General information for g4920.t12
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Probable 26S proteasome non-ATPase regulatory subunit 3.
Parent gene
- The parent gene g4920 is located on chr_2: 5965405..5966004 (- 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 | g4920 | g4920.t12 | TTS | g4920.t12 | 5963285 | 5963285 |
| chr_2 | g4920 | g4920.t12 | isoform | g4920.t12 | 5963398 | 5965014 |
| chr_2 | g4920 | g4920.t12 | exon | g4920.t12.exon1 | 5963398 | 5964437 |
| chr_2 | g4920 | g4920.t12 | cds | g4920.t12.CDS1 | 5963398 | 5964063 |
| chr_2 | g4920 | g4920.t12 | exon | g4920.t12.exon2 | 5964498 | 5964923 |
| chr_2 | g4920 | g4920.t12 | exon | g4920.t12.exon3 | 5965004 | 5965014 |
| chr_2 | g4920 | g4920.t12 | TSS | g4920.t12 | 5965056 | 5965056 |
Sequences
>g4920.t12 Gene=g4920 Length=1477
AAAATATTAAGTACAAGATGTGGAAATGGAAGTCATTGAAAGTGAAAATACAGAACAGGA
GCAACAGAAGAAAGAATCGGATGTGAATACAATTGTCCAAGAGATTCGAGAACATGTAAA
GCAAATTGATAAAGCAGTAGCAAGCAAAGAACCGCGTTTTATTCTTCGTGTTTTAAGATC
TCTACCAAATACACGTAGAAAATTGACTCCCGTTGTTCTTAGATCACTCGCAAATCAAAT
CTATCCTGTATCTGAACGAGATGCTATTCTTGTATATGTCGAGGAAGTAACTAGTGGAGA
GCAGCAAAATGAAAGTGCAAGTGCACGTCCTCGCGCAACAATTAAAACTCCACTTCCAGA
AGTTGATGCATATTTTCACTTATTAGCTCTTGTTCGTTTGTTAGACGCGAAATTGCTTGA
TAAAGCATCTCATTGTGCTCAACAGCTCATGACAAAAATTATGTCTCAGAATCGTAGATC
ATTAGATCTTATTGCTGCAAAGAGCTATTTCTATCATTCACGAGTTGCAGAATTAACAAA
TAAATTGGATACAATTCGTGGATTTTTACATGCTCGTCTAAGAACTGCAACTCTACGTAA
TGATTTTGAGGGATAAGCTGTCCTAATTAATTGTCTTTTACGCAATTACTTGCATTATTC
ATTATATGATCAAGCTGATAAATTAGTTAACAAATCAGTCTTTCCTGAAACTGCAAGTAA
CAATGAATGGGCCCGTTTTCTTTATTATTTGGGTCGTATAAAGGCTGCAAAATTGGAATA
TAGTGTTGCACATAAGCATCTTATTCAGGCTATGCGAAAGGCTCCACAAAATGCTGCAAT
TGGTTTCCGTCAAACAGTTCAGAAACTTGTAGTTGTTGTTGAATTACTTTTGGGTGATAT
CCCAGAACGACAAATTTTCAGACAAGCAGCTCTTCGTCGTTCACTCGTTCCTTATTTTCA
ACTTACACAAGCTGTAAGATTGGGAAATCTGAAACGTTTCGGTGAAGTGCTTACCAATTA
TGGTGAAAAATTCCGTCAAGATCATACATTTACACTCATCATTCGTTTGAGACATAATGT
CATTAAGACTGCAATAAGATCAATTGGACTCTCATATTCATGCATTTCACCAGCTGATAT
AGCCAAAAAATTAGGAATTGATTCTAAGGAGGATGCAGAATTTATTGTATCGAAAGCTAT
TCGTGATGGTGTTATTGAAGCAACATTAGATCCAGAAAAAGGATATATGCGCAGCAAAGA
GAGCACAGATATATATTCAACTCGTGAGCCTCAATTGGCTTTTCATCAACGCATCACTTT
CTGCTTAGATTTGCATAATCAATCAGTTAAAGCAATGCGATATCCACCAAAATCATATGG
CAAGGATTTGGAAAGTGCTGAAGAACGAATTGAACGTGAGCAACAAGAAGTTGAATTAGC
AAAGGAAATGGCAGAAGATGATGATGATGGTTTTTAA
>g4920.t12 Gene=g4920 Length=221
MRKAPQNAAIGFRQTVQKLVVVVELLLGDIPERQIFRQAALRRSLVPYFQLTQAVRLGNL
KRFGEVLTNYGEKFRQDHTFTLIIRLRHNVIKTAIRSIGLSYSCISPADIAKKLGIDSKE
DAEFIVSKAIRDGVIEATLDPEKGYMRSKESTDIYSTREPQLAFHQRITFCLDLHNQSVK
AMRYPPKSYGKDLESAEERIEREQQEVELAKEMAEDDDDGF
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g4920.t12 | Coils | Coil | Coil | 193 | 217 | - |
| 6 | g4920.t12 | Gene3D | G3DSA:1.25.40.570 | - | 1 | 96 | 7.7E-23 |
| 11 | g4920.t12 | MobiDBLite | mobidb-lite | consensus disorder prediction | 185 | 204 | - |
| 10 | g4920.t12 | MobiDBLite | mobidb-lite | consensus disorder prediction | 190 | 204 | - |
| 3 | g4920.t12 | PANTHER | PTHR10758:SF2 | 26S PROTEASOME NON-ATPASE REGULATORY SUBUNIT 3 | 1 | 221 | 2.1E-109 |
| 4 | g4920.t12 | PANTHER | PTHR10758 | 26S PROTEASOME NON-ATPASE REGULATORY SUBUNIT 3/COP9 SIGNALOSOME COMPLEX SUBUNIT 3 | 1 | 221 | 2.1E-109 |
| 2 | g4920.t12 | Pfam | PF01399 | PCI domain | 47 | 149 | 3.7E-21 |
| 1 | g4920.t12 | Pfam | PF08375 | Proteasome regulatory subunit C-terminal | 153 | 219 | 2.0E-28 |
| 12 | g4920.t12 | ProSiteProfiles | PS50250 | PCI domain profile. | 1 | 153 | 22.531 |
| 8 | g4920.t12 | SMART | SM00088 | PINT_4 | 81 | 171 | 6.6E-26 |
| 9 | g4920.t12 | SMART | SM00753 | motif in proteasome subunits, Int-6, Nip-1 and TRIP-15 | 81 | 171 | 6.6E-26 |
| 5 | g4920.t12 | SUPERFAMILY | SSF46785 | Winged helix DNA-binding domain | 86 | 153 | 7.89E-8 |
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:0000502 | proteasome complex | CC |
| GO:0042176 | regulation of protein catabolic process | BP |
| GO:0030234 | enzyme regulator 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.
