General information for g11202.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as X-ray repair cross-complementing protein 5.
Parent gene
- The parent gene g11202 is located on chr_1: 14557451..14559403 (+ 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 | g11202 | g11202.t1 | TSS | g11202.t1 | 14557362 | 14557362 |
| chr_1 | g11202 | g11202.t1 | isoform | g11202.t1 | 14557451 | 14559403 |
| chr_1 | g11202 | g11202.t1 | exon | g11202.t1.exon1 | 14557451 | 14557538 |
| chr_1 | g11202 | g11202.t1 | cds | g11202.t1.CDS1 | 14557451 | 14557538 |
| chr_1 | g11202 | g11202.t1 | exon | g11202.t1.exon2 | 14557594 | 14557724 |
| chr_1 | g11202 | g11202.t1 | cds | g11202.t1.CDS2 | 14557594 | 14557724 |
| chr_1 | g11202 | g11202.t1 | exon | g11202.t1.exon3 | 14557781 | 14559403 |
| chr_1 | g11202 | g11202.t1 | cds | g11202.t1.CDS3 | 14557781 | 14559403 |
| chr_1 | g11202 | g11202.t1 | TTS | g11202.t1 | 14559467 | 14559467 |
Sequences
>g11202.t1 Gene=g11202 Length=1842
ATGGCAACATCGCTTTATCAATTTACTCAGTATAACGATGATGATGAACAAGAAGACATT
AAACATTTTATTACAGGAAAAGATATCACTCTTTTCGTTATTGATGTTGGAAAATCTATG
TTTAAAGAGATAATTGAAAATGAGACGCCTTTTGACGTTTGTCTTACGGTTCTTGAGAAA
TTGTTTTTAGCTAAAATTCGTCACAATTCTAACGATCAAATAGCAGTGATATTTTATAAT
ACACAACATTCACCAGAACCAAAATCTGATGTACAGATTGCTTGTCCAGATCAATGTGCT
ATTCTTTTTACTCTTCAATCAATTGAATCAGATATTATTCGCTTTATCAAAAATATGAAA
GCGTCAGGCGATTATCACGATTTTGCAACAAAGTATGGTCATTCAAAAGATACACAGTTA
TCAGAAGTTCTCTGGCTCTGTAATGCTTTAGTTTCAAATTCTGGTATTTTTGTACGAAAT
TGTACTATCGTGTGGTTCACAGATAATGACCAGCCTCATCAGTTGAATACACCTGAATAT
ACTTCAGTTATGCAAAAAACTGCAGATCTGCACAATCTTCATCCAGATTTTCAATTGGTT
CCATTAAAAGAAACTTTCAAAAAAGATTTGTTCTATAATGAATTCCTGCAGAATATTATG
AAGGACCGTGATGAAATAGAATTTCCGACACCAACAATTGACACAGATGAACTTGCAAGA
CGACTTTTAACTCGCAGTTATCGTAATAGAGCTCTATCTTATCTCACTGTTGAGATACTT
GATAGACCACAATTTAGTGTCGGCATCTACACTTTCACATCAAAAAAATCCGGACCACGT
TCAGAAACAATTTCACGTGTGACGAAGGAAGTAGTAAAATCTAAGCGTTCTTATAAATAT
GGACACTTTAAAGAAGATAATGAAGATGACTTGAATGTCAGTTTTAATGAAAAGTTAACT
GCTGAGAAAACGATTAAATATTTAGAAGTTGGTGGCGAGAAAGTTAAATTTACACCATTA
GAGACATATGAAATGAAGCAATTTATGCAGCCAGCTATTAAAATTCTTGGTTTTAAACCA
CTAGAAACGTTCAATCCACTCAATCATAAAAGAAGTCCATATTTTGTGTATCCAAGTGAA
AATCAAATTAAACATTCCACTAAGACGTTTCGAGCACTTTGGGAAACTTGTTTAAATAAA
AGCAAGTATATTCTTTGTATTGTTTGTTTGCGTCTTAAAAGTAATCCTCGATTTGTTGCT
TTGATACCGCAACGTGAAAATGCAAACCAAACACAATTCGATGGTTTTCGGATGGAATTT
CTTCCTTTCGCTGGTGAAATTCGTGATTTAAGCCAAAAAATGCCCGTACGTAAAGAAGTC
AGTGACAAAGCTTTGACAGAAATGGCTAAAGCTATTTCAAAGCTTACCATTAATTATGAT
GTTACAATGTTTAAAAATCCTGCTATCTCAAAATTATACAACAAGATCGAACGAATTGAA
TTTAGCGAAGATGTAGAGGATCCACCTGAGGATGTAACATTGCCCAAAGTTGAAGAACAA
GATCGTCGTATAGATGCTTATGCTTCAGTTTTGAAAGAGATGTATAGTGATTTAACAGAT
AAATCATCTAAACGCAAAGCAACATGCACACAGGGTGGCTCTTCAGCGAAGAAACCGGCT
CTTGATATTAATGAAGACATGCTTGTTGAGTTATGCAAGAAAGACGATGTAAAAAATATT
AATGTTCCAGTTTTAAGAGAATACTTAAAAAGCAAAAATGTAAGTGGTCTTTCAAAAATG
AACAAAGAGCAGTTGGTCAGAAAAATTGTTGAGATCTCTTAA
>g11202.t1 Gene=g11202 Length=613
MATSLYQFTQYNDDDEQEDIKHFITGKDITLFVIDVGKSMFKEIIENETPFDVCLTVLEK
LFLAKIRHNSNDQIAVIFYNTQHSPEPKSDVQIACPDQCAILFTLQSIESDIIRFIKNMK
ASGDYHDFATKYGHSKDTQLSEVLWLCNALVSNSGIFVRNCTIVWFTDNDQPHQLNTPEY
TSVMQKTADLHNLHPDFQLVPLKETFKKDLFYNEFLQNIMKDRDEIEFPTPTIDTDELAR
RLLTRSYRNRALSYLTVEILDRPQFSVGIYTFTSKKSGPRSETISRVTKEVVKSKRSYKY
GHFKEDNEDDLNVSFNEKLTAEKTIKYLEVGGEKVKFTPLETYEMKQFMQPAIKILGFKP
LETFNPLNHKRSPYFVYPSENQIKHSTKTFRALWETCLNKSKYILCIVCLRLKSNPRFVA
LIPQRENANQTQFDGFRMEFLPFAGEIRDLSQKMPVRKEVSDKALTEMAKAISKLTINYD
VTMFKNPAISKLYNKIERIEFSEDVEDPPEDVTLPKVEEQDRRIDAYASVLKEMYSDLTD
KSSKRKATCTQGGSSAKKPALDINEDMLVELCKKDDVKNINVPVLREYLKSKNVSGLSKM
NKEQLVRKIVEIS
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 13 | g11202.t1 | CDD | cd00788 | KU70 | 250 | 524 | 0e+00 |
| 10 | g11202.t1 | Gene3D | G3DSA:3.40.50.410 | - | 27 | 246 | 0e+00 |
| 11 | g11202.t1 | Gene3D | G3DSA:2.40.290.10 | - | 250 | 443 | 0e+00 |
| 8 | g11202.t1 | Gene3D | G3DSA:4.10.970.10 | Ku70 | 275 | 349 | 0e+00 |
| 9 | g11202.t1 | Gene3D | G3DSA:1.10.1600.10 | - | 444 | 537 | 0e+00 |
| 4 | g11202.t1 | PANTHER | PTHR12604 | KU AUTOANTIGEN DNA HELICASE | 12 | 609 | 0e+00 |
| 5 | g11202.t1 | PANTHER | PTHR12604:SF2 | X-RAY REPAIR CROSS-COMPLEMENTING PROTEIN 6 | 12 | 609 | 0e+00 |
| 12 | g11202.t1 | PIRSF | PIRSF003033 | Ku70 | 5 | 612 | 0e+00 |
| 3 | g11202.t1 | Pfam | PF03731 | Ku70/Ku80 N-terminal alpha/beta domain | 30 | 251 | 0e+00 |
| 2 | g11202.t1 | Pfam | PF02735 | Ku70/Ku80 beta-barrel domain | 264 | 453 | 0e+00 |
| 1 | g11202.t1 | Pfam | PF03730 | Ku70/Ku80 C-terminal arm | 479 | 559 | 1e-07 |
| 14 | g11202.t1 | SMART | SM00559 | ku_4 | 316 | 458 | 0e+00 |
| 7 | g11202.t1 | SUPERFAMILY | SSF53300 | vWA-like | 26 | 221 | 0e+00 |
| 6 | g11202.t1 | SUPERFAMILY | SSF100939 | SPOC domain-like | 250 | 534 | 0e+00 |
| 15 | g11202.t1 | TIGRFAM | TIGR00578 | ku70: ATP-dependent DNA helicase II, 70 kDa subunit (ku70) | 25 | 606 | 0e+00 |
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:0003678 | DNA helicase activity | MF |
| GO:0006303 | double-strand break repair via nonhomologous end joining | BP |
| GO:0000723 | telomere maintenance | BP |
KEGG
Orthology
- This transcript has been annotated with K10884 (ATP-dependent DNA helicase 2 subunit 1)
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.
