General information for g3920.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Beta-glucuronidase.
Parent gene
- The parent gene g3920 is located on chr_3: 28904901..28910681 (- 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 | g3920 | g3920.t2 | TTS | g3920.t2 | 28902789 | 28902789 |
| chr_3 | g3920 | g3920.t2 | isoform | g3920.t2 | 28902856 | 28903715 |
| chr_3 | g3920 | g3920.t2 | exon | g3920.t2.exon1 | 28902856 | 28903046 |
| chr_3 | g3920 | g3920.t2 | cds | g3920.t2.CDS1 | 28902856 | 28903046 |
| chr_3 | g3920 | g3920.t2 | exon | g3920.t2.exon2 | 28903113 | 28903218 |
| chr_3 | g3920 | g3920.t2 | cds | g3920.t2.CDS2 | 28903113 | 28903218 |
| chr_3 | g3920 | g3920.t2 | exon | g3920.t2.exon3 | 28903277 | 28903715 |
| chr_3 | g3920 | g3920.t2 | cds | g3920.t2.CDS3 | 28903277 | 28903630 |
| chr_3 | g3920 | g3920.t2 | TSS | g3920.t2 | NA | NA |
Sequences
>g3920.t2 Gene=g3920 Length=736
AAATTATAGTCAAAAATTACTCGAAAACCACAAATATAGTATTGAGCAGCTTATTCATCG
TGATATAAATCATCCATCCGTGGTGATGTGGTCAATAGCAAATGAGCCCAGAACTCAGCA
AGTGAATGCTGACCAATATTTTGCAGAGGTTGCGCGCTATACACGATTTCTGGATCCAAC
ACGGCCAGTGACTGCAGCAATTGCCGTTAATTCTAAGCAAGATCAAGCAGCACAGTATTT
GGATATAATAAGTTTTAATAGATATAATGCATGGTACCAAAATACAGGCAGATTAGATAT
GGTAACAAGTTATGTGATGAATGAGGCTAGAACTTGGCATGAGAAACACAATAAGCCAGT
GCTAATGAGTGAATATGGTAGTGACACTGTTGAAGGACTTCACATTTTACCTGCTTACGT
ATGGTCGGAAGAATTCCAGAGTCAACAATTTTCAAAGCACTTCAAAGCATTCGATCAACT
GAGAAATGAGGGATTTTTCATTGGTGAATTTGTTTGGAATTTCGCTGATTTTAAAACAGC
ACAAACTTATACACGTGTCGGTGGAAATAAGAAGGGAGTTTTTACTCGTAATAGACAGCC
AAAAGCAGCTGCTCATCTTTTGAGAAAGCGATACTATGAATTAGCATCAGAATTAGATAG
TATTCATCAAAAACCTGATAATCTTTACGAATACACTAGTCAAAGTCAGAACAAATTGCA
AAAGAATGAACTTTAA
>g3920.t2 Gene=g3920 Length=216
MWSIANEPRTQQVNADQYFAEVARYTRFLDPTRPVTAAIAVNSKQDQAAQYLDIISFNRY
NAWYQNTGRLDMVTSYVMNEARTWHEKHNKPVLMSEYGSDTVEGLHILPAYVWSEEFQSQ
QFSKHFKAFDQLRNEGFFIGEFVWNFADFKTAQTYTRVGGNKKGVFTRNRQPKAAAHLLR
KRYYELASELDSIHQKPDNLYEYTSQSQNKLQKNEL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 4 | g3920.t2 | Gene3D | G3DSA:3.20.20.80 | Glycosidases | 1 | 192 | 0 |
| 2 | g3920.t2 | PANTHER | PTHR10066 | BETA-GLUCURONIDASE | 1 | 198 | 0 |
| 1 | g3920.t2 | Pfam | PF02836 | Glycosyl hydrolases family 2, TIM barrel domain | 1 | 186 | 0 |
| 3 | g3920.t2 | SUPERFAMILY | SSF51445 | (Trans)glycosidases | 1 | 183 | 0 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0004553 | hydrolase activity, hydrolyzing O-glycosyl compounds | MF |
| GO:0005975 | carbohydrate metabolic process | 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.
