General information for g5384.t11
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as 26S proteasome non-ATPase regulatory subunit 14.
Parent gene
- The parent gene g5384 is located on chr_2: 9308700..9309914 (- 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 | g5384 | g5384.t11 | TTS | g5384.t11 | 9308578 | 9308578 |
| chr_2 | g5384 | g5384.t11 | isoform | g5384.t11 | 9308700 | 9309914 |
| chr_2 | g5384 | g5384.t11 | exon | g5384.t11.exon1 | 9308700 | 9309457 |
| chr_2 | g5384 | g5384.t11 | cds | g5384.t11.CDS1 | 9308700 | 9309457 |
| chr_2 | g5384 | g5384.t11 | exon | g5384.t11.exon2 | 9309519 | 9309914 |
| chr_2 | g5384 | g5384.t11 | cds | g5384.t11.CDS2 | 9309519 | 9309573 |
| chr_2 | g5384 | g5384.t11 | TSS | g5384.t11 | 9310094 | 9310094 |
Sequences
>g5384.t11 Gene=g5384 Length=1154
ATGGATCGTTTGTTGAGTTTAGGACGTAAGTAAAATTTATATTTATGGATTTTTTTAATT
AATCGGTTTAGTTTCAATATTTCAAGTGATTACAATAAAACAAACTTAGAATTATCAATT
TCTTATGATCCAGTTGCATTAAAATTATTAATTTGTGAAAAATAACAATGGGGTTATTAA
TGCAAAATGATTTGCATAATTTTGAAAACTATAAAGAATAACATTATTTCTTCTTTATTC
TTATAGGATTACCTGGTATATCTCAACCACCTCCTCCCTCGGATGCTCCAGTAGTTGATA
CAGCTGAACAAGTTTATATTTCATCATTAGCTTTATTGAAAATGCTTAAACACGGTCGAG
CTGGGGTGCCAATGGAGGTCATGGGTCTCATGTTGGGTGAATTTGTTGATGATTATACAG
TACAAGTCATCGATGTATTTGCTATGCCACAAACTGGCACTGGAGTCTCCGTAGAAACAG
TTGATCCTGTGTTTCAGGCAAAAATGTTGGACATGCTTAAGCAAACTGGTCGTCCCGAAA
TGGTTGTAGGCTGGTATCACTCTCATCCTGGTTTTGGTTGTTGGCTTTCTGGTGTCGACA
TTAATACACAACAGTCGTTTGAAGCATTAAGTGAAAGAGCAGTTGCTGTCGTTGTCGATC
CTATTCAATCTGTAAAAGGAAAAGTAGTTATTGACGCTTTTCGTTTGATTAATCCAAACA
TGTTGGTACTTGGACAAGAACCTCGTCAAACTACATCAAATTTGGGTCATTTACAGAAAC
CATCAGTGCAAGCACTTATTCATGGTCTCAATCGCCATTACTATTCAATCAGCATCAATT
ATAGAAAGAATGAATTAGAACAAAAGATGCTTCTTAATTTGCATAAAAAATCATGGATGG
ATGGACTTACACTCGCAAATTATGAAGAACATTGCAGCATTAATGAAAGTACTGTAGGTG
AAATGCTTGAATTGGCAAAGAATTACAATAAAGCACTCGAAGATGAAGAGAAAATGACAC
CAGAACAGCTGGCTATTAAGAATGTAGGAAAACAAGATCCAAAGAGACATTTGGAAGAAA
AAGTCGATACACTTATGTCCAATAATATTGTTCAATGTTTGGGAGCAATGTTAGACACTG
TTGTCTTTAAGTAA
>g5384.t11 Gene=g5384 Length=270
MLKHGRAGVPMEVMGLMLGEFVDDYTVQVIDVFAMPQTGTGVSVETVDPVFQAKMLDMLK
QTGRPEMVVGWYHSHPGFGCWLSGVDINTQQSFEALSERAVAVVVDPIQSVKGKVVIDAF
RLINPNMLVLGQEPRQTTSNLGHLQKPSVQALIHGLNRHYYSISINYRKNELEQKMLLNL
HKKSWMDGLTLANYEEHCSINESTVGEMLELAKNYNKALEDEEKMTPEQLAIKNVGKQDP
KRHLEEKVDTLMSNNIVQCLGAMLDTVVFK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g5384.t11 | CDD | cd08069 | MPN_RPN11_CSN5 | 1 | 246 | 0.000 |
| 7 | g5384.t11 | Gene3D | G3DSA:3.40.140.10 | Cytidine Deaminase | 1 | 194 | 0.000 |
| 3 | g5384.t11 | PANTHER | PTHR10410 | EUKARYOTIC TRANSLATION INITIATION FACTOR 3 -RELATED | 1 | 269 | 0.000 |
| 4 | g5384.t11 | PANTHER | PTHR10410:SF22 | 26S PROTEASOME NON-ATPASE REGULATORY SUBUNIT 14 HOMOLOG | 1 | 269 | 0.000 |
| 2 | g5384.t11 | Pfam | PF01398 | JAB1/Mov34/MPN/PAD-1 ubiquitin protease | 1 | 98 | 0.000 |
| 1 | g5384.t11 | Pfam | PF13012 | Maintenance of mitochondrial structure and function | 133 | 254 | 0.000 |
| 8 | g5384.t11 | ProSiteProfiles | PS50249 | MPN domain profile. | 1 | 126 | 33.477 |
| 6 | g5384.t11 | SMART | SM00232 | pad1_6 | 1 | 125 | 0.000 |
| 5 | g5384.t11 | SUPERFAMILY | SSF102712 | JAB1/MPN domain | 1 | 127 | 0.000 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5384/g5384.t11; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5384.t11.fa.iupred3.txt does not exist
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0061578 | Lys63-specific deubiquitinase activity | MF |
| GO:0008237 | metallopeptidase activity | MF |
| GO:0005515 | protein binding | MF |
| GO:0070122 | isopeptidase activity | MF |
KEGG
Orthology
This gene did not have any KEGG ortholog annotations (KAAS, GHOSTZ).
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.
