General information for g5634.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as hypothetical.
Parent gene
- The parent gene g5634 is located on chr_2: 10782735..10783233 (+ 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 | g5634 | g5634.t1 | TSS | g5634.t1 | 10782658 | 10782658 |
| chr_2 | g5634 | g5634.t1 | isoform | g5634.t1 | 10782735 | 10783233 |
| chr_2 | g5634 | g5634.t1 | exon | g5634.t1.exon1 | 10782735 | 10783023 |
| chr_2 | g5634 | g5634.t1 | cds | g5634.t1.CDS1 | 10782735 | 10783023 |
| chr_2 | g5634 | g5634.t1 | exon | g5634.t1.exon2 | 10783157 | 10783233 |
| chr_2 | g5634 | g5634.t1 | cds | g5634.t1.CDS2 | 10783157 | 10783233 |
| chr_2 | g5634 | g5634.t1 | TTS | g5634.t1 | 10783899 | 10783899 |
Sequences
>g5634.t1 Gene=g5634 Length=366
ATGAATCGACAACATTCAGAAGATTTAGAAAGTGATAAGGAGTACAATGAGGAACAACAG
GATAAAGAAGACATTATAAGAAAATTATCAGTTGACATTACATTTGAAAGATCATTTTGG
GAAAAATTTTACGAAATTGAGAATGAATTAGTTAATGAATTAATGGAAATAGACTTTCTG
AAAGATAATAACATCGATGCTATTTATAATCCACTTGATTATGCTGCAGATATTCATATT
AACTATTTGAAGAAATTTCTGAAACGAACTCCTTCAGTTTTATTTGTAAGCATGAATCCT
GGTCTTTTGGGCATGTGTCAAACTGGTGTGCCTTTCGGAAATGTTTCGTCAGTTAAAATT
GGATGA
>g5634.t1 Gene=g5634 Length=121
MNRQHSEDLESDKEYNEEQQDKEDIIRKLSVDITFERSFWEKFYEIENELVNELMEIDFL
KDNNIDAIYNPLDYAADIHINYLKKFLKRTPSVLFVSMNPGLLGMCQTGVPFGNVSSVKI
G
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 4 | g5634.t1 | Gene3D | G3DSA:3.40.470.10 | - | 36 | 120 | 4.3E-27 |
| 3 | g5634.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 21 | - |
| 1 | g5634.t1 | PANTHER | PTHR13235 | SINGLE-STRAND SELECTIVE MONOFUNCTIONAL URACIL DNA GLYCOSYLASE | 35 | 119 | 4.2E-19 |
| 2 | g5634.t1 | SUPERFAMILY | SSF52141 | Uracil-DNA glycosylase-like | 38 | 116 | 1.77E-13 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5634/g5634.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5634.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.
