General information for g4555.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative DNA repair protein XRCC1.
Parent gene
- The parent gene g4555 is located on chr_2: 3231409..3232228 (+ 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_2 | g4555 | g4555.t2 | TSS | g4555.t2 | 3230058 | 3230058 |
| chr_2 | g4555 | g4555.t2 | isoform | g4555.t2 | 3230121 | 3231036 |
| chr_2 | g4555 | g4555.t2 | exon | g4555.t2.exon1 | 3230121 | 3230171 |
| chr_2 | g4555 | g4555.t2 | cds | g4555.t2.CDS1 | 3230121 | 3230171 |
| chr_2 | g4555 | g4555.t2 | exon | g4555.t2.exon2 | 3230230 | 3231036 |
| chr_2 | g4555 | g4555.t2 | cds | g4555.t2.CDS2 | 3230230 | 3231036 |
| chr_2 | g4555 | g4555.t2 | TTS | g4555.t2 | 3231248 | 3231248 |
Sequences
>g4555.t2 Gene=g4555 Length=858
ATGCCACAGATTAAAAATATAAAAATTCACAGTTTTAGTAGCGAAGATCCAAATTTCCCG
GCAAAAAATTTAATAAACACTGATGTTACAAAAAGATGGAAATGCGCAAAACCTGGTGAA
AAGAGTGCTTTTGTGGTACTAAAATTAGACAAACCTTATCAAATTACACAAATTGACATT
GGAAATGAATTTTCATCAATGATAGAAATTTTGGTCGGTAATAGCCAACAAGAACCACCT
GATTTTCGAGAAATTTTAATGTCAACAAGCTTTATGACTTTAATTGAAGCCAGAAATGAA
ACAAATCCTCATAGATTGAGAATCTTTAATAAAGGCTTATTTGTTTCTGGTGTGGCTGAG
AAAAAATGGGATTTAATTAAAATTTTGTGTGTTCAAAATTATAACAATCGAAAACAATAC
GGCATCTCTTTTATTAATCTATTTACAAATGATGAAGTGACTTCAAAAGAGGAAGAATCT
CCAATTAAGCTTAATCATATTATACATCAAACACCCAAGCCAATGTCTGCATCTAAACCA
GTTAAAACTCTTGGCAAATTTCATTTTCGTGATTCAAGTTCAGATGAAGAAAAAGATGAA
GACTCGTCGCCCTTTGCAAAATGGAAGGCCAAAAAAAATGAGTTTAAAAATTCTACTAAC
GATTTAGACAAATTGCCAGAAAATTCTAAATCTGGTCTAAAGGAGCATTTAAAAGAAAAA
CTAGCATCTGAAAATCGTAAACGAAATCGGTCAATTGATGAGAAAGATGAGAAAGAAATT
GTGAAAAATCGCAATCGTTCTAAAGGCTTAATGTATGAAAGTAGTGACGATGAACCAAAT
GAAAAATTACAAAAGAAA
>g4555.t2 Gene=g4555 Length=286
MPQIKNIKIHSFSSEDPNFPAKNLINTDVTKRWKCAKPGEKSAFVVLKLDKPYQITQIDI
GNEFSSMIEILVGNSQQEPPDFREILMSTSFMTLIEARNETNPHRLRIFNKGLFVSGVAE
KKWDLIKILCVQNYNNRKQYGISFINLFTNDEVTSKEEESPIKLNHIIHQTPKPMSASKP
VKTLGKFHFRDSSSDEEKDEDSSPFAKWKAKKNEFKNSTNDLDKLPENSKSGLKEHLKEK
LASENRKRNRSIDEKDEKEIVKNRNRSKGLMYESSDDEPNEKLQKK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g4555.t2 | Coils | Coil | Coil | 234 | 254 | - |
| 5 | g4555.t2 | Gene3D | G3DSA:2.60.120.260 | - | 1 | 150 | 2.5E-54 |
| 4 | g4555.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 189 | 286 | - |
| 2 | g4555.t2 | PANTHER | PTHR11370 | DNA-REPAIR PROTEIN XRCC1 | 1 | 261 | 1.4E-53 |
| 1 | g4555.t2 | Pfam | PF01834 | XRCC1 N terminal domain | 1 | 147 | 3.2E-50 |
| 3 | g4555.t2 | SUPERFAMILY | SSF49785 | Galactose-binding domain-like | 1 | 148 | 1.44E-49 |
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:0005634 | nucleus | CC |
| GO:0003684 | damaged DNA binding | MF |
| GO:0000012 | single strand break repair | BP |
KEGG
Orthology
- This transcript has been annotated with K10803 (DNA-repair protein XRCC1)
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.
