General information for g5270.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Ubiquitin carboxyl-terminal hydrolase 7.
Parent gene
- The parent gene g5270 is located on chr_2: 8331997..8335461 (+ 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_2 | g5270 | g5270.t2 | TSS | g5270.t2 | 8331805 | 8331805 |
| chr_2 | g5270 | g5270.t2 | isoform | g5270.t2 | 8331997 | 8334084 |
| chr_2 | g5270 | g5270.t2 | exon | g5270.t2.exon1 | 8331997 | 8332024 |
| chr_2 | g5270 | g5270.t2 | cds | g5270.t2.CDS1 | 8331997 | 8332024 |
| chr_2 | g5270 | g5270.t2 | exon | g5270.t2.exon2 | 8332154 | 8332924 |
| chr_2 | g5270 | g5270.t2 | cds | g5270.t2.CDS2 | 8332154 | 8332924 |
| chr_2 | g5270 | g5270.t2 | exon | g5270.t2.exon3 | 8332986 | 8334084 |
| chr_2 | g5270 | g5270.t2 | cds | g5270.t2.CDS3 | 8332986 | 8334082 |
| chr_2 | g5270 | g5270.t2 | TTS | g5270.t2 | NA | NA |
Sequences
>g5270.t2 Gene=g5270 Length=1898
ATGGAGACCGAAGAAAATGAAACTCCAGATATCACTCCTTCAGATCATAATATGGAGGAT
GAACTAAGAAGCGAGGCAACGTTTCAATTGACGATTGAAAACTTTAGTAAAATGTCTGAG
ACTATGCTCTCAGAGGCACATTATGTGCGTGGATTACCGTGGAAAATTATGGCTATGCCA
CGATCGTCGAATGACAAAGACAAAAGTTTAGGATTTTTCCTACAATGTAATGCCGAATGT
GACTCAAATTGGAACTGTTCTGCTACAGCAGATTTGCGTTTATTGAGTTTCAAAAAAGAA
ACACCGCCAGTTTCAAGAAAAATTAAACATGTCTTTTACAACAAGGAAAATGACTGGGGA
TTTTCAACCTTTCAATCTTTTGCTGACATTCTTGATCCAGAAAAAGGCTACATACAGAAT
GACACAATAGTTTTGGAAGTACATGTACAAGCGGAAGCACCGCATAATGCTTATTGGGAC
TCAAAGAAATTGACAGGATACGTTGGCCTTAAGAATCAGGGAGCAACTTGCTACATGAAT
TCTCTCTTGCAAACACTTTACTTCACAAATGAACTCAGAAAAGCTGTCTATAAAATGCCG
ACAGAGGCTGATGACAGCAGTAAATCCGTAGCTCTTGCATTACAAAGAGTATTTCATGAG
CTACAGTCGTCCAACAAGCCTGTTGGCACAAAAAAACTCACAAAAAGTTTTGGGTGGGAG
ACGCTCGACTCGTTTATGCAACATGATGTGCAAGAATTTTTACGTGTCCTTCTTGATAAG
TTAGAAATCAAAATGAAAGGTACTTCCATTGAAGGAACTATACCAAGATTATTTGCAGGT
AAAATGATTTCATTCATCAAATGCAAGAATGTCAACTACAAAAGTACCAAAACGGAGACC
TTTTATGATATTCAACTAAATATCAAGGGCAAAAAGAATGTTTATGAATCATTTGACGAT
TATGTATCTACGGAAATTTTAGACGATGAAAATAAGTATGATGCTGGTGAATATGGACTA
CAAAAGGCTGAAAAAGGTGTGATTTTTGCTTCGTTTCCACCCGTTTTGCATTTACATTTG
CTTCGCTTCCAATATGACCCTATGACAAACAATTCAGTCAAGTTTAATGATCGTTTTGAG
TTTCATGAGAAAATCAATTTAGATAAGTACTTGGAGAAACCAGAAGAAACACCAGCGAAT
TATATTTTGCATGCCGTACTAGTGCATTCAGGTGATAATCATGGGGGACATTATGTTGTT
TTCATTAATCCACGAGGTGATGGAAATTGGTGCAAATTTGATGATGATGTAGTTTCAGCT
GTTCCTAAAACAGCAGCAATTGATCAAAATTATGGCGGTACTGAAGATGATTTTATGCTT
AATGTGCGTAATTGTACAAACGCTTATATGTTGGTTTATGTACGTGAAGCACAAATGAAA
ACAATTCTTCAAGAAATCGCTGAAGAAGACATTCCCTCGGAGCTTAATGATAAATTAAAC
GAGGAAAAACGTATGGAAATGGCAAAACGAAAGGAACGCAATGAAGCATCAAATTACATC
AATGTAAATGTGATTTTGGAAGATTATTTTGATGGTCATCATGCAAACGATCTATTCAAT
CCTGACGCAACACATTATAGATGTTTTAAAATCAAACAAAATTCTCCGCTTCATGAGCTT
GTCAGTCTTATTCAAAGTACATTTAAAGTATCTCCTTTAAAAATGCGTTTATGGTCATTT
TCGTATATGGGTAGTCATAGTGGTGGACAAATGTATCATAACTCGACAAGTGGCAGTGGT
GGTTTACTCTCAAATGGTCTTTACAACATAGACATTAATGATCCCGAGTTATTAAACAAT
CCAGTTACATATTTATCACGCGACCATAATCCATGGAC
>g5270.t2 Gene=g5270 Length=632
METEENETPDITPSDHNMEDELRSEATFQLTIENFSKMSETMLSEAHYVRGLPWKIMAMP
RSSNDKDKSLGFFLQCNAECDSNWNCSATADLRLLSFKKETPPVSRKIKHVFYNKENDWG
FSTFQSFADILDPEKGYIQNDTIVLEVHVQAEAPHNAYWDSKKLTGYVGLKNQGATCYMN
SLLQTLYFTNELRKAVYKMPTEADDSSKSVALALQRVFHELQSSNKPVGTKKLTKSFGWE
TLDSFMQHDVQEFLRVLLDKLEIKMKGTSIEGTIPRLFAGKMISFIKCKNVNYKSTKTET
FYDIQLNIKGKKNVYESFDDYVSTEILDDENKYDAGEYGLQKAEKGVIFASFPPVLHLHL
LRFQYDPMTNNSVKFNDRFEFHEKINLDKYLEKPEETPANYILHAVLVHSGDNHGGHYVV
FINPRGDGNWCKFDDDVVSAVPKTAAIDQNYGGTEDDFMLNVRNCTNAYMLVYVREAQMK
TILQEIAEEDIPSELNDKLNEEKRMEMAKRKERNEASNYINVNVILEDYFDGHHANDLFN
PDATHYRCFKIKQNSPLHELVSLIQSTFKVSPLKMRLWSFSYMGSHSGGQMYHNSTSGSG
GLLSNGLYNIDINDPELLNNPVTYLSRDHNPW
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 11 | g5270.t2 | CDD | cd02659 | peptidase_C19C | 166 | 476 | 3.47918E-152 |
| 10 | g5270.t2 | Coils | Coil | Coil | 495 | 515 | - |
| 9 | g5270.t2 | Gene3D | G3DSA:2.60.210.10 | Apoptosis | 21 | 164 | 1.8E-41 |
| 8 | g5270.t2 | Gene3D | G3DSA:3.90.70.10 | Cysteine proteinases | 165 | 478 | 1.5E-88 |
| 7 | g5270.t2 | Gene3D | G3DSA:3.10.20.90 | - | 490 | 590 | 6.0E-25 |
| 15 | g5270.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 20 | - |
| 3 | g5270.t2 | PANTHER | PTHR24006:SF793 | UBIQUITIN CARBOXYL-TERMINAL HYDROLASE 7 | 14 | 597 | 3.2E-261 |
| 4 | g5270.t2 | PANTHER | PTHR24006 | UBIQUITIN CARBOXYL-TERMINAL HYDROLASE | 14 | 597 | 3.2E-261 |
| 1 | g5270.t2 | Pfam | PF00917 | MATH domain | 32 | 150 | 7.3E-17 |
| 2 | g5270.t2 | Pfam | PF00443 | Ubiquitin carboxyl-terminal hydrolase | 168 | 473 | 1.3E-49 |
| 14 | g5270.t2 | ProSitePatterns | PS00972 | Ubiquitin specific protease (USP) domain signature 1. | 169 | 184 | - |
| 13 | g5270.t2 | ProSitePatterns | PS00973 | Ubiquitin specific protease (USP) domain signature 2. | 401 | 418 | - |
| 16 | g5270.t2 | ProSiteProfiles | PS50144 | MATH/TRAF domain profile. | 25 | 149 | 24.047 |
| 17 | g5270.t2 | ProSiteProfiles | PS50235 | Ubiquitin specific protease (USP) domain profile. | 168 | 476 | 42.034 |
| 12 | g5270.t2 | SMART | SM00061 | math_3 | 30 | 130 | 9.0E-12 |
| 5 | g5270.t2 | SUPERFAMILY | SSF49599 | TRAF domain-like | 25 | 152 | 2.13E-27 |
| 6 | g5270.t2 | SUPERFAMILY | SSF54001 | Cysteine proteinases | 163 | 503 | 2.55E-97 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5270/g5270.t2; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5270.t2.fa.iupred3.txt does not exist
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0004843 | thiol-dependent deubiquitinase | MF |
| GO:0006511 | ubiquitin-dependent protein catabolic process | BP |
| GO:0005515 | protein binding | MF |
| GO:0016579 | protein deubiquitination | BP |
KEGG
Orthology
- This transcript has been annotated with K11838 (ubiquitin carboxyl-terminal hydrolase 7)
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.
