Human Gene C1orf56 (ENST00000368926.6) from GENCODE V44
  Description: Homo sapiens chromosome 1 open reading frame 56 (C1orf56), mRNA. (from RefSeq NM_017860)
RefSeq Summary (NM_017860): This gene is a proto-oncogene whose promoter is methylated by DNA methyltransferase 3B (DNMT3B), which represses the proto-oncogene. However, a catalytically inactive isoform of DNMT3B is overexpressed in lymphomas, leading to hypomethylation of the proto-oncogene's promoter and derepression of the proto-oncogene. [provided by RefSeq, Sep 2016].
Gencode Transcript: ENST00000368926.6
Gencode Gene: ENSG00000143443.10
Transcript (Including UTRs)
   Position: hg38 chr1:151,047,751-151,051,420 Size: 3,670 Total Exon Count: 2 Strand: +
Coding Region
   Position: hg38 chr1:151,047,848-151,050,458 Size: 2,611 Coding Exon Count: 2 

Page IndexSequence and LinksUniProtKB CommentsPrimersRNA-Seq ExpressionMicroarray Expression
RNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA DescriptionsOther Names
Methods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr1:151,047,751-151,051,420)mRNA (may differ from genome)Protein (341 aa)
Gene SorterGenome BrowserOther Species FASTATable SchemaAlphaFoldBioGPS
EnsemblEntrez GeneExonPrimerGencodeGeneCardsHGNC
HPRDLynxMalacardsMGIneXtProtPubMed
UniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: MENT_HUMAN
DESCRIPTION: RecName: Full=Protein MENT; AltName: Full=Methylated in normal thymocytes protein; Flags: Precursor;
FUNCTION: Involved in control of cellular proliferation. Onconcogenic modifier contributing to the tumor suppressor function of DNMT3B.
SUBCELLULAR LOCATION: Secreted (Potential).
TISSUE SPECIFICITY: Plasma. Overexpressed in lymphomas.
PTM: Phosphorylation sites are present in the extracellular medium.

-  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


-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 124.01 RPKM in Testis
Total median expression: 309.48 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 -38.9097-0.401 Picture PostScript Text
3' UTR -227.10962-0.236 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 Q9BUN1
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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
Genome BrowserGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
MGIRGD    
Protein SequenceProtein Sequence    
AlignmentAlignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003674 molecular_function

Biological Process:
GO:0042127 regulation of cell proliferation

Cellular Component:
GO:0005575 cellular_component
GO:0005576 extracellular region


-  Descriptions from all associated GenBank mRNAs
  AK301712 - Homo sapiens cDNA FLJ56800 complete cds.
AY358436 - Homo sapiens clone DNA59616 VPAA547 (UNQ547) mRNA, complete cds.
AK315680 - Homo sapiens cDNA, FLJ96774.
AK000526 - Homo sapiens cDNA FLJ20519 fis, clone KAT10365.
BC002469 - Homo sapiens chromosome 1 open reading frame 56, mRNA (cDNA clone MGC:1029 IMAGE:3347975), complete cds.
KJ899040 - Synthetic construct Homo sapiens clone ccsbBroadEn_08434 C1orf56 gene, encodes complete protein.
JD457877 - Sequence 438901 from Patent EP1572962.
JD166117 - Sequence 147141 from Patent EP1572962.
JD551015 - Sequence 532039 from Patent EP1572962.
JD037178 - Sequence 18202 from Patent EP1572962.
JD241479 - Sequence 222503 from Patent EP1572962.
JD556768 - Sequence 537792 from Patent EP1572962.
JD378471 - Sequence 359495 from Patent EP1572962.
JD486232 - Sequence 467256 from Patent EP1572962.
JD197419 - Sequence 178443 from Patent EP1572962.
JD237986 - Sequence 219010 from Patent EP1572962.
JD503762 - Sequence 484786 from Patent EP1572962.
JD324542 - Sequence 305566 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: B2RDU8, ENST00000368926.1, ENST00000368926.2, ENST00000368926.3, ENST00000368926.4, ENST00000368926.5, MENT, MENT_HUMAN, NM_017860, Q9BUN1, Q9NWZ4, uc001ewn.1, uc001ewn.2, uc001ewn.3, uc001ewn.4, uc001ewn.5, UNQ547/PRO1104
UCSC ID: ENST00000368926.6
RefSeq Accession: NM_017860
Protein: Q9BUN1 (aka MENT_HUMAN)
CCDS: CCDS980.1

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.