Human Gene PABIR2 (uc004exq.3)
  Description: Homo sapiens family with sequence similarity 122B (PABIR2), transcript variant 4, mRNA.
Transcript (Including UTRs)
   Position: hg19 chrX:133,903,596-133,930,385 Size: 26,790 Total Exon Count: 10 Strand: -
Coding Region
   Position: hg19 chrX:133,906,169-133,930,235 Size: 24,067 Coding Exon Count: 10 

Page IndexSequence and LinksPrimersGene AllelesRNA-Seq ExpressionMicroarray Expression
RNA StructureProtein StructureOther SpeciesmRNA DescriptionsOther NamesModel Information
Methods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chrX:133,903,596-133,930,385)mRNA (may differ from genome)Protein (266 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsH-INV
LynxMGIPubMedTreefamUniProtKBWikipedia
BioGrid 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: 25.39 RPKM in Testis
Total median expression: 687.31 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 -40.50150-0.270 Picture PostScript Text
3' UTR -663.482573-0.258 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 Q7Z309-3
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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
  BX538218 - Homo sapiens mRNA; cDNA DKFZp686L20116 (from clone DKFZp686L20116); complete cds.
AK124940 - Homo sapiens cDNA FLJ42950 fis, clone BRSTN2007284.
AL832218 - Homo sapiens mRNA; cDNA DKFZp686E0936 (from clone DKFZp686E0936).
AK026809 - Homo sapiens cDNA: FLJ23156 fis, clone LNG09609.
AK125991 - Homo sapiens cDNA FLJ44003 fis, clone TESTI4022936.
AK124650 - Homo sapiens cDNA FLJ42659 fis, clone BRAMY2003008.
JD526898 - Sequence 507922 from Patent EP1572962.
AK297720 - Homo sapiens cDNA FLJ57750 complete cds.
AB541015 - Homo sapiens SPACIA2 mRNA for synoviocyte proliferation associated in collagen-induced arthritis 2, isoform 2, complete cds.
AK292517 - Homo sapiens cDNA FLJ76450 complete cds.
BC019221 - Homo sapiens family with sequence similarity 122B, mRNA (cDNA clone MGC:11157 IMAGE:3841054), complete cds.
BC032419 - Homo sapiens family with sequence similarity 122B, mRNA (cDNA clone IMAGE:5222139), complete cds.
JD086629 - Sequence 67653 from Patent EP1572962.
JD244440 - Sequence 225464 from Patent EP1572962.
JD563654 - Sequence 544678 from Patent EP1572962.
JD299243 - Sequence 280267 from Patent EP1572962.
AB541014 - Homo sapiens SPACIA2 mRNA for synoviocyte proliferation associated in collagen-induced arthritis 2, isoform 1, complete cds.
CU676388 - Synthetic construct Homo sapiens gateway clone IMAGE:100021816 5' read FAM122B mRNA.
AM393279 - Synthetic construct Homo sapiens clone IMAGE:100002156 for hypothetical protein (FAM122B gene).
KJ895706 - Synthetic construct Homo sapiens clone ccsbBroadEn_05100 FAM122B gene, encodes complete protein.
AB528130 - Synthetic construct DNA, clone: pF1KE0166, Homo sapiens FAM122B gene for family with sequence similarity 122B, without stop codon, in Flexi system.
JD185615 - Sequence 166639 from Patent EP1572962.
JD176860 - Sequence 157884 from Patent EP1572962.
JD294293 - Sequence 275317 from Patent EP1572962.
JD226383 - Sequence 207407 from Patent EP1572962.
JD405707 - Sequence 386731 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: FAM122B, NM_001170756, NP_001164227, Q7Z309-3
UCSC ID: uc004exq.3
RefSeq Accession: NM_001170756
Protein: Q7Z309-3, splice isoform of Q7Z309 CCDS: CCDS55499.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_001170756.1
exon count: 10CDS single in 3' UTR: no RNA size: 3534
ORF size: 801CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 1740.00frame shift in genome: no % Coverage: 99.72
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: 1877# 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.