General information for g5830.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Ubiquitin-conjugating enzyme E2 W.
Parent gene
- The parent gene g5830 is located on chr_2: 12119017..12119609 (- 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 | g5830 | g5830.t1 | TTS | g5830.t1 | 12118852 | 12118852 |
| chr_2 | g5830 | g5830.t1 | isoform | g5830.t1 | 12119017 | 12119609 |
| chr_2 | g5830 | g5830.t1 | exon | g5830.t1.exon1 | 12119017 | 12119168 |
| chr_2 | g5830 | g5830.t1 | cds | g5830.t1.CDS1 | 12119017 | 12119168 |
| chr_2 | g5830 | g5830.t1 | exon | g5830.t1.exon2 | 12119225 | 12119513 |
| chr_2 | g5830 | g5830.t1 | cds | g5830.t1.CDS2 | 12119225 | 12119513 |
| chr_2 | g5830 | g5830.t1 | exon | g5830.t1.exon3 | 12119592 | 12119609 |
| chr_2 | g5830 | g5830.t1 | cds | g5830.t1.CDS3 | 12119592 | 12119609 |
| chr_2 | g5830 | g5830.t1 | TSS | g5830.t1 | 12119703 | 12119703 |
Sequences
>g5830.t1 Gene=g5830 Length=459
ATGACGTCTCCTTCGGAGCGACGTTTGAGAAAGGAGTTCCTTGAATTAATAAAAAATCCA
ATACCTGGAGTGATTATTGATGGTGAAAAGATTGAAAAGAATATAAATGAATGGAATGTG
ACAATCATTGGAGCCGAAGGAACAATTTACCAAGGAGAAACTTTTGAATTGCAATTTTTA
TTTAATGATAAATATCCATTTGATAGTCCAAGTGTTGTGTTCATTGGTAAAAACATTCCT
GAGCATTCCCATATCTATTCAAATGGTCACATTTGTTTATCGATTTTATCACAAGACTGG
ACTCCAGCTTTGTCTGTTGGTGCTGTTTGTCTTTCAATTCGATCAATGCTGAGTTCTGCC
ACAAAAAAAGAAAGACCTCCGGATGATTTAATTTACACCAAAACCTGCTCAAAAAATCCT
AAGAAAACGAAATGGTTCTTTCATGATGATAATGTCTAA
>g5830.t1 Gene=g5830 Length=152
MTSPSERRLRKEFLELIKNPIPGVIIDGEKIEKNINEWNVTIIGAEGTIYQGETFELQFL
FNDKYPFDSPSVVFIGKNIPEHSHIYSNGHICLSILSQDWTPALSVGAVCLSIRSMLSSA
TKKERPPDDLIYTKTCSKNPKKTKWFFHDDNV
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g5830.t1 | CDD | cd00195 | UBCc | 6 | 119 | 0.000 |
| 6 | g5830.t1 | Gene3D | G3DSA:3.10.110.10 | Ubiquitin Conjugating Enzyme | 3 | 152 | 0.000 |
| 2 | g5830.t1 | PANTHER | PTHR24068:SF153 | UBIQUITIN-CONJUGATING ENZYME E2 W | 5 | 151 | 0.000 |
| 3 | g5830.t1 | PANTHER | PTHR24068 | UBIQUITIN-CONJUGATING ENZYME E2 | 5 | 151 | 0.000 |
| 1 | g5830.t1 | Pfam | PF00179 | Ubiquitin-conjugating enzyme | 8 | 139 | 0.000 |
| 7 | g5830.t1 | ProSiteProfiles | PS50127 | Ubiquitin-conjugating enzymes family profile. | 7 | 128 | 25.701 |
| 5 | g5830.t1 | SMART | SM00212 | ubc_7 | 7 | 152 | 0.000 |
| 4 | g5830.t1 | SUPERFAMILY | SSF54495 | UBC-like | 1 | 122 | 0.000 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5830/g5830.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5830.t1.fa.iupred3.txt does not exist
GO terms from InterProScan
There are no GO annotations for this transcript.
KEGG
Orthology
- This transcript has been annotated with K10688 (ubiquitin-conjugating enzyme E2 W)
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.
