General information for g5635.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Single-strand selective monofunctional uracil DNA glycosylase.
Parent gene
- The parent gene g5635 is located on chr_2: 10783275..10783787 (+ 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 | g5635 | g5635.t1 | TSS | g5635.t1 | 10782658 | 10782658 |
| chr_2 | g5635 | g5635.t1 | isoform | g5635.t1 | 10783275 | 10783787 |
| chr_2 | g5635 | g5635.t1 | exon | g5635.t1.exon1 | 10783275 | 10783457 |
| chr_2 | g5635 | g5635.t1 | cds | g5635.t1.CDS1 | 10783275 | 10783457 |
| chr_2 | g5635 | g5635.t1 | exon | g5635.t1.exon2 | 10783518 | 10783787 |
| chr_2 | g5635 | g5635.t1 | cds | g5635.t1.CDS2 | 10783518 | 10783787 |
| chr_2 | g5635 | g5635.t1 | TTS | g5635.t1 | 10783899 | 10783899 |
Sequences
>g5635.t1 Gene=g5635 Length=453
ATGAAACCAATCGAAGGATTAGAGTGTAAGCGGAAAGAACAAAGTGGAAAACGATTTTGG
GGATTGATGGAAGAACTTTGTGGAGAACCTGAAAATTTCTTTCGTCATTGCTTTATGTAC
AACATTTGTCCGTTTGCATTTTTAAACAAAAATGGTCGCAATATTACACCACCTGAACTA
AAGGGTGAATGTAAAAGTGCACTAAACAAAATCTGTTTAAATTATCTTTCAAAAAGTATA
AAAATATTCAAACCAAAAATAATTATCGCCATCGGTTCATATGCAAATCAAAAGTTAAAT
GATTTAAGAAAAAAGAGTCTCATTTCTGAATCAATTGATTACAAATTGCTTCCACATCCA
TCACCTCGAGCCTTTCATAATAACGATTGGGTTGATAGAGCACGAAAATGGATGCTTGAA
AATGATATGCTTAAATATTTTAAAGCAGAATAA
>g5635.t1 Gene=g5635 Length=150
MKPIEGLECKRKEQSGKRFWGLMEELCGEPENFFRHCFMYNICPFAFLNKNGRNITPPEL
KGECKSALNKICLNYLSKSIKIFKPKIIIAIGSYANQKLNDLRKKSLISESIDYKLLPHP
SPRAFHNNDWVDRARKWMLENDMLKYFKAE
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 4 | g5635.t1 | Gene3D | G3DSA:3.40.470.10 | - | 1 | 149 | 0 |
| 2 | g5635.t1 | PANTHER | PTHR13235 | SINGLE-STRAND SELECTIVE MONOFUNCTIONAL URACIL DNA GLYCOSYLASE | 2 | 148 | 0 |
| 1 | g5635.t1 | Pfam | PF03167 | Uracil DNA glycosylase superfamily | 14 | 132 | 0 |
| 3 | g5635.t1 | SUPERFAMILY | SSF52141 | Uracil-DNA glycosylase-like | 3 | 134 | 0 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5635/g5635.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5635.t1.fa.iupred3.txt does not exist
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0017065 | single-strand selective uracil DNA N-glycosylase activity | MF |
| GO:0006284 | base-excision repair | 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.
