Human Gene LOC643387 (uc010znu.2)
  Description: Homo sapiens TAR DNA binding protein pseudogene (LOC643387), non-coding RNA.
Transcript (Including UTRs)
   Position: hg19 chr2:239,140,327-239,142,985 Size: 2,659 Total Exon Count: 1 Strand: +
Coding Region
   Position: hg19 chr2:239,140,522-239,140,860 Size: 339 Coding Exon Count: 1 

Page IndexSequence and LinksPrimersMalaCardsGene AllelesMicroarray Expression
RNA StructureOther SpeciesmRNA DescriptionsOther NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr2:239,140,327-239,142,985)mRNA (may differ from genome)Protein (112 aa)
Gene SorterGenome BrowserOther Species FASTATable SchemaBioGPSExonPrimer
GeneCardsLynxMalacardsMGIPubMed

-  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


-  MalaCards Disease Associations
  MalaCards Gene Search: LOC643387
Diseases sorted by gene-association score: frontotemporal lobar degeneration with ubiquitin-positive inclusions (3)

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

+  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 -67.90195-0.348 Picture PostScript Text
3' UTR -647.442125-0.305 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.

-  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
  BC059397 - Homo sapiens cDNA clone IMAGE:5268977, **** WARNING: chimeric clone ****.
JD200426 - Sequence 181450 from Patent EP1572962.
DQ580109 - Homo sapiens piRNA piR-48221, complete sequence.
JD215286 - Sequence 196310 from Patent EP1572962.
JD499029 - Sequence 480053 from Patent EP1572962.
JD213728 - Sequence 194752 from Patent EP1572962.
JD089146 - Sequence 70170 from Patent EP1572962.
JD093354 - Sequence 74378 from Patent EP1572962.
JD225854 - Sequence 206878 from Patent EP1572962.
LF348438 - JP 2014500723-A/155941: Polycomb-Associated Non-Coding RNAs.
JD290976 - Sequence 272000 from Patent EP1572962.
LF348439 - JP 2014500723-A/155942: Polycomb-Associated Non-Coding RNAs.
LF348441 - JP 2014500723-A/155944: Polycomb-Associated Non-Coding RNAs.
JD393059 - Sequence 374083 from Patent EP1572962.
LF348442 - JP 2014500723-A/155945: Polycomb-Associated Non-Coding RNAs.
JD151573 - Sequence 132597 from Patent EP1572962.
JD250187 - Sequence 231211 from Patent EP1572962.
JD436986 - Sequence 418010 from Patent EP1572962.
JD252875 - Sequence 233899 from Patent EP1572962.
JD558038 - Sequence 539062 from Patent EP1572962.
JD255269 - Sequence 236293 from Patent EP1572962.
JD399944 - Sequence 380968 from Patent EP1572962.
JD339413 - Sequence 320437 from Patent EP1572962.
JD080681 - Sequence 61705 from Patent EP1572962.
JD279300 - Sequence 260324 from Patent EP1572962.
JD547866 - Sequence 528890 from Patent EP1572962.
JD272469 - Sequence 253493 from Patent EP1572962.
MA584015 - JP 2018138019-A/155941: Polycomb-Associated Non-Coding RNAs.
MA584016 - JP 2018138019-A/155942: Polycomb-Associated Non-Coding RNAs.
MA584018 - JP 2018138019-A/155944: Polycomb-Associated Non-Coding RNAs.
MA584019 - JP 2018138019-A/155945: Polycomb-Associated Non-Coding RNAs.
MA823565 - WO 2019013141-A/3: Antisense oligonucleotide for regulating TDP-43 expression level and use thereof.
MA823627 - WO 2019013141-A/65: Antisense oligonucleotide for regulating TDP-43 expression level and use thereof.
MA823567 - WO 2019013141-A/5: Antisense oligonucleotide for regulating TDP-43 expression level and use thereof.

-  Other Names for This Gene
  Alternate Gene Symbols: NR_026923
UCSC ID: uc010znu.2
RefSeq Accession: NR_026923

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NR_026923.1
exon count: 1CDS single in 3' UTR: no RNA size: 2660
ORF size: 339CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 787.00frame shift in genome: no % Coverage: 99.96
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.