General information for g1602.t12
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as 26S proteasome regulatory subunit 4.
Parent gene
- The parent gene g1602 is located on chr_3: 12086969..12087946 (- 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_3 | g1602 | g1602.t12 | TTS | g1602.t12 | 12086105 | 12086105 |
| chr_3 | g1602 | g1602.t12 | isoform | g1602.t12 | 12086169 | 12087914 |
| chr_3 | g1602 | g1602.t12 | exon | g1602.t12.exon1 | 12086169 | 12086623 |
| chr_3 | g1602 | g1602.t12 | exon | g1602.t12.exon2 | 12086705 | 12086869 |
| chr_3 | g1602 | g1602.t12 | cds | g1602.t12.CDS1 | 12086737 | 12086869 |
| chr_3 | g1602 | g1602.t12 | exon | g1602.t12.exon3 | 12086934 | 12087171 |
| chr_3 | g1602 | g1602.t12 | cds | g1602.t12.CDS2 | 12086934 | 12087171 |
| chr_3 | g1602 | g1602.t12 | exon | g1602.t12.exon4 | 12087358 | 12087784 |
| chr_3 | g1602 | g1602.t12 | cds | g1602.t12.CDS3 | 12087358 | 12087784 |
| chr_3 | g1602 | g1602.t12 | exon | g1602.t12.exon5 | 12087912 | 12087914 |
| chr_3 | g1602 | g1602.t12 | cds | g1602.t12.CDS4 | 12087912 | 12087914 |
| chr_3 | g1602 | g1602.t12 | TSS | g1602.t12 | 12088004 | 12088004 |
Sequences
>g1602.t12 Gene=g1602 Length=1288
ATGGGCCAAAATCAATCTTCTGGTAGTGGAGATAAAAAAGATGATAAAGACAAGAAGAAG
AAGTACGAGCCACCAATTCCAACTCGCGTTGGTAAAAAGAAGCGAAAACAGAAGGGACCA
GATGCTGCATTAAAACTTCCGCAAGTCACTCCGCATACTCGTTGTCGTTTGAAATTGCTT
AAACTTGAACGCATCAAAGATTACCTTCTTATGGAAGAGGAATTTATTCGTAATCAAGAG
CGTTTGAAGCCTCAAGAAGAGAAGAATGAAGAAGAAAGGTCGAAAGTTGATGATTTGAGA
GGAACACCAATGTCTGTTGGTAATCTGGAAGAAATCATTGATGATAATCATGCAATTGTT
TCAACATCAGTTGGTAGTGAGCATTACGTTAGCATATTATCATTTGTCGATAAAGATCAA
CTTGAACCAGGATGTTCGGTCTTATTAAATCATAAAGTTCATGCTGTAGTTGGTGTATTA
AGTGATGATACAGATCCAATGGTTACGGTAATGAAATTAGAAAAAGCTCCACAAGAAACT
TATGCCGATATTGGCGGATTAGATACGCAAATTCAAGAAATTAAAGAGTCTGTTGAATTA
CCTTTAACACATCCTGAATATTATGAAGAAATGGGTATTAAACCACCAAAAGGAGTCATT
TTATATGGTCCACCAGGTACAGGCAAAACTTTACTTGCTAAAGCTGTAGCTAATCAGACA
TCAGCTACTTTCCTACGTGTTGTTGGATCAGAATTAATTCAAAAGTATTTGGTAAGATTA
ATTAGACTGATGTTTAAATGAAAATTAATATTTCTTTCATTCATAGGGTGATGTTGGCAC
AAAACGTTATGATTCAAATTCAGGCGGTGAGAGAGAAATTCAAAGAACTATGTTGGAGTT
GCTTAATCAATTAGATGGTTTTGATTCACGTGGTGATGTGAAAGTTATTATGGCAACAAA
TAGAATTGAAACTCTTGATCCTGCTCTCATTCGTCCCGGACGTATTGATCGTAAAATTGA
ATTCCCTCTGCCAGATGAGAAGACAAAGAGAAGAATTTTCAATATTCACACTTCAAAAAT
GACACTCGCATCCGATGTCAATCTTTCTGAATTAATTATGGCAAAAGATGATTTGTCTGG
GGCTGATATAAAAGCTATTTGTACTGAAGCTGGTTTGATGGCTTTGCGTGAACGTCGAAT
GAAGGTTACAAATGATGACTTTAAGAAATCGAAAGAGAGTGTACTTTATCGTAAAAAAGA
AGGAACCCCAGATGGTTTATATTTGTAA
>g1602.t12 Gene=g1602 Length=266
MGQNQSSGSGDKKDDKDKKKKYEPPIPTRVGKKKRKQKGPDAALKLPQVTPHTRCRLKLL
KLERIKDYLLMEEEFIRNQERLKPQEEKNEEERSKVDDLRGTPMSVGNLEEIIDDNHAIV
STSVGSEHYVSILSFVDKDQLEPGCSVLLNHKVHAVVGVLSDDTDPMVTVMKLEKAPQET
YADIGGLDTQIQEIKESVELPLTHPEYYEEMGIKPPKGVILYGPPGTGKTLLAKAVANQT
SATFLRVVGSELIQKYLVRLIRLMFK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 10 | g1602.t12 | CDD | cd00009 | AAA | 185 | 265 | 3.13432E-11 |
| 9 | g1602.t12 | Gene3D | G3DSA:2.40.50.140 | - | 104 | 171 | 2.7E-29 |
| 8 | g1602.t12 | Gene3D | G3DSA:3.40.50.300 | - | 172 | 266 | 1.4E-28 |
| 6 | g1602.t12 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 47 | - |
| 7 | g1602.t12 | MobiDBLite | mobidb-lite | consensus disorder prediction | 9 | 30 | - |
| 3 | g1602.t12 | PANTHER | PTHR23073 | 26S PROTEASOME REGULATORY SUBUNIT | 28 | 258 | 5.8E-138 |
| 4 | g1602.t12 | PANTHER | PTHR23073:SF77 | 26S PROTEASOME REGULATORY SUBUNIT 4 | 28 | 258 | 5.8E-138 |
| 1 | g1602.t12 | Pfam | PF16450 | Proteasomal ATPase OB C-terminal domain | 106 | 160 | 2.3E-11 |
| 2 | g1602.t12 | Pfam | PF00004 | ATPase family associated with various cellular activities (AAA) | 219 | 257 | 2.0E-11 |
| 5 | g1602.t12 | SUPERFAMILY | SSF52540 | P-loop containing nucleoside triphosphate hydrolases | 170 | 255 | 1.52E-24 |
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:0005524 | ATP binding | MF |
| GO:0036402 | proteasome-activating activity | MF |
| GO:0016887 | ATP hydrolysis 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.
