General information for g13409.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Ubiquitin-conjugating enzyme E2 R2.
Parent gene
- The parent gene g13409 is located on chr_1: 29888360..29889337 (- 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_1 | g13409 | g13409.t1 | TTS | g13409.t1 | 29885566 | 29885566 |
| chr_1 | g13409 | g13409.t1 | isoform | g13409.t1 | 29886521 | 29888805 |
| chr_1 | g13409 | g13409.t1 | exon | g13409.t1.exon1 | 29886521 | 29886625 |
| chr_1 | g13409 | g13409.t1 | cds | g13409.t1.CDS1 | 29886521 | 29886625 |
| chr_1 | g13409 | g13409.t1 | exon | g13409.t1.exon2 | 29886688 | 29886802 |
| chr_1 | g13409 | g13409.t1 | cds | g13409.t1.CDS2 | 29886688 | 29886802 |
| chr_1 | g13409 | g13409.t1 | exon | g13409.t1.exon3 | 29886953 | 29887132 |
| chr_1 | g13409 | g13409.t1 | cds | g13409.t1.CDS3 | 29886953 | 29887132 |
| chr_1 | g13409 | g13409.t1 | exon | g13409.t1.exon4 | 29887227 | 29887366 |
| chr_1 | g13409 | g13409.t1 | cds | g13409.t1.CDS4 | 29887227 | 29887366 |
| chr_1 | g13409 | g13409.t1 | exon | g13409.t1.exon5 | 29888367 | 29888417 |
| chr_1 | g13409 | g13409.t1 | cds | g13409.t1.CDS5 | 29888367 | 29888417 |
| chr_1 | g13409 | g13409.t1 | exon | g13409.t1.exon6 | 29888692 | 29888805 |
| chr_1 | g13409 | g13409.t1 | cds | g13409.t1.CDS6 | 29888692 | 29888805 |
| chr_1 | g13409 | g13409.t1 | TSS | g13409.t1 | 29889048 | 29889048 |
Sequences
>g13409.t1 Gene=g13409 Length=705
ATGAATTCGTCTTCGCTAAGAGCACTTGCATTAGAATACAAAAGTCTACAAGAAGAGCCA
GTTGAAGGCTTTAAAGTGAAATTATTAAATGATGATAACTTTTACGAATGGAGTGTTGGA
ATTTTTGGCCCTCCTCAGACACTTTATGCTGGTGGTTATTTTAAGGCTACTATGAAATTT
CCGCAAGATTACCCTTATTCACCACCATCAATTCGTTTCATAACAAAAGTCTGGCATCCG
AATGTTTATGAAAATGGGGACTTGTGTATTTCAATTTTACATCCGCCAGTTGATGATCCT
CAGAGTGGTGAGTTGCCGTGCGAACGATGGAATCCAACTCAAAATGTCCGCACCATTCTC
CTCTCTGTAATCTCATTGCTCAATGAACCCAACACATTTTCACCAGCTAATGTAGACGCA
AGTGTTATGTACAGAAGATGGCGTGAATCAAATGGTCGCGATAACGAATATCCAAACATA
ATCAGGAAACAAGCGTTACAAGCTAAGTTAGAAGCTGAAAAAGAAGGAATTGTTGTTCCA
TTAACATTAGAGGAATATTGCCTGAAACCTAAAACGAACCCAAATAATCAGGAACCTCAA
CTCGATATGACAGACTTTTATGACGATTTCGATGATGATGAGTGTAGCGAATCTGAAACA
GAATCACAAAATGGTGATGGAGAAGATTCGGGGAACGCTGAATAA
>g13409.t1 Gene=g13409 Length=234
MNSSSLRALALEYKSLQEEPVEGFKVKLLNDDNFYEWSVGIFGPPQTLYAGGYFKATMKF
PQDYPYSPPSIRFITKVWHPNVYENGDLCISILHPPVDDPQSGELPCERWNPTQNVRTIL
LSVISLLNEPNTFSPANVDASVMYRRWRESNGRDNEYPNIIRKQALQAKLEAEKEGIVVP
LTLEEYCLKPKTNPNNQEPQLDMTDFYDDFDDDECSESETESQNGDGEDSGNAE
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g13409.t1 | CDD | cd00195 | UBCc | 7 | 150 | 7.23402E-62 |
| 5 | g13409.t1 | Gene3D | G3DSA:3.10.110.10 | Ubiquitin Conjugating Enzyme | 1 | 180 | 3.5E-79 |
| 9 | g13409.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 190 | 234 | - |
| 10 | g13409.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 204 | 224 | - |
| 2 | g13409.t1 | PANTHER | PTHR24067 | UBIQUITIN-CONJUGATING ENZYME E2 | 2 | 215 | 3.9E-103 |
| 3 | g13409.t1 | PANTHER | PTHR24067:SF157 | FI11905P | 2 | 215 | 3.9E-103 |
| 1 | g13409.t1 | Pfam | PF00179 | Ubiquitin-conjugating enzyme | 9 | 148 | 1.4E-44 |
| 7 | g13409.t1 | ProSitePatterns | PS00183 | Ubiquitin-conjugating enzymes active site. | 78 | 93 | - |
| 11 | g13409.t1 | ProSiteProfiles | PS50127 | Ubiquitin-conjugating enzymes family profile. | 7 | 153 | 38.354 |
| 8 | g13409.t1 | SMART | SM00212 | ubc_7 | 7 | 170 | 1.2E-61 |
| 4 | g13409.t1 | SUPERFAMILY | SSF54495 | UBC-like | 4 | 149 | 2.96E-52 |
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 K02207 (ubiquitin-conjugating enzyme E2 R)
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.
