Gene loci information

Transcript annotation

  • This transcript has been annotated as Ubiquitin thioesterase OTU1.

Parent gene

Gene structure

  • The exon-intron structure of all isoforms are indicated below. CDS regions are colored in green. TSS and TTs that were predicted with CTR-Seq data are indicated in solid circle and squares, respectively. More specific data are shown in the table below.

Chromosome Gene Transcript Category ID Start End
chr_1 g9931 g9931.t3 TTS g9931.t3 6067754 6067754
chr_1 g9931 g9931.t3 isoform g9931.t3 6067911 6068903
chr_1 g9931 g9931.t3 exon g9931.t3.exon1 6067911 6068653
chr_1 g9931 g9931.t3 cds g9931.t3.CDS1 6067911 6068653
chr_1 g9931 g9931.t3 exon g9931.t3.exon2 6068744 6068903
chr_1 g9931 g9931.t3 cds g9931.t3.CDS2 6068744 6068885
chr_1 g9931 g9931.t3 TSS g9931.t3 6069074 6069074

Sequences

>g9931.t3 Gene=g9931 Length=903
GATTTAAATGAAGATTCAATGATTTCGGAAATAAAAGATAAAATTCATACTATTACGGAG
ATTCCTCTTGCTTCAATAGAAATTCGTTATGGCTTCCCACCAAAAGTGCTATCTGTTGAA
GATAATTGTACATTAAAAAGTTCTGGAATAAAATCAGGAGAAACACTAATTGTTGATGTA
AAGCCTCTCACACAAGAAGAAAAGGATGCAATTGAGCGTGCAAAAAGACTTGCAGAAGAT
GAAATTTTAGCGCGACAATTGGCAGAAACATCTGAAAGTGGCAGTAGTGTAGCAAATGGA
ATATTATTAAAACAAGTTGTTGCAGCTGATAACAGTTGTCTATTTACAAGCATTGGATTT
CTTGTTTCAGGAAAAGTTGATACAAGCATTGGACCATATTTGCGACAAATCATAGCTCAA
ACTGTTCACAATGAAAGAGAAACATACAACGATGGTATCTTAGGTCGAAATAATGCAGAT
TATGTTGCATGGATTATTCAAGAGTCTTCATGGGGAGGTGCGATAGAAGTTGGTATCCTA
TCTGCTCATTATGGAATTGAATTCGACGTCGTTGACATAACTAATGCAGCAATATGCAGA
TTTGGTGAAGACAAAAAATATCCAATGAGAGGATTCTTGCTATATGATGGAATTCATTAT
GATCCGTTATATCTCGAATCACTTAATGGTGATGGACAAAAGACTTTGTTTTCAGTTGAA
GATGAAGAATACGTATATGAAATGGCTCAGAACTTAGCAAAAGAGGCTCAAAGTAGTCGA
CAATTTACAGATGTCGATAAATTTACATTACGTTGCATACAGTGCGATAAGAAATTAAAA
GGTCAAGTCCAAGCCACAGAACATGCTAAAGAAACAGGTCACACTCAGTTTGGAGAATTT
TGA

>g9931.t3 Gene=g9931 Length=294
MISEIKDKIHTITEIPLASIEIRYGFPPKVLSVEDNCTLKSSGIKSGETLIVDVKPLTQE
EKDAIERAKRLAEDEILARQLAETSESGSSVANGILLKQVVAADNSCLFTSIGFLVSGKV
DTSIGPYLRQIIAQTVHNERETYNDGILGRNNADYVAWIIQESSWGGAIEVGILSAHYGI
EFDVVDITNAAICRFGEDKKYPMRGFLLYDGIHYDPLYLESLNGDGQKTLFSVEDEEYVY
EMAQNLAKEAQSSRQFTDVDKFTLRCIQCDKKLKGQVQATEHAKETGHTQFGEF

Protein features from InterProScan

Transcript Database ID Name Start End E.value
6 g9931.t3 Gene3D G3DSA:3.10.20.90 - 1 55 1.3E-12
7 g9931.t3 Gene3D G3DSA:3.90.70.80 - 79 260 1.0E-56
1 g9931.t3 PANTHER PTHR13312:SF0 UBIQUITIN THIOESTERASE OTU1 2 293 3.4E-82
2 g9931.t3 PANTHER PTHR13312 HIV-INDUCED PROTEIN-7-LIKE PROTEASE 2 293 3.4E-82
5 g9931.t3 ProSitePatterns PS00028 Zinc finger C2H2 type domain signature. 266 288 -
8 g9931.t3 ProSiteProfiles PS50802 OTU domain profile. 96 220 10.273
3 g9931.t3 SUPERFAMILY SSF54236 Ubiquitin-like 2 57 5.07E-6
4 g9931.t3 SUPERFAMILY SSF54001 Cysteine proteinases 99 218 8.93E-11

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

GO terms from InterProScan

GOID TERM ONTOLOGY
GO:0101005 deubiquitinase activity MF
GO:0004843 thiol-dependent deubiquitinase MF
GO:0030433 ubiquitin-dependent ERAD pathway BP
GO:0016579 protein deubiquitination BP

KEGG

Orthology

Pathway

  • This transcript belongs to the following pathways

Expression

Transcript expression in Pv11 cells

TPM values are indicated as average +/- STDEV.

Differential expression

Differentially expressed genes were identified with DESeq2 using the ‘run_DE_analysis.pl’ script from Trinity. Transcripts were determined as differentially expressed when (1) FDR < 0.05 (2) fold change > 2 (TPM calculated by RSEM). DE information and fold change between conditions are indicated in the plot below.

Raw TPM values