General information for g4920.t1
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.t1 | TTS | g4920.t1 | 5963285 | 5963285 |
| chr_2 | g4920 | g4920.t1 | isoform | g4920.t1 | 5963398 | 5965772 |
| chr_2 | g4920 | g4920.t1 | exon | g4920.t1.exon1 | 5963398 | 5964200 |
| chr_2 | g4920 | g4920.t1 | cds | g4920.t1.CDS1 | 5963398 | 5964200 |
| chr_2 | g4920 | g4920.t1 | exon | g4920.t1.exon2 | 5964279 | 5964437 |
| chr_2 | g4920 | g4920.t1 | cds | g4920.t1.CDS2 | 5964279 | 5964437 |
| chr_2 | g4920 | g4920.t1 | exon | g4920.t1.exon3 | 5964498 | 5964937 |
| chr_2 | g4920 | g4920.t1 | cds | g4920.t1.CDS3 | 5964498 | 5964937 |
| chr_2 | g4920 | g4920.t1 | exon | g4920.t1.exon4 | 5965004 | 5965014 |
| chr_2 | g4920 | g4920.t1 | cds | g4920.t1.CDS4 | 5965004 | 5965014 |
| chr_2 | g4920 | g4920.t1 | TSS | g4920.t1 | 5965056 | 5965056 |
| chr_2 | g4920 | g4920.t1 | exon | g4920.t1.exon5 | 5965405 | 5965604 |
| chr_2 | g4920 | g4920.t1 | cds | g4920.t1.CDS5 | 5965405 | 5965604 |
| chr_2 | g4920 | g4920.t1 | exon | g4920.t1.exon6 | 5965664 | 5965772 |
| chr_2 | g4920 | g4920.t1 | cds | g4920.t1.CDS6 | 5965664 | 5965772 |
Sequences
>g4920.t1 Gene=g4920 Length=1722
ATGGAATCAAAAGCTAATGCATTTCAAATTAAACCAGAACTTGAAAATATTATCCCCCCA
GGAGAAGTGAAAAAGTTAATTCAAAAAACACTTAATGATACACTCCTAAACAAATGTTAT
TCTGTTGAAAATGCAAAAGTTTGGACAAAAAGTATAGCTGATGATATAAATAGGAATTTA
AATTATTCAACACAACGATATAAGCATGTCGTTCAAGTTTTGCTTACTCAAAAGTTAGGA
CAAGGCTTCAAATTTACAGCACGTAGTCGTTGGGATACTGATACAGATCGTCAAATAACA
GATTCGTTCAAAATATTAAGCAAAATGGTTGCAGTACAAGATGTGGAAATGGAAGTCATT
GAAAGTGAAAATACAGAACAGGAGCAACAGAAGAAAGAATCGGATGTGAATACAATTGTC
CAAGAGATTCGAGAACATGTAAAGCAAATTGATAAAGCAGTAGCAAGCAAAGAACCGCGT
TTTATTCTTCGTGTTTTAAGATCTCTACCAAATACACGTAGAAAATTGACTCCCGTTGTT
CTTAGATCACTCGCAAATCAAATCTATCCTGTATCTGAACGAGATGCTATTCTTGTATAT
GTCGAGGAAGTAACTAGTGGAGAGCAGCAAAATGAAAGTGCAAGTGCACGTCCTCGCGCA
ACAATTAAAACTCCACTTCCAGAAGTTGATGCATATTTTCACTTATTAGCTCTTGTTCGT
TTGTTAGACGCGAAATTGCTTGATAAAGCATCTCATTGTGCTCAACAGCTCATGACAAAA
ATTATGTCTCAGAATCGTAGATCATTAGATCTTATTGCTGCAAAGAGCTATTTCTATCAT
TCACGAGTTGCAGAATTAACAAATAAATTGGATACAATTCGTGGATTTTTACATGCTCGT
CTAAGAACTGCAACTCTACCTGATAAATTAGTTAACAAATCAGTCTTTCCTGAAACTGCA
AGTAACAATGAATGGGCCCGTTTTCTTTATTATTTGGGTCGTATAAAGGCTGCAAAATTG
GAATATAGTGTTGCACATAAGCATCTTATTCAGGCTATGCGAAAGGCTCCACAAAATGCT
GCAATTGGTTTCCGTCAAACAGTTCAGAAACTTGTAGTTGTTGTTGAATTACTTTTGGGT
GATATCCCAGAACGACAAATTTTCAGACAAGCAGCTCTTCGTCGTTCACTCGTTCCTTAT
TTTCAACTTACACAAGCTGTAAGATTGGGAAATCTGAAACGTTTCGGTGAAGTGCTTACC
AATTATGGTGAAAAATTCCGTCAAGATCATACATTTACACTCATCATTCGTTTGAGACAT
AATGTCATTAAGACTGCAATAAGATCAATTGGACTCTCATATTCATGCATTTCACCAGCT
GATATAGCCAAAAAATTAGGAATTGATTCTAAGGAGGATGCAGAATTTATTGTATCGAAA
GCTATTCGTGATGGTGTTATTGAAGCAACATTAGATCCAGAAAAAGGATATATGCGCAGC
AAAGAGAGCACAGATATATATTCAACTCGTGAGCCTCAATTGGCTTTTCATCAACGCATC
ACTTTCTGCTTAGATTTGCATAATCAATCAGTTAAAGCAATGCGATATCCACCAAAATCA
TATGGCAAGGATTTGGAAAGTGCTGAAGAACGAATTGAACGTGAGCAACAAGAAGTTGAA
TTAGCAAAGGAAATGGCAGAAGATGATGATGATGGTTTTTAA
>g4920.t1 Gene=g4920 Length=573
MESKANAFQIKPELENIIPPGEVKKLIQKTLNDTLLNKCYSVENAKVWTKSIADDINRNL
NYSTQRYKHVVQVLLTQKLGQGFKFTARSRWDTDTDRQITDSFKILSKMVAVQDVEMEVI
ESENTEQEQQKKESDVNTIVQEIREHVKQIDKAVASKEPRFILRVLRSLPNTRRKLTPVV
LRSLANQIYPVSERDAILVYVEEVTSGEQQNESASARPRATIKTPLPEVDAYFHLLALVR
LLDAKLLDKASHCAQQLMTKIMSQNRRSLDLIAAKSYFYHSRVAELTNKLDTIRGFLHAR
LRTATLPDKLVNKSVFPETASNNEWARFLYYLGRIKAAKLEYSVAHKHLIQAMRKAPQNA
AIGFRQTVQKLVVVVELLLGDIPERQIFRQAALRRSLVPYFQLTQAVRLGNLKRFGEVLT
NYGEKFRQDHTFTLIIRLRHNVIKTAIRSIGLSYSCISPADIAKKLGIDSKEDAEFIVSK
AIRDGVIEATLDPEKGYMRSKESTDIYSTREPQLAFHQRITFCLDLHNQSVKAMRYPPKS
YGKDLESAEERIEREQQEVELAKEMAEDDDDGF
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 11 | g4920.t1 | Coils | Coil | Coil | 112 | 132 | - |
| 12 | g4920.t1 | Coils | Coil | Coil | 545 | 569 | - |
| 9 | g4920.t1 | Gene3D | G3DSA:3.30.1140.40 | - | 21 | 116 | 9.1E-17 |
| 10 | g4920.t1 | Gene3D | G3DSA:1.25.40.570 | - | 314 | 448 | 1.1E-37 |
| 16 | g4920.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 537 | 556 | - |
| 15 | g4920.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 542 | 556 | - |
| 4 | g4920.t1 | PANTHER | PTHR10758:SF2 | 26S PROTEASOME NON-ATPASE REGULATORY SUBUNIT 3 | 114 | 306 | 6.1E-175 |
| 6 | g4920.t1 | PANTHER | PTHR10758 | 26S PROTEASOME NON-ATPASE REGULATORY SUBUNIT 3/COP9 SIGNALOSOME COMPLEX SUBUNIT 3 | 114 | 306 | 6.1E-175 |
| 5 | g4920.t1 | PANTHER | PTHR10758:SF2 | 26S PROTEASOME NON-ATPASE REGULATORY SUBUNIT 3 | 308 | 573 | 6.1E-175 |
| 7 | g4920.t1 | PANTHER | PTHR10758 | 26S PROTEASOME NON-ATPASE REGULATORY SUBUNIT 3/COP9 SIGNALOSOME COMPLEX SUBUNIT 3 | 308 | 573 | 6.1E-175 |
| 1 | g4920.t1 | Pfam | PF03645 | Tctex-1 family | 22 | 104 | 2.6E-14 |
| 3 | g4920.t1 | Pfam | PF01399 | PCI domain | 399 | 501 | 2.4E-20 |
| 2 | g4920.t1 | Pfam | PF08375 | Proteasome regulatory subunit C-terminal | 505 | 571 | 9.5E-28 |
| 17 | g4920.t1 | ProSiteProfiles | PS50250 | PCI domain profile. | 326 | 505 | 24.724 |
| 13 | g4920.t1 | SMART | SM00088 | PINT_4 | 433 | 523 | 6.6E-26 |
| 14 | g4920.t1 | SMART | SM00753 | motif in proteasome subunits, Int-6, Nip-1 and TRIP-15 | 433 | 523 | 6.6E-26 |
| 8 | g4920.t1 | SUPERFAMILY | SSF46785 | Winged helix DNA-binding domain | 438 | 505 | 9.25E-7 |
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 transcript has been annotated with K03033 (26S proteasome regulatory subunit N3)
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.
