General information for g4362.t3
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Probable proteasome subunit beta type-2.
Parent gene
- The parent gene g4362 is located on chr_2: 1575013..1577207 (+ 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 | g4362 | g4362.t3 | TSS | g4362.t3 | 1565845 | 1565845 |
| chr_2 | g4362 | g4362.t3 | isoform | g4362.t3 | 1565994 | 1575013 |
| chr_2 | g4362 | g4362.t3 | exon | g4362.t3.exon1 | 1565994 | 1566001 |
| chr_2 | g4362 | g4362.t3 | exon | g4362.t3.exon2 | 1571758 | 1571785 |
| chr_2 | g4362 | g4362.t3 | exon | g4362.t3.exon3 | 1574250 | 1574362 |
| chr_2 | g4362 | g4362.t3 | cds | g4362.t3.CDS1 | 1574272 | 1574362 |
| chr_2 | g4362 | g4362.t3 | exon | g4362.t3.exon4 | 1574439 | 1574795 |
| chr_2 | g4362 | g4362.t3 | cds | g4362.t3.CDS2 | 1574439 | 1574795 |
| chr_2 | g4362 | g4362.t3 | exon | g4362.t3.exon5 | 1574856 | 1575013 |
| chr_2 | g4362 | g4362.t3 | cds | g4362.t3.CDS3 | 1574856 | 1575013 |
| chr_2 | g4362 | g4362.t3 | TTS | g4362.t3 | 1575148 | 1575148 |
Sequences
>g4362.t3 Gene=g4362 Length=664
AAAACAGAGCATGTGAATCGTGTTTCTGGATCAAATTATCTTTTGAAAATAAATAGCAAT
GGAGACCATTATCGGAATAAAAGGAAAAGATTTTGTTATGTTAGCTGCTGATAGCACTCA
TCCACATTCAATTATGGTTCTCAAAGACGATGAGAATAAAATTCACAAAATATCTGATTC
TTTGCTTATTGCTGCTACTGGCGATCAAGGAGACACGGTTCAGTTTGTTGAATACATCTC
TAAAAATATTCTTTTATATAAAATGAGAAATGGATATGAACTTGGTCCAAAGGCAGCAGC
ATATTTCACTCGTAAAAATCTGGCTGATTACTTAAGAACTCGCTATGCTTATCAAGTTTG
GTTGCTTGTTGCTGGTTACGATAAAAAAGAAGGTCCACAATTAACATTCATTGATTATCT
CGCAAATACTCTCTCCGTTAATCATGGAGCCCACGGTTATGGTGGGATGTTTTGTGGAAG
CATTTTTGACCAATATCATTATGAGAATATAACTCAAGATGAAGCTTATGAAGTTATGCG
AAAGTGTGCACGTGAAATTCAAAAGCGACTGATTATTTCTCAACAGAAATTCCATGTAAC
AGTTGTTGATGCTAATGGTGTTCGTAGATTGGATGATATCACAGCTGAAAATTTGAAGAA
TTAA
>g4362.t3 Gene=g4362 Length=201
METIIGIKGKDFVMLAADSTHPHSIMVLKDDENKIHKISDSLLIAATGDQGDTVQFVEYI
SKNILLYKMRNGYELGPKAAAYFTRKNLADYLRTRYAYQVWLLVAGYDKKEGPQLTFIDY
LANTLSVNHGAHGYGGMFCGSIFDQYHYENITQDEAYEVMRKCAREIQKRLIISQQKFHV
TVVDANGVRRLDDITAENLKN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g4362.t3 | CDD | cd03758 | proteasome_beta_type_2 | 1 | 193 | 4.23588E-109 |
| 6 | g4362.t3 | Gene3D | G3DSA:3.60.20.10 | Glutamine Phosphoribosylpyrophosphate | 1 | 199 | 1.1E-48 |
| 2 | g4362.t3 | PANTHER | PTHR11599:SF6 | PROTEASOME SUBUNIT BETA TYPE-2 | 1 | 191 | 2.1E-65 |
| 3 | g4362.t3 | PANTHER | PTHR11599 | PROTEASOME SUBUNIT ALPHA/BETA | 1 | 191 | 2.1E-65 |
| 1 | g4362.t3 | Pfam | PF00227 | Proteasome subunit | 3 | 183 | 8.8E-41 |
| 5 | g4362.t3 | ProSitePatterns | PS00854 | Proteasome beta-type subunits signature. | 5 | 52 | - |
| 7 | g4362.t3 | ProSiteProfiles | PS51476 | Proteasome beta-type subunit profile. | 1 | 183 | 38.698 |
| 4 | g4362.t3 | SUPERFAMILY | SSF56235 | N-terminal nucleophile aminohydrolases (Ntn hydrolases) | 1 | 199 | 3.87E-51 |
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:0051603 | proteolysis involved in cellular protein catabolic process | BP |
| GO:0004298 | threonine-type endopeptidase activity | MF |
| GO:0005839 | proteasome core complex | CC |
KEGG
Orthology
- This transcript has been annotated with K02734 (20S proteasome subunit beta 4)
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.
