sequence 318135 from Patent EP1572962.
JD187665 - Sequence 168689 from Patent EP1572962.
JD515755 - Sequence 496779 from Patent EP1572962.
JD062773 - Sequence 43797 from Patent EP1572962.
JD259439 - Sequence 240463 from Patent EP1572962.
JD059373 - Sequence 40397 from Patent EP1572962.
JD424299 - Sequence 405323 from Patent EP1572962.
JD444145 - Sequence 425169 from Patent EP1572962.
JD267817 - Sequence 248841 from Patent EP1572962.
JD443456 - Sequence 424480 from Patent EP1572962.
JD069210 - Sequence 50234 from Patent EP1572962.
LF377199 - JP 2014500723-A/184702: Polycomb-Associated Non-Coding RNAs.
MA612776 - JP 2018138019-A/184702: Polycomb-Associated Non-Coding RNAs.

-  Other Names for This Gene
  Alternate Gene Symbols: AK128205, B3KWI3, C9J888, CO039_HUMAN, ENST00000360639.1, ENST00000360639.2, ENST00000360639.3, ENST00000360639.4, ENST00000360639.5, FP6578, Q6ZRI6, Q71JB1, Q7L3S0, Q8N3F2, Q96FB6, Q9NTU5, uc002azp.1, uc002azp.2, uc002azp.3, uc002azp.4
UCSC ID: ENST00000360639.6
RefSeq Accession: NM_015492
Protein: Q6ZRI6 (aka CO039_HUMAN)
CCDS: CCDS10276.1

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