General information for g3324.t4
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as DNA-dependent protein kinase catalytic subunit.
Parent gene
- The parent gene g3324 is located on chr_3: 24660935..24662531 (+ 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 | g3324 | g3324.t4 | isoform | g3324.t4 | 24660935 | 24662531 |
| chr_3 | g3324 | g3324.t4 | exon | g3324.t4.exon1 | 24660935 | 24661940 |
| chr_3 | g3324 | g3324.t4 | cds | g3324.t4.CDS1 | 24660950 | 24661940 |
| chr_3 | g3324 | g3324.t4 | exon | g3324.t4.exon2 | 24661999 | 24662531 |
| chr_3 | g3324 | g3324.t4 | cds | g3324.t4.CDS2 | 24661999 | 24662531 |
| chr_3 | g3324 | g3324.t4 | TSS | g3324.t4 | NA | NA |
| chr_3 | g3324 | g3324.t4 | TTS | g3324.t4 | NA | NA |
Sequences
>g3324.t4 Gene=g3324 Length=1539
AAACATAACAATGACATGAAAGGTAGCGATTTCAGTAAAATTCAAAGAACATATTATAAA
TTGATTGTTGAGTTGAAAAAGTTCAATTGGGATACCGAAAAAGAAAAAGCATATAAACAA
ATAAGAGAAATTCAAAAGACAATAAGAAATGGAACAAGAATTCAGCAGTCACAGACAGTT
GAACTTAATAAATTATGTCAATGGCTTGCTGAATACAAATGGAGTGGTAATGAGGATTTT
ATTGAAATTCCTGGACAATATAAAGGCAATATTAAACCGTTCATTGAGAATCATGTGAAA
ATTGTTCGTTTTGAGACACGATTAGATGTTTTTAATTCAAAGCAATTGCCTATCAAAGTT
GGAATATATGGCAGTGATGGTAAAATCTACAATTTCATAGTGAAATATGGTGAAGATCTT
CGTCAAGATCAAAGAATTCAAGAAGTAATGGATTTGATGTCAAGCAAACTTACTTTAGAT
AAAAATTGTAGAAAAAATCGTCTAAAAATTGACACTTATCAAGTCATTCCCATAAATTCG
ACATGTGGACTTTTGCAAATGGTTACGAATACTGCGACAATAAGTGAATTTATGCAAAAA
TCTGGCAAATCATTTCTTCAAAAAGATTTCAATGAATATGTGCTAGAAGCACGCAATAAA
TTTCGTGAATTACTTCTTGCTGGAAATAAATTTACTGGATGGATTGAAACTTTTGAAAAG
GCTCTGATAACACACAGTCGTGACCGATTGATTGAAATATTTGAAGAAATCAGCAATCAA
GTACCATTAAATATTATCCAAAAATCATTAACAGGATTATCACTTACGCTTCATTCTTAT
TATATTTTACGAAAAAATTTTGTAACAAGTTTAGCTGCGATGAATGTTACTCATTGGCTT
CTTGGTATTGGTGATCGACATCTGAATAATATTCTAATCAATACATCAAATGCACGTTTA
ATTGCTATTGATTTTGGTATAGCATTTGGAACAGCAGCATCATTAGGTATCGCAGAATTA
ATTCCTTTTCGTCTTACACCACATTTCGTTAGTGTTCTTTATCCAATGGAAATTAATGGT
TTACTAAAAGAAAATATGAATCATACATTAAAATGCTACCGTGATCATAGAGAGACAATC
GTTGTATGTCTTGAAGTTTTTGTGAAAGAACCAACTCTTGATTGGTTAAAAGAAACAAAG
AAAAAGAGCATTGGGAGCATAAATGTAGAAAATGAAAGTGTTGCATCATCTACTTGGGAA
CCTGAATCACGTATTGATATTGTTAAACGAAAATTAAATGGTCATAATCCAACAAAAATT
TTAATTGAAGAATTAAATTCAGGACATGTAGGCTCAAAACGAGAAATTTTTAATGCATAT
AAAAACTTGATTTATGGAGAAGAGAATTGCACAAGATATAAATATCAACATGAAGAGCTG
AATTTAAGGACTGAAGATCAGATCGAATGTTTGATTGAAATAGCTACAGATAAGGCAGTT
TTGGCAACTACTTATGTAGGATGGGACAGTTGGTTTTAA
>g3324.t4 Gene=g3324 Length=507
MKGSDFSKIQRTYYKLIVELKKFNWDTEKEKAYKQIREIQKTIRNGTRIQQSQTVELNKL
CQWLAEYKWSGNEDFIEIPGQYKGNIKPFIENHVKIVRFETRLDVFNSKQLPIKVGIYGS
DGKIYNFIVKYGEDLRQDQRIQEVMDLMSSKLTLDKNCRKNRLKIDTYQVIPINSTCGLL
QMVTNTATISEFMQKSGKSFLQKDFNEYVLEARNKFRELLLAGNKFTGWIETFEKALITH
SRDRLIEIFEEISNQVPLNIIQKSLTGLSLTLHSYYILRKNFVTSLAAMNVTHWLLGIGD
RHLNNILINTSNARLIAIDFGIAFGTAASLGIAELIPFRLTPHFVSVLYPMEINGLLKEN
MNHTLKCYRDHRETIVVCLEVFVKEPTLDWLKETKKKSIGSINVENESVASSTWEPESRI
DIVKRKLNGHNPTKILIEELNSGHVGSKREIFNAYKNLIYGEENCTRYKYQHEELNLRTE
DQIECLIEIATDKAVLATTYVGWDSWF
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g3324.t4 | CDD | cd05172 | PIKKc_DNA-PK | 96 | 392 | 5.88633E-102 |
| 6 | g3324.t4 | Gene3D | G3DSA:3.30.1010.10 | - | 27 | 184 | 7.6E-16 |
| 7 | g3324.t4 | Gene3D | G3DSA:1.10.1070.11 | - | 240 | 418 | 4.4E-25 |
| 3 | g3324.t4 | PANTHER | PTHR11139:SF68 | DNA-DEPENDENT PROTEIN KINASE CATALYTIC SUBUNIT | 36 | 503 | 9.6E-106 |
| 4 | g3324.t4 | PANTHER | PTHR11139 | ATAXIA TELANGIECTASIA MUTATED ATM -RELATED | 36 | 503 | 9.6E-106 |
| 1 | g3324.t4 | Pfam | PF00454 | Phosphatidylinositol 3- and 4-kinase | 125 | 390 | 2.8E-42 |
| 2 | g3324.t4 | Pfam | PF02260 | FATC domain | 477 | 507 | 1.6E-8 |
| 9 | g3324.t4 | ProSitePatterns | PS00916 | Phosphatidylinositol 3- and 4-kinases signature 2. | 285 | 305 | - |
| 12 | g3324.t4 | ProSiteProfiles | PS50290 | Phosphatidylinositol 3- and 4-kinases family profile. | 125 | 507 | 36.179 |
| 13 | g3324.t4 | ProSiteProfiles | PS51190 | FATC domain profile. | 475 | 507 | 11.676 |
| 11 | g3324.t4 | SMART | SM00146 | pi3k_hr1_6 | 126 | 445 | 1.9E-37 |
| 10 | g3324.t4 | SMART | SM01343 | FATC_2 | 475 | 507 | 1.6E-7 |
| 5 | g3324.t4 | SUPERFAMILY | SSF56112 | Protein kinase-like (PK-like) | 39 | 398 | 2.3E-65 |
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:0004677 | DNA-dependent protein kinase activity | MF |
| GO:0006281 | DNA repair | BP |
| GO:0005515 | protein binding | MF |
| GO:0016301 | kinase 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.
