Human Gene PRXL2A (uc001kcc.4)
  Description: Homo sapiens family with sequence similarity 213, member A (PRXL2A), transcript variant 1, mRNA.
Transcript (Including UTRs)
   Position: hg19 chr10:82,168,242-82,192,753 Size: 24,512 Total Exon Count: 6 Strand: +
Coding Region
   Position: hg19 chr10:82,180,224-82,191,855 Size: 11,632 Coding Exon Count: 5 

Page IndexSequence and LinksUniProtKB CommentsPrimersGene AllelesRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
Other NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr10:82,168,242-82,192,753)mRNA (may differ from genome)Protein (229 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsGeneNetwork
H-INVHPRDLynxMGIneXtProtOMIM
PubMedTreefamUniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: F213A_HUMAN
DESCRIPTION: RecName: Full=Redox-regulatory protein FAM213A; AltName: Full=Peroxiredoxin-like 2 activated in M-CSF stimulated monocytes; Short=Protein PAMM;
FUNCTION: Involved in redox regulation of the cell. Acts as an antioxidant. Inhibits TNFSF11-induced NFKB1 and JUN activation and osteoclast differentiation. May affect bone resorption and help to maintain bone mass.
SUBCELLULAR LOCATION: Cytoplasm.
TISSUE SPECIFICITY: Expressed in CSF1 and TNFSF11-stimulated CD14(+) peripheral blood mononuclear cells (PBMCs).
INDUCTION: By CSF1 in peripheral blood mononuclear cells (PBMCs). This induction is reduced in the presence of TNFSF11.
MISCELLANEOUS: The active site cysteines correspond to the redox- active cysteines of peroxiredoxins.
SIMILARITY: Belongs to the peroxiredoxin-like FAM213 family. FAM213A subfamily.
SEQUENCE CAUTION: Sequence=AAK55527.1; Type=Erroneous initiation; Note=Translation N-terminally extended; Sequence=BAG37828.1; Type=Erroneous initiation; Note=Translation N-terminally extended;

-  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: 116.10 RPKM in Adipose - Subcutaneous
Total median expression: 1751.78 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 -77.40160-0.484 Picture PostScript Text
3' UTR -247.90898-0.276 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
IPR012336 - Thioredoxin-like_fold

Pfam Domains:
PF13911 - AhpC/TSA antioxidant enzyme

SCOP Domains:
52833 - Thioredoxin-like

ModBase Predicted Comparative 3D Structure on Q9BRX8
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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 orthologGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGD    
 Protein Sequence    
 Alignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0016209 antioxidant activity

Biological Process:
GO:0045670 regulation of osteoclast differentiation
GO:0055114 oxidation-reduction process
GO:0098869 cellular oxidant detoxification

Cellular Component:
GO:0005576 extracellular region
GO:0005737 cytoplasm


-  Descriptions from all associated GenBank mRNAs
  AK075447 - Homo sapiens cDNA PSEC0139 fis, clone PLACE1005760.
LF210018 - JP 2014500723-A/17521: Polycomb-Associated Non-Coding RNAs.
AK074643 - Homo sapiens cDNA FLJ90162 fis, clone HEMBB1002693.
AK315440 - Homo sapiens cDNA, FLJ96497.
AY359059 - Homo sapiens clone DNA60622 SFLQ611 (UNQ611) mRNA, complete cds.
AK225387 - Homo sapiens mRNA for Protein C10orf58 precursor variant, clone: HRC03732.
BC005871 - Homo sapiens chromosome 10 open reading frame 58, mRNA (cDNA clone MGC:4248 IMAGE:3010078), complete cds.
BC071938 - Homo sapiens chromosome 10 open reading frame 58, mRNA (cDNA clone IMAGE:4904753), with apparent retained intron.
AK027858 - Homo sapiens cDNA FLJ14952 fis, clone PLACE3000070.
BC024308 - Homo sapiens chromosome 10 open reading frame 58, mRNA (cDNA clone IMAGE:4905111), with apparent retained intron.
KJ903409 - Synthetic construct Homo sapiens clone ccsbBroadEn_12803 FAM213A gene, encodes complete protein.
MA445595 - JP 2018138019-A/17521: Polycomb-Associated Non-Coding RNAs.
LF212565 - JP 2014500723-A/20068: Polycomb-Associated Non-Coding RNAs.
LF334073 - JP 2014500723-A/141576: Polycomb-Associated Non-Coding RNAs.
MA448142 - JP 2018138019-A/20068: Polycomb-Associated Non-Coding RNAs.
MA569650 - JP 2018138019-A/141576: Polycomb-Associated Non-Coding RNAs.
AF305824 - Homo sapiens PRO2290 mRNA, complete cds.
BC045777 - Homo sapiens chromosome 10 open reading frame 58, mRNA (cDNA clone IMAGE:4791477).
LF334071 - JP 2014500723-A/141574: Polycomb-Associated Non-Coding RNAs.
LF334069 - JP 2014500723-A/141572: Polycomb-Associated Non-Coding RNAs.
LF334067 - JP 2014500723-A/141570: Polycomb-Associated Non-Coding RNAs.
AF086462 - Homo sapiens full length insert cDNA clone ZD85G07.
LF334066 - JP 2014500723-A/141569: Polycomb-Associated Non-Coding RNAs.
LF334065 - JP 2014500723-A/141568: Polycomb-Associated Non-Coding RNAs.
LF334064 - JP 2014500723-A/141567: Polycomb-Associated Non-Coding RNAs.
JD305914 - Sequence 286938 from Patent EP1572962.
JD315163 - Sequence 296187 from Patent EP1572962.
JD558094 - Sequence 539118 from Patent EP1572962.
JD481270 - Sequence 462294 from Patent EP1572962.
JD381146 - Sequence 362170 from Patent EP1572962.
JD362322 - Sequence 343346 from Patent EP1572962.
JD105387 - Sequence 86411 from Patent EP1572962.
JD420990 - Sequence 402014 from Patent EP1572962.
JD420991 - Sequence 402015 from Patent EP1572962.
JD531914 - Sequence 512938 from Patent EP1572962.
JD176648 - Sequence 157672 from Patent EP1572962.
JD444378 - Sequence 425402 from Patent EP1572962.
JD531427 - Sequence 512451 from Patent EP1572962.
JD175606 - Sequence 156630 from Patent EP1572962.
JD331784 - Sequence 312808 from Patent EP1572962.
JD182521 - Sequence 163545 from Patent EP1572962.
JD351000 - Sequence 332024 from Patent EP1572962.
JD351001 - Sequence 332025 from Patent EP1572962.
JD231685 - Sequence 212709 from Patent EP1572962.
JD486957 - Sequence 467981 from Patent EP1572962.
JD491794 - Sequence 472818 from Patent EP1572962.
JD512544 - Sequence 493568 from Patent EP1572962.
JD545673 - Sequence 526697 from Patent EP1572962.
JD512545 - Sequence 493569 from Patent EP1572962.
JD097472 - Sequence 78496 from Patent EP1572962.
JD050876 - Sequence 31900 from Patent EP1572962.
JD364709 - Sequence 345733 from Patent EP1572962.
BC034631 - Homo sapiens cDNA clone IMAGE:4831290, **** WARNING: chimeric clone ****.
JD292173 - Sequence 273197 from Patent EP1572962.
LF334063 - JP 2014500723-A/141566: Polycomb-Associated Non-Coding RNAs.
MA569648 - JP 2018138019-A/141574: Polycomb-Associated Non-Coding RNAs.
MA569646 - JP 2018138019-A/141572: Polycomb-Associated Non-Coding RNAs.
MA569644 - JP 2018138019-A/141570: Polycomb-Associated Non-Coding RNAs.
MA569643 - JP 2018138019-A/141569: Polycomb-Associated Non-Coding RNAs.
MA569642 - JP 2018138019-A/141568: Polycomb-Associated Non-Coding RNAs.
MA569641 - JP 2018138019-A/141567: Polycomb-Associated Non-Coding RNAs.
MA569640 - JP 2018138019-A/141566: Polycomb-Associated Non-Coding RNAs.

-  Other Names for This Gene
  Alternate Gene Symbols: B2RD81, C10orf58, F213A_HUMAN, FAM213A, NM_032333, NP_001230710, PAMM, PRO2290, PSEC0139, Q6UW08, Q8N2K3, Q8NBK9, Q96JR0, Q9BRX8, UNQ611/PRO1198
UCSC ID: uc001kcc.4
RefSeq Accession: NM_032333
Protein: Q9BRX8 (aka F213A_HUMAN)
CCDS: CCDS58089.1, CCDS7368.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_032333.4
exon count: 6CDS single in 3' UTR: no RNA size: 1773
ORF size: 690CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 1462.00frame shift in genome: no % Coverage: 98.59
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.