Human Gene PRXL2B (uc010nzf.2)
  Description: Homo sapiens family with sequence similarity 213, member B (PRXL2B), transcript variant 6, mRNA.
Transcript (Including UTRs)
   Position: hg19 chr1:2,518,189-2,522,908 Size: 4,720 Total Exon Count: 6 Strand: +
Coding Region
   Position: hg19 chr1:2,518,235-2,520,866 Size: 2,632 Coding Exon Count: 6 

Page IndexSequence and LinksPrimersGene AllelesRNA-Seq ExpressionMicroarray Expression
RNA StructureProtein StructureOther SpeciesmRNA DescriptionsPathwaysOther Names
Model InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr1:2,518,189-2,522,908)mRNA (may differ from genome)Protein (191 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsH-INV
LynxMGIPubMedReactomeUniProtKBBioGrid 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


+  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: 8.60 RPKM in Colon - Transverse
Total median expression: 180.40 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 -12.6046-0.274 Picture PostScript Text
3' UTR -876.652042-0.429 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:
PF13911 - AhpC/TSA antioxidant enzyme

ModBase Predicted Comparative 3D Structure on Q8TBF2-5
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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
  AK303504 - Homo sapiens cDNA FLJ54774 complete cds.
AK291908 - Homo sapiens cDNA FLJ78325 complete cds.
AK298926 - Homo sapiens cDNA FLJ52973 complete cds.
AK075273 - Homo sapiens cDNA FLJ90792 fis, clone THYRO1001608.
AF425266 - Homo sapiens unknown protein mRNA, complete cds.
BC022547 - Homo sapiens chromosome 1 open reading frame 93, mRNA (cDNA clone MGC:26818 IMAGE:4812314), complete cds.
AK057027 - Homo sapiens cDNA FLJ32465 fis, clone SKNMC1000264.
JD459039 - Sequence 440063 from Patent EP1572962.
AK308034 - Homo sapiens cDNA, FLJ97982.
AK316243 - Homo sapiens cDNA, FLJ79142 complete cds.
KJ903733 - Synthetic construct Homo sapiens clone ccsbBroadEn_13127 FAM213B gene, encodes complete protein.
AK094901 - Homo sapiens cDNA FLJ37582 fis, clone BRCOC2004354.
DL491353 - Novel nucleic acids.
DL489983 - Novel nucleic acids.
CR749706 - Homo sapiens mRNA; cDNA DKFZp547M123 (from clone DKFZp547M123).
JD140961 - Sequence 121985 from Patent EP1572962.
JD132743 - Sequence 113767 from Patent EP1572962.
JD424440 - Sequence 405464 from Patent EP1572962.
JD138582 - Sequence 119606 from Patent EP1572962.
JD278940 - Sequence 259964 from Patent EP1572962.
JD306753 - Sequence 287777 from Patent EP1572962.
JD103218 - Sequence 84242 from Patent EP1572962.
JD339625 - Sequence 320649 from Patent EP1572962.
JD372950 - Sequence 353974 from Patent EP1572962.
JD544632 - Sequence 525656 from Patent EP1572962.
JD449941 - Sequence 430965 from Patent EP1572962.
JD355983 - Sequence 337007 from Patent EP1572962.
JD093255 - Sequence 74279 from Patent EP1572962.
JD551056 - Sequence 532080 from Patent EP1572962.
JD387013 - Sequence 368037 from Patent EP1572962.
JD382465 - Sequence 363489 from Patent EP1572962.
JD107182 - Sequence 88206 from Patent EP1572962.
JD336199 - Sequence 317223 from Patent EP1572962.
JD534906 - Sequence 515930 from Patent EP1572962.
JD146451 - Sequence 127475 from Patent EP1572962.
JD270714 - Sequence 251738 from Patent EP1572962.
JD093757 - Sequence 74781 from Patent EP1572962.
JD387829 - Sequence 368853 from Patent EP1572962.
JD187587 - Sequence 168611 from Patent EP1572962.
JD426972 - Sequence 407996 from Patent EP1572962.
JD545694 - Sequence 526718 from Patent EP1572962.
JD466093 - Sequence 447117 from Patent EP1572962.
JD470586 - Sequence 451610 from Patent EP1572962.
JD439771 - Sequence 420795 from Patent EP1572962.
JD159783 - Sequence 140807 from Patent EP1572962.
JD387861 - Sequence 368885 from Patent EP1572962.
JD545876 - Sequence 526900 from Patent EP1572962.
JD259051 - Sequence 240075 from Patent EP1572962.
JD155986 - Sequence 137010 from Patent EP1572962.
JD185643 - Sequence 166667 from Patent EP1572962.
JD065835 - Sequence 46859 from Patent EP1572962.
JD076107 - Sequence 57131 from Patent EP1572962.
JD220578 - Sequence 201602 from Patent EP1572962.
JD231577 - Sequence 212601 from Patent EP1572962.
JD328251 - Sequence 309275 from Patent EP1572962.
JD254827 - Sequence 235851 from Patent EP1572962.
JD190065 - Sequence 171089 from Patent EP1572962.
JD168234 - Sequence 149258 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q8TBF2 (Reactome details) participates in the following event(s):

R-HSA-2161612 PGH2 is reduced to PGF2a by FAM213B
R-HSA-2162123 Synthesis of Prostaglandins (PG) and Thromboxanes (TX)
R-HSA-2142753 Arachidonic acid metabolism
R-HSA-8978868 Fatty acid metabolism
R-HSA-556833 Metabolism of lipids
R-HSA-1430728 Metabolism

-  Other Names for This Gene
  Alternate Gene Symbols: C1orf93, FAM213B, NM_001195741, NP_001182670, Q8TBF2-5
UCSC ID: uc010nzf.2
RefSeq Accession: NM_001195741
Protein: Q8TBF2-5, splice isoform of Q8TBF2 CCDS: CCDS55564.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_001195741.1
exon count: 6CDS single in 3' UTR: no RNA size: 2680
ORF size: 576CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 1237.00frame shift in genome: no % Coverage: 99.40
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.