General information for g5272.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Beta-galactosidase.
Parent gene
- The parent gene g5272 is located on chr_2: 8342268..8343718 (+ 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 | g5272 | g5272.t2 | TSS | g5272.t2 | 8341436 | 8341436 |
| chr_2 | g5272 | g5272.t2 | isoform | g5272.t2 | 8341476 | 8342268 |
| chr_2 | g5272 | g5272.t2 | exon | g5272.t2.exon1 | 8341476 | 8341583 |
| chr_2 | g5272 | g5272.t2 | exon | g5272.t2.exon2 | 8341681 | 8341957 |
| chr_2 | g5272 | g5272.t2 | cds | g5272.t2.CDS1 | 8341709 | 8341957 |
| chr_2 | g5272 | g5272.t2 | exon | g5272.t2.exon3 | 8342028 | 8342268 |
| chr_2 | g5272 | g5272.t2 | cds | g5272.t2.CDS2 | 8342028 | 8342267 |
| chr_2 | g5272 | g5272.t2 | TTS | g5272.t2 | NA | NA |
Sequences
>g5272.t2 Gene=g5272 Length=626
ATGACACAAGGCTTCTGTGGTAGACATAAATGTCTTATCTCAATTGCTGCTGCAATCATT
GTAATCGCAGCAATTGTAGGAATCGGTAATAGATTAATTTTATGTCTCTATTGATTATGA
ACATGATACATTTTTGATGGATGGAAAACCTTTTAGATATGTCGCAGGATCTTTTCATTA
TTTTAGAGCTTTACCACAAACATGGCGTCAAAAATTAAAGACTTTAAAAGCTGGTGGACT
TAATGCAGTTGACCTTTATATTCAATGGTCACTTCATAATCCAGAAGATGGAATTTATAA
TTGGGATGGAATTGCTGATGTTGAAAGAGTTGTAGAAATTGCAACTGAAGAAGGACTTTT
CGTTATTTTAAGACCAGGACCATATATCTGTGCAGAAATTGACAATGGTGGACTGCCTTA
TTGGCTTGCAACGAAATATCCAAACATTAAAGTTCGTACGAATGACACAAATTATCTTTT
TGAAGTCGAAAGATGGTACTCAAAGCTTATGCCAAAGTTTGAGAAACATCTTTATGGAAA
TGGCGGCAATATCATTATGGTGCAAGTTGAAAATGAATATGGAGCATTTGGTGCATGCGA
TGAAGAATATAAAGAATTTTTGAGAG
>g5272.t2 Gene=g5272 Length=163
MDGKPFRYVAGSFHYFRALPQTWRQKLKTLKAGGLNAVDLYIQWSLHNPEDGIYNWDGIA
DVERVVEIATEEGLFVILRPGPYICAEIDNGGLPYWLATKYPNIKVRTNDTNYLFEVERW
YSKLMPKFEKHLYGNGGNIIMVQVENEYGAFGACDEEYKEFLR
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g5272.t2 | Gene3D | G3DSA:3.20.20.80 | Glycosidases | 1 | 163 | 0 |
| 2 | g5272.t2 | PANTHER | PTHR23421:SF65 | BETA GALACTOSIDASE, ISOFORM A | 1 | 163 | 0 |
| 3 | g5272.t2 | PANTHER | PTHR23421 | BETA-GALACTOSIDASE RELATED | 1 | 163 | 0 |
| 7 | g5272.t2 | PRINTS | PR00742 | Glycosyl hydrolase family 35 signature | 2 | 19 | 0 |
| 6 | g5272.t2 | PRINTS | PR00742 | Glycosyl hydrolase family 35 signature | 23 | 41 | 0 |
| 5 | g5272.t2 | PRINTS | PR00742 | Glycosyl hydrolase family 35 signature | 78 | 97 | 0 |
| 4 | g5272.t2 | PRINTS | PR00742 | Glycosyl hydrolase family 35 signature | 134 | 149 | 0 |
| 1 | g5272.t2 | Pfam | PF01301 | Glycosyl hydrolases family 35 | 1 | 160 | 0 |
| 8 | g5272.t2 | SUPERFAMILY | SSF51445 | (Trans)glycosidases | 2 | 161 | 0 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5272/g5272.t2; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5272.t2.fa.iupred3.txt does not exist
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. There were no conditions that were differentially expressed