Human Gene UBAP2 (uc003ztp.2)
  Description: Homo sapiens ubiquitin associated protein 2 (UBAP2), mRNA.
RefSeq Summary (NM_018449): The protein encoded by this gene contains a UBA (ubiquitin associated) domain, which is characteristic of proteins that function in the ubiquitination pathway. This gene may show increased expression in the adrenal gland and lymphatic tissues. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Sep 2013].
Transcript (Including UTRs)
   Position: hg19 chr9:33,921,691-33,935,189 Size: 13,499 Total Exon Count: 12 Strand: -
Coding Region
   Position: hg19 chr9:33,922,502-33,927,882 Size: 5,381 Coding Exon Count: 10 

Page IndexSequence and LinksPrimersGenetic AssociationsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesmRNA Descriptions
Other NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr9:33,921,691-33,935,189)mRNA (may differ from genome)Protein (358 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsGeneNetwork
H-INVHGNCLynxMGIPubMedTreefam
UniProtKBWikipediaBioGrid 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): UBAP2
CDC HuGE Published Literature: UBAP2

-  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: 13.58 RPKM in Testis
Total median expression: 207.41 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 -578.101877-0.308 Picture PostScript Text
3' UTR -266.22811-0.328 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 Q5JV03
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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
  AF157327 - Homo sapiens AD-012 protein mRNA, complete cds.
AK302754 - Homo sapiens cDNA FLJ61492 complete cds, highly similar to Homo sapiens ubiquitin associated protein 2 (UBAP2), transcript variant 1, mRNA.
LF383860 - JP 2014500723-A/191363: Polycomb-Associated Non-Coding RNAs.
AK026088 - Homo sapiens cDNA: FLJ22435 fis, clone HRC09181.
AB040924 - Homo sapiens mRNA for KIAA1491 protein, partial cds.
AK025801 - Homo sapiens cDNA: FLJ22148 fis, clone HEP22268.
AK303493 - Homo sapiens cDNA FLJ61517 complete cds, highly similar to Homo sapiens ubiquitin associated protein 2 (UBAP2), transcript variant 1, mRNA.
AK299183 - Homo sapiens cDNA FLJ59394 complete cds, highly similar to Homo sapiens ubiquitin associated protein 2 (UBAP2), transcript variant 1, mRNA.
AK294952 - Homo sapiens cDNA FLJ59508 complete cds, highly similar to Homo sapiens ubiquitin associated protein 2 (UBAP2), transcript variant 1, mRNA.
BC169323 - Synthetic construct Homo sapiens clone IMAGE:9093247 ubiquitin associated protein 2 (UBAP2) gene, partial cds.
AK302335 - Homo sapiens cDNA FLJ61633 complete cds, highly similar to Homo sapiens ubiquitin associated protein 2 (UBAP2), transcript variant 1, mRNA.
BC111762 - Homo sapiens ubiquitin associated protein 2, mRNA (cDNA clone IMAGE:40011328), partial cds.
BC111409 - Homo sapiens ubiquitin associated protein 2, mRNA (cDNA clone IMAGE:40000983), with apparent retained intron.
MA619437 - JP 2018138019-A/191363: Polycomb-Associated Non-Coding RNAs.
AK074884 - Homo sapiens cDNA FLJ90403 fis, clone NT2RP2006042, weakly similar to GLUCOAMYLASE S1/S2 PRECURSOR (EC 3.2.1.3).
LF354238 - JP 2014500723-A/161741: Polycomb-Associated Non-Coding RNAs.
BC037416 - Homo sapiens, Similar to AD-012 protein, clone IMAGE:5122712, mRNA.
JD221253 - Sequence 202277 from Patent EP1572962.
JD149961 - Sequence 130985 from Patent EP1572962.
JD363686 - Sequence 344710 from Patent EP1572962.
LF354239 - JP 2014500723-A/161742: Polycomb-Associated Non-Coding RNAs.
BC007890 - Homo sapiens ubiquitin associated protein 2, mRNA (cDNA clone IMAGE:4126670), partial cds.
AK025357 - Homo sapiens cDNA: FLJ21704 fis, clone COL09929.
BC041077 - Homo sapiens ubiquitin associated protein 2, mRNA (cDNA clone IMAGE:5926003), with apparent retained intron.
AK128424 - Homo sapiens cDNA FLJ46567 fis, clone THYMU3040830, moderately similar to Homo sapiens AD-012 protein mRNA.
AK057564 - Homo sapiens cDNA FLJ33002 fis, clone THYMU1000217, highly similar to Homo sapiens ubiquitin associated protein 2 (UBAP2), transcript variant 1, mRNA.
AK125935 - Homo sapiens cDNA FLJ43947 fis, clone TESTI4014818, highly similar to Homo sapiens ubiquitin associated protein 2 (UBAP2), transcript variant 1, mRNA.
JD428713 - Sequence 409737 from Patent EP1572962.
JD549812 - Sequence 530836 from Patent EP1572962.
JD375390 - Sequence 356414 from Patent EP1572962.
JD165145 - Sequence 146169 from Patent EP1572962.
JD386271 - Sequence 367295 from Patent EP1572962.
JD115821 - Sequence 96845 from Patent EP1572962.
JD334872 - Sequence 315896 from Patent EP1572962.
JD181504 - Sequence 162528 from Patent EP1572962.
JD506370 - Sequence 487394 from Patent EP1572962.
JD330271 - Sequence 311295 from Patent EP1572962.
JD080392 - Sequence 61416 from Patent EP1572962.
JD193452 - Sequence 174476 from Patent EP1572962.
JD536895 - Sequence 517919 from Patent EP1572962.
JD090632 - Sequence 71656 from Patent EP1572962.
JD077689 - Sequence 58713 from Patent EP1572962.
JD410221 - Sequence 391245 from Patent EP1572962.
JD058616 - Sequence 39640 from Patent EP1572962.
JD316095 - Sequence 297119 from Patent EP1572962.
BC169324 - Synthetic construct Homo sapiens clone IMAGE:9093260 ubiquitin associated protein 2 (UBAP2) gene, partial cds.
JD324197 - Sequence 305221 from Patent EP1572962.
JD115533 - Sequence 96557 from Patent EP1572962.
JD478737 - Sequence 459761 from Patent EP1572962.
JD108379 - Sequence 89403 from Patent EP1572962.
JD288460 - Sequence 269484 from Patent EP1572962.
JD500936 - Sequence 481960 from Patent EP1572962.
JD329994 - Sequence 311018 from Patent EP1572962.
JD121307 - Sequence 102331 from Patent EP1572962.
JD171621 - Sequence 152645 from Patent EP1572962.
JD383114 - Sequence 364138 from Patent EP1572962.
JD351056 - Sequence 332080 from Patent EP1572962.
JD103918 - Sequence 84942 from Patent EP1572962.
JD371037 - Sequence 352061 from Patent EP1572962.
JD319708 - Sequence 300732 from Patent EP1572962.
JD097490 - Sequence 78514 from Patent EP1572962.
JD253645 - Sequence 234669 from Patent EP1572962.
JD086034 - Sequence 67058 from Patent EP1572962.
JD197467 - Sequence 178491 from Patent EP1572962.
JD139255 - Sequence 120279 from Patent EP1572962.
JD547048 - Sequence 528072 from Patent EP1572962.
JD348238 - Sequence 329262 from Patent EP1572962.
JD402670 - Sequence 383694 from Patent EP1572962.
JD375254 - Sequence 356278 from Patent EP1572962.
JD377876 - Sequence 358900 from Patent EP1572962.
LF354240 - JP 2014500723-A/161743: Polycomb-Associated Non-Coding RNAs.
JD155648 - Sequence 136672 from Patent EP1572962.
JD145788 - Sequence 126812 from Patent EP1572962.
LF354241 - JP 2014500723-A/161744: Polycomb-Associated Non-Coding RNAs.
JD150939 - Sequence 131963 from Patent EP1572962.
JD495970 - Sequence 476994 from Patent EP1572962.
LF354242 - JP 2014500723-A/161745: Polycomb-Associated Non-Coding RNAs.
JD519177 - Sequence 500201 from Patent EP1572962.
MA589815 - JP 2018138019-A/161741: Polycomb-Associated Non-Coding RNAs.
MA589816 - JP 2018138019-A/161742: Polycomb-Associated Non-Coding RNAs.
MA589817 - JP 2018138019-A/161743: Polycomb-Associated Non-Coding RNAs.
MA589818 - JP 2018138019-A/161744: Polycomb-Associated Non-Coding RNAs.
MA589819 - JP 2018138019-A/161745: Polycomb-Associated Non-Coding RNAs.

-  Other Names for This Gene
  Alternate Gene Symbols: AK125935, NM_018449, NP_060919, Q5JV03, Q5JV03_HUMAN, RP11-176F3.6-007
UCSC ID: uc003ztp.2
RefSeq Accession: NM_018449
Protein: Q5JV03

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: AK125935.1
exon count: 12CDS single in 3' UTR: no RNA size: 3602
ORF size: 1077CDS single in intron: no Alignment % ID: 99.86
txCdsPredict score: 641.00frame shift in genome: no % Coverage: 99.92
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: yes # AT/AC introns 0
selenocysteine: no end bleed into intron: 1563# 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.