Human Gene C1orf52 (uc001dkv.3)
  Description: Homo sapiens chromosome 1 open reading frame 52 (C1orf52), transcript variant 1, mRNA.
Transcript (Including UTRs)
   Position: hg19 chr1:85,715,637-85,725,355 Size: 9,719 Total Exon Count: 3 Strand: -
Coding Region
   Position: hg19 chr1:85,718,312-85,725,316 Size: 7,005 Coding Exon Count: 3 

Page IndexSequence and LinksUniProtKB CommentsPrimersGenetic AssociationsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsOther NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr1:85,715,637-85,725,355)mRNA (may differ from genome)Protein (182 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMGI
neXtProtPubMedTreefamUniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: CA052_HUMAN
DESCRIPTION: RecName: Full=UPF0690 protein C1orf52; AltName: Full=BCL10-associated gene protein;
TISSUE SPECIFICITY: Expressed in all tissues tested including heart, placenta, liver, skeletal muscle, kidney and pancreas. Weak expression in brain and lung.
SIMILARITY: Belongs to the UPF0690 family.

-  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


-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): C1orf52
CDC HuGE Published Literature: C1orf52

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  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: 11.46 RPKM in Brain - Frontal Cortex (BA9)
Total median expression: 334.47 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 -13.1039-0.336 Picture PostScript Text
3' UTR -744.802675-0.278 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:
PF15559 - Domain of unknown function (DUF4660)

ModBase Predicted Comparative 3D Structure on Q8N6N3
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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     
      
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003723 RNA binding

Cellular Component:
GO:0005634 nucleus


-  Descriptions from all associated GenBank mRNAs
  AK126929 - Homo sapiens cDNA FLJ44982 fis, clone BRAWH3003975.
LF206361 - JP 2014500723-A/13864: Polycomb-Associated Non-Coding RNAs.
AY486331 - Homo sapiens BCL10-associated protein variant 1 (BAG) mRNA, complete cds, alternatively spliced.
AY486332 - Homo sapiens BCL10-associated protein variant 2 (BAG) mRNA, complete cds, alternatively spliced.
BC029538 - Homo sapiens chromosome 1 open reading frame 52, mRNA (cDNA clone MGC:33961 IMAGE:5303467), complete cds.
MA441938 - JP 2018138019-A/13864: Polycomb-Associated Non-Coding RNAs.
BC051692 - Homo sapiens cDNA clone IMAGE:5287350.
JD101849 - Sequence 82873 from Patent EP1572962.
JD276459 - Sequence 257483 from Patent EP1572962.
JD536216 - Sequence 517240 from Patent EP1572962.
JD276458 - Sequence 257482 from Patent EP1572962.
JD376141 - Sequence 357165 from Patent EP1572962.
JD498038 - Sequence 479062 from Patent EP1572962.
LF353537 - JP 2014500723-A/161040: Polycomb-Associated Non-Coding RNAs.
LF353536 - JP 2014500723-A/161039: Polycomb-Associated Non-Coding RNAs.
AK024939 - Homo sapiens cDNA: FLJ21286 fis, clone COL01915.
JD536798 - Sequence 517822 from Patent EP1572962.
JD046476 - Sequence 27500 from Patent EP1572962.
JD316415 - Sequence 297439 from Patent EP1572962.
JD327123 - Sequence 308147 from Patent EP1572962.
JD525260 - Sequence 506284 from Patent EP1572962.
JD220882 - Sequence 201906 from Patent EP1572962.
LF353535 - JP 2014500723-A/161038: Polycomb-Associated Non-Coding RNAs.
MA589114 - JP 2018138019-A/161040: Polycomb-Associated Non-Coding RNAs.
MA589113 - JP 2018138019-A/161039: Polycomb-Associated Non-Coding RNAs.
MA589112 - JP 2018138019-A/161038: Polycomb-Associated Non-Coding RNAs.
AF387611 - Homo sapiens gm117 form A mRNA, partial cds, alternatively spliced.
AF387612 - Homo sapiens gm117 form B mRNA, partial cds, alternatively spliced.
LF353531 - JP 2014500723-A/161034: Polycomb-Associated Non-Coding RNAs.
MA589108 - JP 2018138019-A/161034: Polycomb-Associated Non-Coding RNAs.

-  Other Names for This Gene
  Alternate Gene Symbols: B3KX89, BAG, CA052_HUMAN, GM117, NM_198077, NP_932343, Q8N6N3, Q8TDK5, Q8TDK6
UCSC ID: uc001dkv.3
RefSeq Accession: NM_198077
Protein: Q8N6N3 (aka CA052_HUMAN)
CCDS: CCDS703.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_198077.3
exon count: 3CDS single in 3' UTR: no RNA size: 3275
ORF size: 549CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 1298.00frame shift in genome: no % Coverage: 99.63
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.