General information for g9372.t3
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative X-ray repair cross-complementing protein 5.
Parent gene
- The parent gene g9372 is located on chr_1: 2290620..2291380 (+ 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_1 | g9372 | g9372.t3 | TSS | g9372.t3 | 2288982 | 2288982 |
| chr_1 | g9372 | g9372.t3 | isoform | g9372.t3 | 2289145 | 2291380 |
| chr_1 | g9372 | g9372.t3 | exon | g9372.t3.exon1 | 2289145 | 2289572 |
| chr_1 | g9372 | g9372.t3 | cds | g9372.t3.CDS1 | 2289445 | 2289572 |
| chr_1 | g9372 | g9372.t3 | exon | g9372.t3.exon2 | 2289631 | 2291380 |
| chr_1 | g9372 | g9372.t3 | cds | g9372.t3.CDS2 | 2289631 | 2291380 |
| chr_1 | g9372 | g9372.t3 | TTS | g9372.t3 | 2291443 | 2291443 |
Sequences
>g9372.t3 Gene=g9372 Length=2178
ATGTCAAGAACACAAAGGGTAAGTTTAAAAATATTGTGAAATTCAAAACATAAACAAATA
TGAGTAAATTATTTTTAGGAAGCTCTTGTGATTATAATTGATGTTGGTGCAAATACAACA
GCTCTATCAGGAAAAAGCGGCAAGACATTCTTTGAAAGAGCAAAAGAATGCGCTAAGAAA
ATTATTTTAAGAAGAATTTTAACAAAACCTGAAGATGAAATTGGTGTAATTTTATTTGGC
ACTGGTGAGACAAAGAATGATTTAAATTCGTCTGATTTAGGCTTTGAGAATATTGTTGAA
ATGGATTTTCTTCAATGTGGCACATGGAAATTAGTCAAAGCACTTGATAATGTTAAACCG
GGAAATGCAACTTGTGATTGGATTGATGCTTTACTTGTTGGCATTAATTACATTAAAAAT
GAAACTGGAGCCAAAAACTTTTGCAAAACTCGCATCATTTTGATAACAAATTTTCAAGTT
GAGGCACACGATGATGAATTGAACGTTGTTGCAGCAAATATCAGTGATAATATGATTGAG
TTGATTGGAGTATCAGATACTGTTCAATATGAAAATAGCAACACTAATTTAACAAGTTGC
CAATTTACACAAAATCCAAACAAAGAAGAAGCTCAAAGCAAGAGTGAAAAAATATTTCAA
GAACTAATTGATCAAATTGAAGATGCAAATTTGTGTCATATCGATTATGTCGAATCTCAA
TTAGCACTTTTTCAAAAGAAAACTACCCGTGCGATGCCATGGAATGCAACTTTATCAATT
GGAAGTCAGTTGTTGATTGAAATTAGTGCATTCGTTTATATTCAAGATGAAAAATTTTTT
GGGAGCTTTAAAACTGAATGTCTCGATCAATTTACTGCTACGAGAATGGTCACAGAATAT
TACAGAAATAATGAGACGATTGAAAAGCCTGATGAAGATGATGTGGTAAAAGCATATATG
TACGGTTCTAAATTCATTGCGATTGATGATCAAGATCTTGCTTACAAAGGAGGAAAAAAA
TGTCTTGCATGCCTAGCATTCTGTAAACGTGATAAAATTCCTCAAGAATATTTCATTGGT
GATGGATGTCACATTGTTGTACCTCAAAAAGATTCAGAGAGAAGTGAAACTCTCTTTTCT
TTATTGGTTCAAGCAATGGCTGTCCGCAATTATCTTATGCTTGCAAGAAAAGTATATCGT
GATGACATAAAACCACAAATTGTTGCTCTTATTCCCCAAATTGAGGATGAAACAAATTAT
TTAATGATGTATGAATTGCCTTATTACGAAGATGTTGAATTCTTTTCCTTTCCAACTCTT
GATCAAATATCAACAAAACCAACTGATCAACAAATGGAAGCAATGAACGAACTTGTTGAA
TTGATGGATTTAACTGATGCAATTGATGATGAAACAGGAATTACTGAAGCATTTACACAA
GATACAATGCAAAATCCTTATCATCAAAATGTATGCAAATCAGTTGCTTATCGTGCACTT
AATCCTACTGAACCTCTGCCACCGATCGACAAAGACTTGTTGAAATTGATTGATACACCA
GAGAAAATCAAACAACGTATTGAAAGTTTTATTATACAATTTGAAGATTTCTTTCCAAGA
GAAATTATACAACGCAAAGATAGAAAGAAACCACTTGGTCAATTACAAAAGGATGGTGAT
ACTGCTATTGATGATACTGAAATTTATGATCATTTGTCATCTGAAAGAACTATAGTTGCC
ATTGGAACAGTAACACCAGCCGAAGATTTTCTTTATTTGCTTAAAAAAGGCGAACGTTTC
AGTGTTTTGTGTGAACAAATGCAATCAATTATTTATGAATACATTTTCAAAAGTATGACA
AAGTTTGAAGATATGGCTGATAAGATAAAGGAAACCATCTTGGCATTTCGTGAGGCAGCA
ACTATTCATGCACCTTTAAATTACAATAAATGGATTGCTGAATTGAAGGCTATGATGACC
AAACGAAATAAAATTGATGAATGGAACTTACTTATCGTAAAAGAAGGCTTAGGTCTAATT
TCACAAAATGAATCGCCTATGTCGACAATTGCACTCGATGAACAAGTTGCATTTTATGAA
ATTATTTCAAAAAATTCATCACGCAATTTCACATCAATTGCTTTAGAAGAAGAAGACGAT
CTTGCTGCATTATTGTAA
>g9372.t3 Gene=g9372 Length=625
MDFLQCGTWKLVKALDNVKPGNATCDWIDALLVGINYIKNETGAKNFCKTRIILITNFQV
EAHDDELNVVAANISDNMIELIGVSDTVQYENSNTNLTSCQFTQNPNKEEAQSKSEKIFQ
ELIDQIEDANLCHIDYVESQLALFQKKTTRAMPWNATLSIGSQLLIEISAFVYIQDEKFF
GSFKTECLDQFTATRMVTEYYRNNETIEKPDEDDVVKAYMYGSKFIAIDDQDLAYKGGKK
CLACLAFCKRDKIPQEYFIGDGCHIVVPQKDSERSETLFSLLVQAMAVRNYLMLARKVYR
DDIKPQIVALIPQIEDETNYLMMYELPYYEDVEFFSFPTLDQISTKPTDQQMEAMNELVE
LMDLTDAIDDETGITEAFTQDTMQNPYHQNVCKSVAYRALNPTEPLPPIDKDLLKLIDTP
EKIKQRIESFIIQFEDFFPREIIQRKDRKKPLGQLQKDGDTAIDDTEIYDHLSSERTIVA
IGTVTPAEDFLYLLKKGERFSVLCEQMQSIIYEYIFKSMTKFEDMADKIKETILAFREAA
TIHAPLNYNKWIAELKAMMTKRNKIDEWNLLIVKEGLGLISQNESPMSTIALDEQVAFYE
IISKNSSRNFTSIALEEEDDLAALL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 13 | g9372.t3 | CDD | cd00873 | KU80 | 153 | 435 | 0 |
| 10 | g9372.t3 | Gene3D | G3DSA:3.40.50.410 | - | 2 | 149 | 0 |
| 11 | g9372.t3 | Gene3D | G3DSA:2.40.290.10 | - | 150 | 343 | 0 |
| 9 | g9372.t3 | Gene3D | G3DSA:1.10.1600.10 | - | 345 | 446 | 0 |
| 12 | g9372.t3 | Gene3D | G3DSA:1.25.40.240 | - | 476 | 610 | 0 |
| 3 | g9372.t3 | PANTHER | PTHR12604 | KU AUTOANTIGEN DNA HELICASE | 10 | 588 | 0 |
| 4 | g9372.t3 | PANTHER | PTHR12604:SF4 | X-RAY REPAIR CROSS-COMPLEMENTING PROTEIN 5 | 10 | 588 | 0 |
| 1 | g9372.t3 | Pfam | PF02735 | Ku70/Ku80 beta-barrel domain | 160 | 353 | 0 |
| 2 | g9372.t3 | Pfam | PF08785 | Ku C terminal domain like | 485 | 599 | 0 |
| 8 | g9372.t3 | SMART | SM00559 | ku_4 | 207 | 343 | 0 |
| 7 | g9372.t3 | SUPERFAMILY | SSF53300 | vWA-like | 11 | 86 | 0 |
| 5 | g9372.t3 | SUPERFAMILY | SSF100939 | SPOC domain-like | 150 | 432 | 0 |
| 6 | g9372.t3 | SUPERFAMILY | SSF101420 | C-terminal domain of Ku80 | 474 | 599 | 0 |
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:0043564 | Ku70:Ku80 complex | CC |
| GO:0005634 | nucleus | CC |
| GO:0003677 | DNA binding | MF |
| GO:0042162 | telomeric DNA binding | MF |
| GO:0003684 | damaged DNA binding | MF |
| GO:0006303 | double-strand break repair via nonhomologous end joining | BP |
| GO:0006310 | DNA recombination | BP |
| GO:0000723 | telomere maintenance | BP |
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.
