General information for g3915.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Probable ubiquitin carboxyl-terminal hydrolase creB.
Parent gene
- The parent gene g3915 is located on chr_3: 28865141..28866173 (- 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_3 | g3915 | g3915.t1 | isoform | g3915.t1 | 28862079 | 28865141 |
| chr_3 | g3915 | g3915.t1 | exon | g3915.t1.exon1 | 28862079 | 28863046 |
| chr_3 | g3915 | g3915.t1 | cds | g3915.t1.CDS1 | 28862079 | 28863046 |
| chr_3 | g3915 | g3915.t1 | exon | g3915.t1.exon2 | 28863107 | 28863239 |
| chr_3 | g3915 | g3915.t1 | cds | g3915.t1.CDS2 | 28863107 | 28863239 |
| chr_3 | g3915 | g3915.t1 | exon | g3915.t1.exon3 | 28863297 | 28864094 |
| chr_3 | g3915 | g3915.t1 | cds | g3915.t1.CDS3 | 28863297 | 28864094 |
| chr_3 | g3915 | g3915.t1 | exon | g3915.t1.exon4 | 28864470 | 28865141 |
| chr_3 | g3915 | g3915.t1 | cds | g3915.t1.CDS4 | 28864470 | 28865141 |
| chr_3 | g3915 | g3915.t1 | TSS | g3915.t1 | 28865732 | 28865732 |
| chr_3 | g3915 | g3915.t1 | TTS | g3915.t1 | NA | NA |
Sequences
>g3915.t1 Gene=g3915 Length=2571
ATGCCAGTTTCGGAAGTTTCAAATAGAATTTCAAGCTTAACTGATGATAATAACATTTAT
AAACAATTAAGCGAGAAGCAAAGAAATTGGAAAAAATCTTCCAGCTTTGACGATAATTGT
GTCAACAATCAATCAATATTGTGCTTATTTAATGAAGATCCTGAATTAAGGTTCTTTAAA
TTAGATAAAAAGTTTAGAAAACAATTTTTATTTCAACAAGTTGAGTCAAGAAAAAATAAG
GAAAACGGAATTGATCGCGTGAAGAAAAGTAAAAAGAGAAAAATAAAAATTGATAAAAGT
GAGCAAAGTGAGAAGCGAAATAAGCTCGAAATGTATGACTATCGTCATAATTCAACATTA
CTCAAGACGACCGAAAACAGTGGAAGTAATAATGACTTTGTGTCCTCATCAAAAAATGAA
GAAGATGAGGAAAATATTATTAATGCATTCTATCAGCAACGATATTTAGGTGGAAGTAAT
AATTCTATTGCGACATTATGCAATATTGGCAATTCATGCTATTTAAATTCTGTCATTTAT
ACACTTCGATTTGCACCATATTTCCTTCATAAACTTCATCATCTTTGCGATGATATGCAC
TTTGTGTACCAAAAAATTGGTCAAAATAAACTGAAAAGTTCTTCATTGGGACGTAATGTT
AGCGGTCTACAGGGTCAAAGTGGACGAAGTTGGAGTTCAAAAGATTTAGCATCATTAAGT
GGAACAAATAATACAATTAGTAATAGTGAACCAGTGCTGCTTAAAAATAATCGCCAATTG
GTGACAGAAAAACTACATGAACTCTACCAAAATCTTCATCGGAATGAGTCAATTGATTCA
AGCGAGTCATTTCATGCTGGAACATTTTTGAATTCAATTCAAGATGTTAGTTCGATTTTT
GAAGGTAATCAACAGCAAGATGCACATGAGCTGCTTATGTGCATTTTAGACAGTATTCGT
GAAACATGTTCAACTCTATCAAAGACTTTAAAAGATAATCCAGAAATTCTCTTGCCACAA
ACAAACTCATCAATAAATGATACCGGTGAACTCACATCACCACCAAATTCAGTGCAAACT
TCACAATCAATCAAATCAATTTTTTCGAGAAAAATCAAGAGAAAAGATACAATGAAAACG
AAAAATGGTTCACCAATGAAGGAAATCAATACTTCTGAAATGTCATCAATTGAGGAATCA
AGCGAGACAAATAATATCAAAAGTAGTCTCAATAGTATAACTAATGAACCATGTGATAGC
AATGGTGTAGATGAAAAAGAAAAAATTGATGAGACAATTAAACGATTGGGATTGGATTTT
TTTAGTGAAGATTTCGAGGGTATTACATTGTCAACCACAAAGTGCTTGACATGTGAAACA
GTCACAGAACAAAAAGAAACAATGATCGACATTTCAATTCCACTAGGCAATGAAAACAAT
CAACCACTGGATCCACAAATATTTTTTCAGAATTCATGTATTACAAAGGAATATTTTCGT
GTTGAGAATCATTATAGATGTGATAAATGTTGTGGCTATACTGAAGCCATTCGTTCAATT
TCTTTTGAAGTACTTCCTCGCCTTCTAGTTCTTCATATAAAAAGATTTTCTGGTGGAATG
GAAAAAATAAGCAGTTATAGTCCAACGCCATTCATTTTGAAATGTTTTTGCAATAAATGT
TATAAAAAGCGCGATGAAGATAAGCTGCACATTTACAAACTTTATAGTGTCATCACACAT
GTTGGTGCGACAATGTCTGTTGGTCATTATATCGCATATACTTGCTCGCTGGATATTTAC
AATGAATATGTGAGTTGTGTTCATGATAAGCGAAGATCATCGTTATCAAATGGTACAAAA
ATTAAATCTCAACATCAGAATCATTCTTCATTAGCAAATAGTGGCAATGGAAGCAGTGGA
AGTGAGAAAAATTCTGGTCTAATGAAGAAATTAATTTATGGAAGAAATAAAGCATCAAGT
AGTGGTGATATGAGCAAAAATCTAAAACCAATTAATGGTCTTAGTAAAATAATGATGAAT
GGCATTGAAAAATTAAATCTCAATTCAGATAAAATTAATGCAACGAATGGCAGTGCTCAA
ATTAATGGCACAACAAACACGAATCAAACCAAGCCTAAAACTGTTTGTAACAGTGCAAAC
TGCTGTGGCATTTATATCAAGGATTTTGCCAATATTGTTGAGAATTATCACAATAACAAT
TCTAGTTGCTTAAATAATGGCACTGAAAAAACTCAAGCTAACGAAAGTAATTGTAATTCA
ACAGACGATGGACATGATTATGATAGCAACAATAGCAACAACATGACATCATCGACCACA
ACGAATACAAACAATAATAATAATAACAGCAGTGCGGGATCAACAAAGCCTTCACTAAAT
GATTTAAACCAAAAAGTTTGGTACATGTGTGATGACGATAAAATAAAAATCATGACACAG
CGGGAATTTGAAGATGCACTGTCAAAGAATCAAAAAGTTATGATAACACCGTATTTGCTG
TTTTATGCGCGCTACAATGTGAAAAATCTTAAAAATGCCGAATATGATTAG
>g3915.t1 Gene=g3915 Length=856
MPVSEVSNRISSLTDDNNIYKQLSEKQRNWKKSSSFDDNCVNNQSILCLFNEDPELRFFK
LDKKFRKQFLFQQVESRKNKENGIDRVKKSKKRKIKIDKSEQSEKRNKLEMYDYRHNSTL
LKTTENSGSNNDFVSSSKNEEDEENIINAFYQQRYLGGSNNSIATLCNIGNSCYLNSVIY
TLRFAPYFLHKLHHLCDDMHFVYQKIGQNKLKSSSLGRNVSGLQGQSGRSWSSKDLASLS
GTNNTISNSEPVLLKNNRQLVTEKLHELYQNLHRNESIDSSESFHAGTFLNSIQDVSSIF
EGNQQQDAHELLMCILDSIRETCSTLSKTLKDNPEILLPQTNSSINDTGELTSPPNSVQT
SQSIKSIFSRKIKRKDTMKTKNGSPMKEINTSEMSSIEESSETNNIKSSLNSITNEPCDS
NGVDEKEKIDETIKRLGLDFFSEDFEGITLSTTKCLTCETVTEQKETMIDISIPLGNENN
QPLDPQIFFQNSCITKEYFRVENHYRCDKCCGYTEAIRSISFEVLPRLLVLHIKRFSGGM
EKISSYSPTPFILKCFCNKCYKKRDEDKLHIYKLYSVITHVGATMSVGHYIAYTCSLDIY
NEYVSCVHDKRRSSLSNGTKIKSQHQNHSSLANSGNGSSGSEKNSGLMKKLIYGRNKASS
SGDMSKNLKPINGLSKIMMNGIEKLNLNSDKINATNGSAQINGTTNTNQTKPKTVCNSAN
CCGIYIKDFANIVENYHNNNSSCLNNGTEKTQANESNCNSTDDGHDYDSNNSNNMTSSTT
TNTNNNNNNSSAGSTKPSLNDLNQKVWYMCDDDKIKIMTQREFEDALSKNQKVMITPYLL
FYARYNVKNLKNAEYD
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g3915.t1 | Gene3D | G3DSA:3.90.70.10 | Cysteine proteinases | 387 | 636 | 4.2E-33 |
| 8 | g3915.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 81 | 102 | - |
| 7 | g3915.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 617 | 642 | - |
| 6 | g3915.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 775 | 798 | - |
| 2 | g3915.t1 | PANTHER | PTHR24006:SF674 | UBIQUITIN CARBOXYL-TERMINAL HYDROLASE 1 | 103 | 603 | 4.3E-68 |
| 3 | g3915.t1 | PANTHER | PTHR24006 | UBIQUITIN CARBOXYL-TERMINAL HYDROLASE | 103 | 603 | 4.3E-68 |
| 1 | g3915.t1 | Pfam | PF00443 | Ubiquitin carboxyl-terminal hydrolase | 166 | 596 | 1.9E-29 |
| 5 | g3915.t1 | ProSitePatterns | PS00973 | Ubiquitin specific protease (USP) domain signature 2. | 572 | 590 | - |
| 10 | g3915.t1 | ProSiteProfiles | PS50235 | Ubiquitin specific protease (USP) domain profile. | 164 | 845 | 29.646 |
| 4 | g3915.t1 | SUPERFAMILY | SSF54001 | Cysteine proteinases | 166 | 844 | 4.32E-57 |
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 K11832 (ubiquitin carboxyl-terminal hydrolase 1)
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.
