General information for g12293.t4
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Ubiquitin carboxyl-terminal hydrolase 30-like protein.
Parent gene
- The parent gene g12293 is located on chr_1: 22214296..22215387 (- strand)
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 | g12293 | g12293.t4 | isoform | g12293.t4 | 22214296 | 22215387 |
| chr_1 | g12293 | g12293.t4 | exon | g12293.t4.exon1 | 22214296 | 22215061 |
| chr_1 | g12293 | g12293.t4 | cds | g12293.t4.CDS1 | 22214296 | 22215061 |
| chr_1 | g12293 | g12293.t4 | exon | g12293.t4.exon2 | 22215140 | 22215212 |
| chr_1 | g12293 | g12293.t4 | cds | g12293.t4.CDS2 | 22215140 | 22215212 |
| chr_1 | g12293 | g12293.t4 | exon | g12293.t4.exon3 | 22215363 | 22215387 |
| chr_1 | g12293 | g12293.t4 | cds | g12293.t4.CDS3 | 22215363 | 22215387 |
| chr_1 | g12293 | g12293.t4 | TSS | g12293.t4 | 22215486 | 22215486 |
| chr_1 | g12293 | g12293.t4 | TTS | g12293.t4 | NA | NA |
Sequences
>g12293.t4 Gene=g12293 Length=864
ATGGAATCTGATAAGCTATTGATGGGTGTGATGGCAGTTGCCGCTGTCGGAGTAACTACA
TTTGTCTTTTGGCCGACTAACACAAAATCTAAATTAAGGCAACGACGCGGTCAAGTGTCA
GGTCTAATCAATTTTGGTAACACATGCTTTCTCAACGCTATTCTTCAAGCCATGGCAGCT
TCTCCCCAATTTCTCACTTGGTTGCAACTTCACGATTCAATGGACAAAAAAACTCTGATT
TCTTCGTTACAAATAATTTTAGATTGCATAAATGGCACTCATCCTACAATAAGAACCGAT
CCTTCAAATCCAGCTCCAGTTATAAGAGCTTTAAGAGAAAATGGTTGGGTAATTCCAGAA
CAAGAACATGATCCACATGAACTGTTGCATGTCATATTAACTTCTCTCGAAGAAGAAGCA
ATGAAACCAAAGAAAATTGGCTGTTTGTCTGATGCATTAGGTGATATTCAGGCCATTCAA
CAGCCTTTACCTGCTCGTCCTTCTTCAGCAATGCTTACAGAATTCGATAAAGACACATAC
AATGAATCGTCGAATCTATTGCGTTTAGTGAGAAGTGAAGCACAAACTCCAGAGTCTAAT
CAAAGCACAGTTGATGAGAATGAATCAATTGATCATTCAATGTTTGATGATGATGAGAAA
GACAAGTCAATTCAAGATTCACCACCATCTATAATTTCATCAACAACCACAGGTCGTGCT
CGAAATATTTCTACGAGTAATGGAGATGCATTTAACAGACGCAATTGTGGATCATACCGT
TCACTCGATAGATTATCACGTGGACCTGGACGAGTATCGATTTGGAATGATAAACTTACT
AAACAAATAGCTATCCCATTTAAG
>g12293.t4 Gene=g12293 Length=288
MESDKLLMGVMAVAAVGVTTFVFWPTNTKSKLRQRRGQVSGLINFGNTCFLNAILQAMAA
SPQFLTWLQLHDSMDKKTLISSLQIILDCINGTHPTIRTDPSNPAPVIRALRENGWVIPE
QEHDPHELLHVILTSLEEEAMKPKKIGCLSDALGDIQAIQQPLPARPSSAMLTEFDKDTY
NESSNLLRLVRSEAQTPESNQSTVDENESIDHSMFDDDEKDKSIQDSPPSIISSTTTGRA
RNISTSNGDAFNRRNCGSYRSLDRLSRGPGRVSIWNDKLTKQIAIPFK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g12293.t4 | CDD | cd02257 | Peptidase_C19 | 41 | 103 | 1.78655E-10 |
| 12 | g12293.t4 | MobiDBLite | mobidb-lite | consensus disorder prediction | 191 | 208 | - |
| 13 | g12293.t4 | MobiDBLite | mobidb-lite | consensus disorder prediction | 191 | 210 | - |
| 10 | g12293.t4 | MobiDBLite | mobidb-lite | consensus disorder prediction | 217 | 249 | - |
| 11 | g12293.t4 | MobiDBLite | mobidb-lite | consensus disorder prediction | 226 | 249 | - |
| 1 | g12293.t4 | Pfam | PF00443 | Ubiquitin carboxyl-terminal hydrolase | 41 | 231 | 3.7E-10 |
| 4 | g12293.t4 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 5 | - |
| 5 | g12293.t4 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 6 | 26 | - |
| 3 | g12293.t4 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 27 | 288 | - |
| 9 | g12293.t4 | ProSitePatterns | PS00972 | Ubiquitin specific protease (USP) domain signature 1. | 41 | 56 | - |
| 14 | g12293.t4 | ProSiteProfiles | PS50235 | Ubiquitin specific protease (USP) domain profile. | 40 | 288 | 11.106 |
| 2 | g12293.t4 | SUPERFAMILY | SSF54001 | Cysteine proteinases | 39 | 154 | 2.94E-17 |
| 7 | g12293.t4 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 6 | 25 | - |
| 8 | g12293.t4 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 38 | 60 | - |
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:0004843 | thiol-dependent deubiquitinase | MF |
| GO:0006511 | ubiquitin-dependent protein catabolic process | BP |
| GO:0016579 | protein deubiquitination | BP |
KEGG
Orthology
- This transcript has been annotated with K11851 (ubiquitin carboxyl-terminal hydrolase 30)
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.
