Human Gene C1orf107 (uc001hhr.1)
  Description: digestive-organ expansion factor homolog
Transcript (Including UTRs)
   Position: hg18 chr1:208,067,956-208,097,531 Size: 29,576 Total Exon Count: 12 Strand: +
Coding Region
   Position: hg18 chr1:208,068,032-208,091,415 Size: 23,384 Coding Exon Count: 12 

Page IndexSequence and LinksUniProtKB CommentsPrimersMicroarray ExpressionRNA Structure
Protein StructureOther SpeciesGO AnnotationsmRNA DescriptionsPathwaysOther Names
Model InformationMethods
Data last updated at UCSC: 2009-03-03

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr1:208,067,956-208,097,531)mRNA (may differ from genome)Protein (756 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHPRDMGIPubMedReactome
TreefamUniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: DIEXF_HUMAN
DESCRIPTION: RecName: Full=Digestive organ expansion factor homolog;
FUNCTION: Regulates the p53 pathway to control the expansion growth of digestive organs (By similarity).
SUBCELLULAR LOCATION: Nucleus (By similarity). Nucleus, nucleolus.
SIMILARITY: Belongs to the def family.
SEQUENCE CAUTION: Sequence=CAI95693.1; Type=Erroneous gene model prediction;

-  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


-  Microarray Expression Data
 
Expression ratio colors:

GNF Expression Atlas 2 Data from U133A and GNF1H Chips

      
      
      
     
    
     
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Affymetrix All Exon Microarrays

           
Ratios

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -15.4076-0.203 Picture PostScript Text
3' UTR -1834.826116-0.300 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
IPR010678 - Digest_organ_expansion_fac-prd

Pfam Domains:
PF06862 - Protein of unknown function (DUF1253)

ModBase Predicted Comparative 3D Structure on Q68CQ4
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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 BrowserNo orthologGenome BrowserGenome BrowserNo orthologGenome Browser
Gene DetailsGene Details Gene Details Gene Details
Gene SorterGene Sorter Gene Sorter Gene Sorter
MGIRGDEnsemblFlyBase SGD
Protein Sequence Protein SequenceProtein Sequence Protein Sequence
Alignment AlignmentAlignment Alignment

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003723 RNA binding
GO:0005515 protein binding
GO:0019843 rRNA binding
GO:0034511 U3 snoRNA binding

Biological Process:
GO:0000462 maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
GO:0006364 rRNA processing
GO:0007275 multicellular organism development

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005730 nucleolus
GO:0032040 small-subunit processome


-  Descriptions from all associated GenBank mRNAs
  AK314061 - Homo sapiens cDNA, FLJ94727.
AK289613 - Homo sapiens cDNA FLJ78223 complete cds.
BC022964 - Homo sapiens chromosome 1 open reading frame 107, mRNA (cDNA clone MGC:29875 IMAGE:5110673), complete cds.
CR749825 - Homo sapiens mRNA; cDNA DKFZp686E19106 (from clone DKFZp686E19106).
BX648514 - Homo sapiens mRNA; cDNA DKFZp686L2372 (from clone DKFZp686L2372).
CU692760 - Synthetic construct Homo sapiens gateway clone IMAGE:100017804 5' read C1orf107 mRNA.
AK096118 - Homo sapiens cDNA FLJ38799 fis, clone LIVER2005198.
AK123674 - Homo sapiens cDNA FLJ41680 fis, clone HCASM2003237.
AK295799 - Homo sapiens cDNA FLJ52627 complete cds.
AK022766 - Homo sapiens cDNA FLJ12704 fis, clone NT2RP1000836.
JD527080 - Sequence 508104 from Patent EP1572962.
JD402310 - Sequence 383334 from Patent EP1572962.
JD566530 - Sequence 547554 from Patent EP1572962.
JD361849 - Sequence 342873 from Patent EP1572962.
JD506793 - Sequence 487817 from Patent EP1572962.
JD505566 - Sequence 486590 from Patent EP1572962.
JD399512 - Sequence 380536 from Patent EP1572962.
JD420446 - Sequence 401470 from Patent EP1572962.
JD563957 - Sequence 544981 from Patent EP1572962.
JD451606 - Sequence 432630 from Patent EP1572962.
JD433015 - Sequence 414039 from Patent EP1572962.
JD435119 - Sequence 416143 from Patent EP1572962.
KJ898654 - Synthetic construct Homo sapiens clone ccsbBroadEn_08048 DIEXF gene, encodes complete protein.
JD322332 - Sequence 303356 from Patent EP1572962.
JD060381 - Sequence 41405 from Patent EP1572962.
JD083561 - Sequence 64585 from Patent EP1572962.
JD235957 - Sequence 216981 from Patent EP1572962.
JD286271 - Sequence 267295 from Patent EP1572962.
JD301043 - Sequence 282067 from Patent EP1572962.
JD039601 - Sequence 20625 from Patent EP1572962.
JD275470 - Sequence 256494 from Patent EP1572962.
JD071991 - Sequence 53015 from Patent EP1572962.
JD141102 - Sequence 122126 from Patent EP1572962.
JD254049 - Sequence 235073 from Patent EP1572962.
JD116681 - Sequence 97705 from Patent EP1572962.
JD059786 - Sequence 40810 from Patent EP1572962.
JD188190 - Sequence 169214 from Patent EP1572962.
JD331445 - Sequence 312469 from Patent EP1572962.
JD122334 - Sequence 103358 from Patent EP1572962.
JD066292 - Sequence 47316 from Patent EP1572962.
JD215006 - Sequence 196030 from Patent EP1572962.
JD303317 - Sequence 284341 from Patent EP1572962.
JD252979 - Sequence 234003 from Patent EP1572962.
JD066027 - Sequence 47051 from Patent EP1572962.
JD102568 - Sequence 83592 from Patent EP1572962.
JD174214 - Sequence 155238 from Patent EP1572962.
JD037889 - Sequence 18913 from Patent EP1572962.
JD214329 - Sequence 195353 from Patent EP1572962.
JD203170 - Sequence 184194 from Patent EP1572962.
JD050192 - Sequence 31216 from Patent EP1572962.
JD174957 - Sequence 155981 from Patent EP1572962.
JD338283 - Sequence 319307 from Patent EP1572962.
JD048254 - Sequence 29278 from Patent EP1572962.
JD132345 - Sequence 113369 from Patent EP1572962.
JD237333 - Sequence 218357 from Patent EP1572962.
JD164624 - Sequence 145648 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q68CQ4 (Reactome details) participates in the following event(s):

R-HSA-6790906 EMG1 of the SSU processome methylates pseudouridine-1248 of 18S rRNA yielding N(1)-methylpseudouridine-1248
R-HSA-6791226 Major pathway of rRNA processing in the nucleolus and cytosol
R-HSA-6790901 rRNA modification in the nucleus and cytosol
R-HSA-8868773 rRNA processing in the nucleus and cytosol
R-HSA-72312 rRNA processing
R-HSA-8953854 Metabolism of RNA

-  Other Names for This Gene
  Alternate Gene Symbols: DEF, DEF_HUMAN, NM_014388, NP_055203, O75992, Q4VY00, Q63HL9, Q68CQ4
UCSC ID: uc001hhr.1
RefSeq Accession: NM_014388
Protein: Q68CQ4 (aka DIEXF_HUMAN)
CCDS: CCDS1493.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_014388.5
exon count: 12CDS single in 3' UTR: no RNA size: 8463
ORF size: 2271CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 4565.00frame shift in genome: no % Coverage: 100.00
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.