Human Gene PABIR3 (uc022ceo.1)
  Description: Homo sapiens family with sequence similarity 122C (PABIR3), transcript variant 6, mRNA.
Transcript (Including UTRs)
   Position: hg19 chrX:133,941,223-133,957,015 Size: 15,793 Total Exon Count: 3 Strand: +
Coding Region
   Position: hg19 chrX:133,941,629-133,955,407 Size: 13,779 Coding Exon Count: 3 

Page IndexSequence and LinksUniProtKB CommentsPrimersGene AllelesRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesmRNA DescriptionsOther Names
Model InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chrX:133,941,223-133,957,015)mRNA (may differ from genome)Protein (79 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsH-INV
LynxMGIPubMedUniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: F5H036_HUMAN
DESCRIPTION: SubName: Full=Protein FAM122C;
CAUTION: The sequence shown here is derived from an Ensembl automatic analysis pipeline and should be considered as preliminary data.

-  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: 3.52 RPKM in Ovary
Total median expression: 32.39 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 -137.10406-0.338 Picture PostScript Text
3' UTR -404.511608-0.252 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
  InterPro Domains: Graphical view of domain structure
IPR026716 - FAM122

ModBase Predicted Comparative 3D Structure on F5H036
FrontTopSide
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
      
      
      
      
      

-  Descriptions from all associated GenBank mRNAs
  AK307219 - Homo sapiens cDNA, FLJ97167.
BC016784 - Homo sapiens hypothetical protein BC017868, mRNA (cDNA clone IMAGE:4072765), partial cds.
BC017868 - Homo sapiens family with sequence similarity 122C, mRNA (cDNA clone MGC:22643 IMAGE:4699951), complete cds.
AK310079 - Homo sapiens cDNA, FLJ17121.
AK295485 - Homo sapiens cDNA FLJ61273 complete cds.
BC063491 - Homo sapiens family with sequence similarity 122C, mRNA (cDNA clone MGC:74677 IMAGE:5229041), complete cds.
BC065225 - Homo sapiens family with sequence similarity 122C, mRNA (cDNA clone MGC:74678 IMAGE:5724414), complete cds.
KJ906441 - Synthetic construct Homo sapiens clone ccsbBroadEn_16111 FAM122C gene, encodes complete protein.
CU676092 - Synthetic construct Homo sapiens gateway clone IMAGE:100022021 5' read FAM122C mRNA.
KJ895708 - Synthetic construct Homo sapiens clone ccsbBroadEn_05102 FAM122C gene, encodes complete protein.
HQ448058 - Synthetic construct Homo sapiens clone IMAGE:100071437; CCSB012125_01 family with sequence similarity 122C (FAM122C) gene, encodes complete protein.
KJ895707 - Synthetic construct Homo sapiens clone ccsbBroadEn_05101 FAM122C gene, encodes complete protein.
CU687752 - Synthetic construct Homo sapiens gateway clone IMAGE:100021604 5' read FAM122C mRNA.
AK090611 - Homo sapiens cDNA FLJ33292 fis, clone BNGH42000130, weakly similar to Homo sapiens beta glucuronidase isoform.
JD088531 - Sequence 69555 from Patent EP1572962.
JD204521 - Sequence 185545 from Patent EP1572962.
JD509503 - Sequence 490527 from Patent EP1572962.
JD111870 - Sequence 92894 from Patent EP1572962.
JD349289 - Sequence 330313 from Patent EP1572962.
JD298870 - Sequence 279894 from Patent EP1572962.
JD365727 - Sequence 346751 from Patent EP1572962.
JD164824 - Sequence 145848 from Patent EP1572962.
JD263181 - Sequence 244205 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: F5H036, F5H036_HUMAN, FAM122C, NM_001170783, NP_001164254
UCSC ID: uc022ceo.1
RefSeq Accession: NM_001170783
Protein: F5H036

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_001170783.1
exon count: 3CDS single in 3' UTR: no RNA size: 2269
ORF size: 240CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 478.00frame shift in genome: no % Coverage: 99.34
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: 347# 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.