General information for g9372.t2
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.t2 | TSS | g9372.t2 | 2288982 | 2288982 |
| chr_1 | g9372 | g9372.t2 | isoform | g9372.t2 | 2289145 | 2290620 |
| chr_1 | g9372 | g9372.t2 | exon | g9372.t2.exon1 | 2289145 | 2289162 |
| chr_1 | g9372 | g9372.t2 | exon | g9372.t2.exon2 | 2289223 | 2290620 |
| chr_1 | g9372 | g9372.t2 | cds | g9372.t2.CDS1 | 2289734 | 2290618 |
| chr_1 | g9372 | g9372.t2 | TTS | g9372.t2 | 2291443 | 2291443 |
Sequences
>g9372.t2 Gene=g9372 Length=1416
ATGTCAAGAACACAAAGGGAAGCTCTTGTGATTATAATTGATGTTGGTGCAAATACAACA
GCTCTATCAGGAAAAAGCGGCAAGACATTCTTTGAAAGAGCAAAAGAATGCGCTAAGAAA
ATTATTTTAAGAAGAATTTTAACAAAACCTGAAGATGAAATTGGTGTAATTTTATTTGGC
ACTGGTGAGACAAAGAATGATTTAAATTCGTCTGATTTAGGCTTTGAGAATATTGTTGAA
ATGGATTTTCTTCAATGTGGCACATGGAAATTAGTCAAAGCACTTGATAATGTTAAACCG
GGAAATGCAACTTGTGATTGGATTGATGCTTTACTTGTTGGCATTAATTACATTAAAAAT
GAAACTGGGTAAGTATTTAATTCAACCCACATAATAATTTCATCATTTTATAAATTTCAA
TTATAGAGCCAAAAACTTTTGCAAAACTCGCATCATTTTGATAACAAATTTTCAAGTTGA
GGCACACGATGATGAATTGAACGTTGTTGCAGCAAATATCAGTGATAATATGATTGAGTT
GATTGGAGTATCAGATACTGTTCAATATGAAAATAGCAACACTAATTTAACAAGTTGCCA
ATTTACACAAAATCCAAACAAAGAAGAAGCTCAAAGCAAGAGTGAAAAAATATTTCAAGA
ACTAATTGATCAAATTGAAGATGCAAATTTGTGTCATATCGATTATGTCGAATCTCAATT
AGCACTTTTTCAAAAGAAAACTACCCGTGCGATGCCATGGAATGCAACTTTATCAATTGG
AAGTCAGTTGTTGATTGAAATTAGTGCATTCGTTTATATTCAAGATGAAAAATTTTTTGG
GAGCTTTAAAACTGAATGTCTCGATCAATTTACTGCTACGAGAATGGTCACAGAATATTA
CAGAAATAATGAGACGATTGAAAAGCCTGATGAAGATGATGTGGTAAAAGCATATATGTA
CGGTTCTAAATTCATTGCGATTGATGATCAAGATCTTGCTTACAAAGGAGGAAAAAAATG
TCTTGCATGCCTAGCATTCTGTAAACGTGATAAAATTCCTCAAGAATATTTCATTGGTGA
TGGATGTCACATTGTTGTACCTCAAAAAGATTCAGAGAGAAGTGAAACTCTCTTTTCTTT
ATTGGTTCAAGCAATGGCTGTCCGCAATTATCTTATGCTTGCAAGAAAAGTATATCGTGA
TGACATAAAACCACAAATTGTTGCTCTTATTCCCCAAATTGAGGATGAAACAAATTATTT
AATGATGTATGAATTGCCTTATTACGAAGATGTTGAATTCTTTTCCTTTCCAACTCTTGA
TCAAATATCAACAAAACCAACTGATCAACAAATGGAAGCAATGAACGAACTTGTTGAATT
GATGGATTTAACTGATGCAATTGATGATGAAACAGG
>g9372.t2 Gene=g9372 Length=295
MIELIGVSDTVQYENSNTNLTSCQFTQNPNKEEAQSKSEKIFQELIDQIEDANLCHIDYV
ESQLALFQKKTTRAMPWNATLSIGSQLLIEISAFVYIQDEKFFGSFKTECLDQFTATRMV
TEYYRNNETIEKPDEDDVVKAYMYGSKFIAIDDQDLAYKGGKKCLACLAFCKRDKIPQEY
FIGDGCHIVVPQKDSERSETLFSLLVQAMAVRNYLMLARKVYRDDIKPQIVALIPQIEDE
TNYLMMYELPYYEDVEFFSFPTLDQISTKPTDQQMEAMNELVELMDLTDAIDDET
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g9372.t2 | Gene3D | G3DSA:2.40.290.10 | - | 73 | 266 | 0 |
| 2 | g9372.t2 | PANTHER | PTHR12604 | KU AUTOANTIGEN DNA HELICASE | 15 | 289 | 0 |
| 3 | g9372.t2 | PANTHER | PTHR12604:SF4 | X-RAY REPAIR CROSS-COMPLEMENTING PROTEIN 5 | 15 | 289 | 0 |
| 1 | g9372.t2 | Pfam | PF02735 | Ku70/Ku80 beta-barrel domain | 83 | 276 | 0 |
| 5 | g9372.t2 | SMART | SM00559 | ku_4 | 130 | 266 | 0 |
| 4 | g9372.t2 | SUPERFAMILY | SSF100939 | SPOC domain-like | 73 | 292 | 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:0003677 | DNA binding | MF |
| GO:0006303 | double-strand break repair via nonhomologous end joining | 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.
