Human Gene C1orf109 (uc001cbp.3)
  Description: Homo sapiens chromosome 1 open reading frame 109 (C1orf109), mRNA.
Transcript (Including UTRs)
   Position: hg19 chr1:38,147,242-38,156,192 Size: 8,951 Total Exon Count: 5 Strand: -
Coding Region
   Position: hg19 chr1:38,148,795-38,155,552 Size: 6,758 Coding Exon Count: 4 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsOther NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr1:38,147,242-38,156,192)mRNA (may differ from genome)Protein (203 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMGI
neXtProtOMIMPubMedTreefamUniProtKBWikipedia
BioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: CA109_HUMAN
DESCRIPTION: RecName: Full=Uncharacterized protein C1orf109;

-  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


-  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: 4.76 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 158.75 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 -69.70190-0.367 Picture PostScript Text
3' UTR -441.051553-0.284 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:
PF15011 - Casein Kinase 2 substrate

ModBase Predicted Comparative 3D Structure on Q9NX04
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 orthologGenome BrowserNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
  Ensembl   
  Protein Sequence   
  Alignment   

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005515 protein binding

Cellular Component:
GO:0005634 nucleus
GO:0005737 cytoplasm


-  Descriptions from all associated GenBank mRNAs
  AK000515 - Homo sapiens cDNA FLJ20508 fis, clone KAT09559.
LF383906 - JP 2014500723-A/191409: Polycomb-Associated Non-Coding RNAs.
BC018109 - Homo sapiens chromosome 1 open reading frame 109, mRNA (cDNA clone MGC:8853 IMAGE:3914920), complete cds.
AK092319 - Homo sapiens cDNA FLJ35000 fis, clone OCBBF2011872.
AX747480 - Sequence 1005 from Patent EP1308459.
BC063843 - Homo sapiens chromosome 1 open reading frame 109, mRNA (cDNA clone MGC:74978 IMAGE:6501461), complete cds.
JD305097 - Sequence 286121 from Patent EP1572962.
JD508608 - Sequence 489632 from Patent EP1572962.
JD106934 - Sequence 87958 from Patent EP1572962.
JD244927 - Sequence 225951 from Patent EP1572962.
JD149998 - Sequence 131022 from Patent EP1572962.
JD360229 - Sequence 341253 from Patent EP1572962.
JD120357 - Sequence 101381 from Patent EP1572962.
JD348965 - Sequence 329989 from Patent EP1572962.
JD514673 - Sequence 495697 from Patent EP1572962.
JD448897 - Sequence 429921 from Patent EP1572962.
JD297375 - Sequence 278399 from Patent EP1572962.
JD175077 - Sequence 156101 from Patent EP1572962.
JD089360 - Sequence 70384 from Patent EP1572962.
JD188034 - Sequence 169058 from Patent EP1572962.
JD454893 - Sequence 435917 from Patent EP1572962.
JD114568 - Sequence 95592 from Patent EP1572962.
JD131312 - Sequence 112336 from Patent EP1572962.
JD552982 - Sequence 534006 from Patent EP1572962.
AK299377 - Homo sapiens cDNA FLJ55172 complete cds.
LF356547 - JP 2014500723-A/164050: Polycomb-Associated Non-Coding RNAs.
JD092987 - Sequence 74011 from Patent EP1572962.
JD446790 - Sequence 427814 from Patent EP1572962.
LF356546 - JP 2014500723-A/164049: Polycomb-Associated Non-Coding RNAs.
JD282572 - Sequence 263596 from Patent EP1572962.
JD110580 - Sequence 91604 from Patent EP1572962.
JD530065 - Sequence 511089 from Patent EP1572962.
JD355200 - Sequence 336224 from Patent EP1572962.
JD195507 - Sequence 176531 from Patent EP1572962.
JD532175 - Sequence 513199 from Patent EP1572962.
AK316093 - Homo sapiens cDNA, FLJ78992 complete cds.
JD550952 - Sequence 531976 from Patent EP1572962.
CU687832 - Synthetic construct Homo sapiens gateway clone IMAGE:100022753 5' read C1orf109 mRNA.
HQ447505 - Synthetic construct Homo sapiens clone IMAGE:100070842; CCSB014291_01 chromosome 1 open reading frame 109 (C1orf109) gene, encodes complete protein.
KJ904786 - Synthetic construct Homo sapiens clone ccsbBroadEn_14180 C1orf109 gene, encodes complete protein.
JD085521 - Sequence 66545 from Patent EP1572962.
AK056029 - Homo sapiens cDNA FLJ31467 fis, clone NT2NE2001397.
JD566570 - Sequence 547594 from Patent EP1572962.
MA619483 - JP 2018138019-A/191409: Polycomb-Associated Non-Coding RNAs.
MA592124 - JP 2018138019-A/164050: Polycomb-Associated Non-Coding RNAs.
MA592123 - JP 2018138019-A/164049: Polycomb-Associated Non-Coding RNAs.

-  Other Names for This Gene
  Alternate Gene Symbols: CA109_HUMAN, D3DPT1, NM_017850, NP_060320, Q8WVD1, Q9NX04
UCSC ID: uc001cbp.3
RefSeq Accession: NM_017850
Protein: Q9NX04 (aka CA109_HUMAN)
CCDS: CCDS423.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_017850.1
exon count: 5CDS single in 3' UTR: no RNA size: 2376
ORF size: 612CDS single in intron: no Alignment % ID: 99.79
txCdsPredict score: 1390.00frame shift in genome: no % Coverage: 99.12
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: 82# 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.