Human Gene UBC (uc001ugw.4) Description and Page Index
  Description: Homo sapiens ubiquitin C (UBC), mRNA.
RefSeq Summary (NM_021009): This gene represents a ubiquitin gene, ubiquitin C. The encoded protein is a polyubiquitin precursor. Conjugation of ubiquitin monomers or polymers can lead to various effects within a cell, depending on the residues to which ubiquitin is conjugated. Ubiquitination has been associated with protein degradation, DNA repair, cell cycle regulation, kinase modification, endocytosis, and regulation of other cell signaling pathways. [provided by RefSeq, Aug 2010]. Publication Note: This RefSeq record includes a subset of the publications that are available for this gene. Please see the Gene record to access additional publications. ##Evidence-Data-START## Transcript exon combination :: BC093445.1, BC039193.1 [ECO:0000332] RNAseq introns :: single sample supports all introns SAMEA1966682, SAMEA1968189 [ECO:0000348] ##Evidence-Data-END## ##RefSeq-Attributes-START## MANE Ensembl match :: ENST00000339647.6/ ENSP00000344818.5 RefSeq Select criteria :: based on single protein-coding transcript ##RefSeq-Attributes-END##
Transcript (Including UTRs)
   Position: hg19 chr12:125,397,236-125,399,587 Size: 2,352 Total Exon Count: 3 Strand: -
Coding Region
   Position: hg19 chr12:125,397,960-125,398,317 Size: 358 Coding Exon Count: 2 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated: 2013-06-15

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr12:125,397,236-125,399,587)mRNA (may differ from genome)Protein (88 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblExonPrimerGeneCardsGeneNetwork
H-INVHGNCLynxMGIPubMedStanford SOURCE
UniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: F5H4D8_HUMAN
DESCRIPTION: SubName: Full=Polyubiquitin-C;
CAUTION: The sequence shown here is derived from an Ensembl automatic analysis pipeline and should be considered as preliminary data.

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

-  MalaCards Disease Associations
  MalaCards Gene Search: UBC
Diseases sorted by gene-association score: apocrine adenoma (4), congenital granular cell tumor (3), cystic fibrosis (3), endometrial small cell carcinoma (2), splenic artery aneurysm (2), cutaneous solitary mastocytoma (1), eumycotic mycetoma (1), malignant skin fibrous histiocytoma (1), malignant dermis tumor (1), retinitis pigmentosa (0)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene
  • D019256 Cadmium Chloride
  • D001564 Benzo(a)pyrene
  • D013749 Tetrachlorodibenzodioxin
  • C037123 cadmium sulfate
  • C517041 (4-amino-1,4-dihydro-3-(2-pyridyl)-5-thioxo-1,2,4-triazole)copper(II)
  • D015632 1-Methyl-4-phenyl-1,2,3,6-tetrahydropyridine
  • C015802 2,6-dichloro-4-nitrophenol
  • C012796 2-butenal
  • C030370 2-methoxy-5-(2',3',4'-trimethoxyphenyl)tropone
  • C054649 3-(2-hydroxy-4-(1,1-dimethylheptyl)phenyl)-4-(3-hydroxypropyl)cyclohexanol
          more ... click here to view the complete list

+  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: 618.04 RPKM in Muscle - Skeletal
Total median expression: 17657.82 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 -200.30458-0.437 Picture PostScript Text
3' UTR -248.00724-0.343 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
IPR000626 - Ubiquitin
IPR019954 - Ubiquitin_CS
IPR019956 - Ubiquitin_subgr
IPR019955 - Ubiquitin_supergroup

Pfam Domains:
PF00240 - Ubiquitin family
PF11976 - Ubiquitin-2 like Rad60 SUMO-like
PF13881 - Ubiquitin-2 like Rad60 SUMO-like
PF14560 - Ubiquitin-like domain

SCOP Domains:
54236 - Ubiquitin-like

ModBase Predicted Comparative 3D Structure on F5H4D8
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 orthologNo orthologNo orthologNo orthologNo ortholog
      
      
      
      
      

-  Descriptions from all associated GenBank mRNAs
  M26880 - Human ubiquitin mRNA, complete cds.
LF206965 - JP 2014500723-A/14468: Polycomb-Associated Non-Coding RNAs.
BC014880 - Homo sapiens ubiquitin C, mRNA (cDNA clone IMAGE:3907070), complete cds.
AF052164 - Homo sapiens clone 24683 mRNA sequence.
BC008955 - Homo sapiens ubiquitin C, mRNA (cDNA clone IMAGE:3030313), partial cds.
BC080583 - Homo sapiens cDNA clone IMAGE:2822684, partial cds.
BC000449 - Homo sapiens ubiquitin C, mRNA (cDNA clone IMAGE:2821375).
BC039193 - Homo sapiens ubiquitin C, mRNA (cDNA clone MGC:14624 IMAGE:4076286), complete cds.
BC093445 - Homo sapiens ubiquitin C, mRNA (cDNA clone IMAGE:5284302).
AK026846 - Homo sapiens cDNA: FLJ23193 fis, clone REC00306, highly similar to AF052164 Homo sapiens clone 24683 mRNA sequence.
AK097415 - Homo sapiens cDNA FLJ40096 fis, clone TESTI2004080, highly similar to Homo sapiens mRNA for polyubiquitin UbC.
AB209782 - Homo sapiens mRNA for ubiquitin C variant protein.
AK056939 - Homo sapiens cDNA FLJ32377 fis, clone SKMUS1000014, highly similar to Polyubiquitin 9.
AK098827 - Homo sapiens cDNA FLJ25961 fis, clone TST09043, highly similar to Polyubiquitin UbC.
AK129749 - Homo sapiens cDNA FLJ26238 fis, clone CBR05440, highly similar to Rattus norvegicus ubiquitin C (Ubc).
AK291539 - Homo sapiens cDNA FLJ75516 complete cds, highly similar to Xenopus tropicalis ubiquitin C, mRNA.
AB009010 - Homo sapiens UbC1 mRNA for polyubiquitin UbC, complete cds.
AY732488 - Homo sapiens ubiquitin C splice variant (UBC) mRNA, complete cds, alternatively spliced.
AY819759 - Homo sapiens ubiquitin C splice variant (UBC) mRNA, complete cds, alternatively spliced.
LF359721 - JP 2014500723-A/167224: Polycomb-Associated Non-Coding RNAs.
JD020871 - Sequence 1895 from Patent EP1572962.
LF359713 - JP 2014500723-A/167216: Polycomb-Associated Non-Coding RNAs.
LF359723 - JP 2014500723-A/167226: Polycomb-Associated Non-Coding RNAs.
JD332594 - Sequence 313618 from Patent EP1572962.
LF359724 - JP 2014500723-A/167227: Polycomb-Associated Non-Coding RNAs.
LF359727 - JP 2014500723-A/167230: Polycomb-Associated Non-Coding RNAs.
LF359729 - JP 2014500723-A/167232: Polycomb-Associated Non-Coding RNAs.
LF359707 - JP 2014500723-A/167210: Polycomb-Associated Non-Coding RNAs.
JD332594 - Sequence 313618 from Patent EP1572962.
LF359730 - JP 2014500723-A/167233: Polycomb-Associated Non-Coding RNAs.
LF359724 - JP 2014500723-A/167227: Polycomb-Associated Non-Coding RNAs.
LF359733 - JP 2014500723-A/167236: Polycomb-Associated Non-Coding RNAs.
LF359735 - JP 2014500723-A/167238: Polycomb-Associated Non-Coding RNAs.
AB362574 - Homo sapiens UBC mRNA for ubiquitin C, partial cds, splicing variant 1.
JD256670 - Sequence 237694 from Patent EP1572962.
MA442542 - JP 2018138019-A/14468: Polycomb-Associated Non-Coding RNAs.
MA595298 - JP 2018138019-A/167224: Polycomb-Associated Non-Coding RNAs.
MA595290 - JP 2018138019-A/167216: Polycomb-Associated Non-Coding RNAs.
MA595300 - JP 2018138019-A/167226: Polycomb-Associated Non-Coding RNAs.
MA595301 - JP 2018138019-A/167227: Polycomb-Associated Non-Coding RNAs.
MA595304 - JP 2018138019-A/167230: Polycomb-Associated Non-Coding RNAs.
MA595306 - JP 2018138019-A/167232: Polycomb-Associated Non-Coding RNAs.
MA595284 - JP 2018138019-A/167210: Polycomb-Associated Non-Coding RNAs.
MA595307 - JP 2018138019-A/167233: Polycomb-Associated Non-Coding RNAs.
MA595301 - JP 2018138019-A/167227: Polycomb-Associated Non-Coding RNAs.
MA595310 - JP 2018138019-A/167236: Polycomb-Associated Non-Coding RNAs.
MA595312 - JP 2018138019-A/167238: Polycomb-Associated Non-Coding RNAs.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa03320 - PPAR signaling pathway

-  Other Names for This Gene
  Alternate Gene Symbols: AK056939, F5H4D8, F5H4D8_HUMAN, uc001ugw.3
UCSC ID: uc001ugw.4
RefSeq Accession: NM_021009
Protein: F5H4D8

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: AK056939.1
exon count: 3CDS single in 3' UTR: no RNA size: 1300
ORF size: 267CDS single in intron: no Alignment % ID: 99.54
txCdsPredict score: 728.00frame shift in genome: no % Coverage: 81.38
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.