General information for g13537.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as DNA repair protein complementing XP-A cells-like protein.
Parent gene
- The parent gene g13537 is located on chr_1: 30762878..30763729 (+ 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 | g13537 | g13537.t2 | TSS | g13537.t2 | 30761938 | 30761938 |
| chr_1 | g13537 | g13537.t2 | isoform | g13537.t2 | 30762023 | 30762878 |
| chr_1 | g13537 | g13537.t2 | exon | g13537.t2.exon1 | 30762023 | 30762878 |
| chr_1 | g13537 | g13537.t2 | cds | g13537.t2.CDS1 | 30762213 | 30762878 |
| chr_1 | g13537 | g13537.t2 | TTS | g13537.t2 | 30763100 | 30763100 |
Sequences
>g13537.t2 Gene=g13537 Length=856
ATGGAAGAATCAAAAAATCAAAAAATGTTGACCGAAGCTCAAAAAGCTCGAATTGAAAGA
AATCGAGTTAAAGCAATGCATTTAAGAGAATCTAAAGTTGCAATGTAAGTTATTTTTACA
TTTTATCATGCTTTATTTATGTTTTTTTTGATTCGTTTATAGATCAAAAGAAACTGAAAA
TGGTGGTAAAATGATTAAAGTCGATGGATCTAAATATGTAGATACTTGTGGTGGCTTTCT
GATAAATGAACATGATCTGGAAACTGAAGAAGAAGAAAAGGCTGCAAAAATCATAAAATT
AGCAGAAGATGAAGCTGAAGATTTGCCGATAACATATTTGAAATGTATTGAATGTGAAGA
AGAGTATGCTGATTCTTATTTATCAAAACATTTTGAATATTCTTGTTGTGATAAATGCAA
AGATTTAGACGAAAAGCATCAGCTAATAACTAAAACTGATGCCCGAAACGAATTTCTCTT
AAAGGATTGTGATTTCGACAAAAGAGAACCACCTCTAAAATTTATTTCACGAAAAAATCC
GCATAAATCAACATGGGCTGAAATGAAGTTATATTTAAAATTGCAAGTCAAAGCAAGAGC
TATGGAAGTTCATGGTAGTGAAGAGAAGCTGCGTGAAGAAATCAAATTACGAGAAGAGAA
GAGAGAAATTGCAAAAGTTAAAAAATACAATACAAAATTAAATGAATTACGAAAAACTGT
TCGGTCTACACTTTATGATAAAACTCATAAAAGCCATGTGCATGAATATGGTCCTAGTAC
CTACAACAAGGATACTGATGAGTACACACACGTTTGTGTATCATGCGGTTTTATTGAAAC
ATACGAGGAAATGTAA
>g13537.t2 Gene=g13537 Length=221
MIKVDGSKYVDTCGGFLINEHDLETEEEEKAAKIIKLAEDEAEDLPITYLKCIECEEEYA
DSYLSKHFEYSCCDKCKDLDEKHQLITKTDARNEFLLKDCDFDKREPPLKFISRKNPHKS
TWAEMKLYLKLQVKARAMEVHGSEEKLREEIKLREEKREIAKVKKYNTKLNELRKTVRST
LYDKTHKSHVHEYGPSTYNKDTDEYTHVCVSCGFIETYEEM
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g13537.t2 | Coils | Coil | Coil | 23 | 43 | - |
| 7 | g13537.t2 | Coils | Coil | Coil | 153 | 173 | - |
| 6 | g13537.t2 | Gene3D | G3DSA:3.90.530.10 | - | 45 | 155 | 3.5E-40 |
| 3 | g13537.t2 | PANTHER | PTHR10142 | DNA REPAIR PROTEIN COMPLEMENTING XP-A CELLS | 2 | 221 | 5.5E-73 |
| 2 | g13537.t2 | Pfam | PF01286 | XPA protein N-terminal | 50 | 78 | 1.8E-10 |
| 1 | g13537.t2 | Pfam | PF05181 | XPA protein C-terminus | 82 | 133 | 2.2E-25 |
| 4 | g13537.t2 | SUPERFAMILY | SSF57716 | Glucocorticoid receptor-like (DNA-binding domain) | 46 | 78 | 4.28E-7 |
| 5 | g13537.t2 | SUPERFAMILY | SSF46955 | Putative DNA-binding domain | 81 | 155 | 1.46E-25 |
| 9 | g13537.t2 | TIGRFAM | TIGR00598 | rad14: DNA repair protein | 52 | 221 | 3.3E-62 |
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:0003684 | damaged DNA binding | MF |
| GO:0006289 | nucleotide-excision repair | BP |
KEGG
Orthology
- This transcript has been annotated with K10847 (DNA-repair protein complementing XP-A cells)
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.
