Human Gene URM1 (uc011may.2)
  Description: Homo sapiens ubiquitin related modifier 1 (URM1), transcript variant 2, mRNA.
Transcript (Including UTRs)
   Position: hg19 chr9:131,133,598-131,154,295 Size: 20,698 Total Exon Count: 4 Strand: +
Coding Region
   Position: hg19 chr9:131,133,660-131,151,792 Size: 18,133 Coding Exon Count: 4 

Page IndexSequence and LinksPrimersCTDGene AllelesRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesmRNA DescriptionsPathways
Other NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr9:131,133,598-131,154,295)mRNA (may differ from genome)Protein (146 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsGeneNetwork
H-INVHGNCHPRDLynxMGIOMIM
PubMedReactomeUniProtKBBioGrid CRISPR DB

-  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: 22.32 RPKM in Spleen
Total median expression: 783.89 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 -20.8062-0.335 Picture PostScript Text
3' UTR -1058.062503-0.423 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:
PF09138 - Urm1 (Ubiquitin related modifier)

ModBase Predicted Comparative 3D Structure on Q9BTM9-2
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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     
      
      
      

-  Descriptions from all associated GenBank mRNAs
  BC003581 - Homo sapiens ubiquitin related modifier 1 homolog (S. cerevisiae), mRNA (cDNA clone MGC:2668 IMAGE:3546655), complete cds.
AK001880 - Homo sapiens cDNA FLJ11018 fis, clone PLACE1003602, highly similar to Homo sapiens mRNA expressed in placenta.
AK097029 - Homo sapiens cDNA FLJ39710 fis, clone SMINT2013031.
AK300877 - Homo sapiens cDNA FLJ58948 complete cds.
BC011620 - Homo sapiens chromosome 9 open reading frame 74, mRNA (cDNA clone IMAGE:3959055), partial cds.
KJ894850 - Synthetic construct Homo sapiens clone ccsbBroadEn_04244 URM1 gene, encodes complete protein.
KJ906339 - Synthetic construct Homo sapiens clone ccsbBroadEn_16009 URM1 gene, encodes complete protein.
D83200 - Homo sapiens mRNA expressed in placenta.
JD020633 - Sequence 1657 from Patent EP1572962.
JD020634 - Sequence 1658 from Patent EP1572962.
JD020635 - Sequence 1659 from Patent EP1572962.
JD035195 - Sequence 16219 from Patent EP1572962.
JD035196 - Sequence 16220 from Patent EP1572962.
JD028963 - Sequence 9987 from Patent EP1572962.
JD023742 - Sequence 4766 from Patent EP1572962.
JD023743 - Sequence 4767 from Patent EP1572962.
JD025891 - Sequence 6915 from Patent EP1572962.
JD033452 - Sequence 14476 from Patent EP1572962.
JD035654 - Sequence 16678 from Patent EP1572962.
JD556603 - Sequence 537627 from Patent EP1572962.
JD226511 - Sequence 207535 from Patent EP1572962.
JD501919 - Sequence 482943 from Patent EP1572962.
JD469030 - Sequence 450054 from Patent EP1572962.
JD170302 - Sequence 151326 from Patent EP1572962.
JD461376 - Sequence 442400 from Patent EP1572962.
JD383139 - Sequence 364163 from Patent EP1572962.
JD020600 - Sequence 1624 from Patent EP1572962.
JD023520 - Sequence 4544 from Patent EP1572962.
JD033621 - Sequence 14645 from Patent EP1572962.
JD495484 - Sequence 476508 from Patent EP1572962.
JD195320 - Sequence 176344 from Patent EP1572962.
JD129804 - Sequence 110828 from Patent EP1572962.
JD140718 - Sequence 121742 from Patent EP1572962.
JD076315 - Sequence 57339 from Patent EP1572962.
JD387023 - Sequence 368047 from Patent EP1572962.
JD174626 - Sequence 155650 from Patent EP1572962.
JD136472 - Sequence 117496 from Patent EP1572962.
JD099123 - Sequence 80147 from Patent EP1572962.
JD097570 - Sequence 78594 from Patent EP1572962.
JD394173 - Sequence 375197 from Patent EP1572962.
JD415838 - Sequence 396862 from Patent EP1572962.
JD250463 - Sequence 231487 from Patent EP1572962.
JD485760 - Sequence 466784 from Patent EP1572962.
JD552776 - Sequence 533800 from Patent EP1572962.
JD460570 - Sequence 441594 from Patent EP1572962.
JD255035 - Sequence 236059 from Patent EP1572962.
JD339265 - Sequence 320289 from Patent EP1572962.
JD021325 - Sequence 2349 from Patent EP1572962.
JD035352 - Sequence 16376 from Patent EP1572962.

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

Protein Q9BTM9 (Reactome details) participates in the following event(s):

R-HSA-6782264 CTU1:CTU2:URM1 thiolates uridine-34 in tRNAs
R-HSA-6782315 tRNA modification in the nucleus and cytosol
R-HSA-72306 tRNA processing
R-HSA-8953854 Metabolism of RNA

-  Other Names for This Gene
  Alternate Gene Symbols: C9orf74, NM_001135947, NP_001129419, Q9BTM9-2, uc011may.1
UCSC ID: uc011may.2
RefSeq Accession: NM_001135947
Protein: Q9BTM9-2, splice isoform of Q9BTM9 CCDS: CCDS48035.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_001135947.2
exon count: 4CDS single in 3' UTR: no RNA size: 3006
ORF size: 441CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 965.00frame 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: yes # 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.