General information for g3123.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Ubiquitin-conjugating enzyme E2-18 kDa.
Parent gene
- The parent gene g3123 is located on chr_3: 23070810..23071621 (+ 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_3 | g3123 | g3123.t1 | isoform | g3123.t1 | 23070143 | 23070960 |
| chr_3 | g3123 | g3123.t1 | exon | g3123.t1.exon1 | 23070143 | 23070166 |
| chr_3 | g3123 | g3123.t1 | cds | g3123.t1.CDS1 | 23070143 | 23070166 |
| chr_3 | g3123 | g3123.t1 | exon | g3123.t1.exon2 | 23070357 | 23070452 |
| chr_3 | g3123 | g3123.t1 | cds | g3123.t1.CDS2 | 23070357 | 23070452 |
| chr_3 | g3123 | g3123.t1 | exon | g3123.t1.exon3 | 23070561 | 23070747 |
| chr_3 | g3123 | g3123.t1 | cds | g3123.t1.CDS3 | 23070561 | 23070747 |
| chr_3 | g3123 | g3123.t1 | exon | g3123.t1.exon4 | 23070809 | 23070960 |
| chr_3 | g3123 | g3123.t1 | cds | g3123.t1.CDS4 | 23070809 | 23070960 |
| chr_3 | g3123 | g3123.t1 | TTS | g3123.t1 | 23071631 | 23071631 |
| chr_3 | g3123 | g3123.t1 | TSS | g3123.t1 | NA | NA |
Sequences
>g3123.t1 Gene=g3123 Length=459
ATGAATAACAGAAGACTTCAAAAAGAATTGGCCGATATCAAAGCAAGTGGCCTCAAATCA
TTTCGTGACATAGAGGTTGATGATCGCAATATTTTATTATGGTCAGGATCAGTTTGTCCT
GATAATCCTCCTTACAATAAAGGTGCATTTCGAATTGAAATCACATTCCCAGCTGAATAT
CCCTTTAAACCACCAAAAATATGCTTCAAAACAAAAATCTACCATCCAAATATCGATGAA
AAAGGACAAGTTTGTTTACCAATAATATCTGCAGAAAATTGGAAACCAGCTACAAAAACA
GATCAAGTAATTCAAGCTTTAGTCGCATTAGTAAATGATCCAGAACCCGAACATCCTTTG
CGTGCAGAATTGGCTGAAGAGTTTCTAAAAGATCGCAAAAAGTTTATGAAAAATGCTGAA
GAATTTACTCGAAAACATAGTGAGAAGCGACATGACTAA
>g3123.t1 Gene=g3123 Length=152
MNNRRLQKELADIKASGLKSFRDIEVDDRNILLWSGSVCPDNPPYNKGAFRIEITFPAEY
PFKPPKICFKTKIYHPNIDEKGQVCLPIISAENWKPATKTDQVIQALVALVNDPEPEHPL
RAELAEEFLKDRKKFMKNAEEFTRKHSEKRHD
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g3123.t1 | CDD | cd00195 | UBCc | 4 | 143 | 1.04584E-56 |
| 5 | g3123.t1 | Gene3D | G3DSA:3.10.110.10 | Ubiquitin Conjugating Enzyme | 1 | 151 | 3.8E-56 |
| 2 | g3123.t1 | PANTHER | PTHR24068:SF170 | UBIQUITIN-CONJUGATING ENZYME E2 L5 | 3 | 148 | 5.9E-74 |
| 3 | g3123.t1 | PANTHER | PTHR24068 | UBIQUITIN-CONJUGATING ENZYME E2 | 3 | 148 | 5.9E-74 |
| 1 | g3123.t1 | Pfam | PF00179 | Ubiquitin-conjugating enzyme | 5 | 142 | 2.7E-42 |
| 7 | g3123.t1 | ProSitePatterns | PS00183 | Ubiquitin-conjugating enzymes active site. | 74 | 89 | - |
| 9 | g3123.t1 | ProSiteProfiles | PS50127 | Ubiquitin-conjugating enzymes family profile. | 4 | 137 | 34.979 |
| 8 | g3123.t1 | SMART | SM00212 | ubc_7 | 4 | 148 | 5.5E-58 |
| 4 | g3123.t1 | SUPERFAMILY | SSF54495 | UBC-like | 3 | 148 | 8.52E-46 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
GO terms from InterProScan
There are no GO annotations for this transcript.
KEGG
Orthology
- This transcript has been annotated with K04552 (ubiquitin-conjugating enzyme E2 L3)
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.
