General information for g5272.t4
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as 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.t4 | TSS | g5272.t4 | 8341436 | 8341436 |
| chr_2 | g5272 | g5272.t4 | isoform | g5272.t4 | 8342268 | 8343718 |
| chr_2 | g5272 | g5272.t4 | exon | g5272.t4.exon1 | 8342268 | 8342616 |
| chr_2 | g5272 | g5272.t4 | cds | g5272.t4.CDS1 | 8342400 | 8342616 |
| chr_2 | g5272 | g5272.t4 | exon | g5272.t4.exon2 | 8342673 | 8342797 |
| chr_2 | g5272 | g5272.t4 | cds | g5272.t4.CDS2 | 8342673 | 8342797 |
| chr_2 | g5272 | g5272.t4 | exon | g5272.t4.exon3 | 8342855 | 8343718 |
| chr_2 | g5272 | g5272.t4 | cds | g5272.t4.CDS3 | 8342855 | 8343718 |
| chr_2 | g5272 | g5272.t4 | TTS | g5272.t4 | 8343868 | 8343868 |
Sequences
>g5272.t4 Gene=g5272 Length=1338
GATGAAACTTTAAAATATACACAAGACAAAGCCATTCTTTTCACAACTGATCGTCCAATT
GATGATGAATTGAAATGTGGTCAAGTTAAAGATGTTTTCGTTACAACTGATTTTGGTCTT
TATAATTTCTCTATGGTCATGTATAATTTCAACAAATTAAGAGAAGTTCAACCTAAAGGT
CCACTTGTCAATACAGAATTTTACACAGGATGGCTGACACATTGGCAAGAAGCAAATGCA
AGAAGAGGTGGTGAAGATTTGGCAAAAACACTTGAATATATGTTAGTTCTTGGCGCAAAT
GTTGACTTTTACATGTACTTTGGTGGCACAAATTTCGGATTTTGGGCAGGAGCAAATGAT
TGGGGTATTGGAAAATATATGGCTGATATAACAAGTTATGATTATGATGCACCAATGGAT
GAAGCAGGAAATCCCACTGAGAAGTACATGATCTTTCGTGATGTTATTAAAAAGTACATT
GATGTCGTCGATGAATCAGAAATTCCTGAGAAAATAAAAACGATGGCTCCCGGATCTCTC
ACAATGACACCAGTAAATTCACTTTTATCAGCAGAAGGCAGAAATATTTTAGGATCACGT
TCAATTGAATCAAATACATTATTGACTTTTGAACAATTGAAACAATTTTCTGGCTTTGTT
CTTTATGAGACAGAATTGCCAAAACTCACTCGAGATCCAGCAAATTTATTAATTACTGAT
TTGAGAGATCGAGCATTAGTTTATGTCGATGAAGAATATGTTGGTTTATTGTCACGTGAA
AATGTCATCAATACTCTTCCTATTAATGCTGATTATGGTTCAAAGCTTTCAATACTTGTT
GAAAATCAGGGACGAATCAATTTCCAAATAGCAGATGATTACAAAGGAATCAGAGGAACA
GTAGCAGTTCAAACTTTTGATGCTTCTTCTAACAATTTATATGAATTCAATAATTGGACA
ATAACAGGATTTCCTTTTGATAAGTCAGTAGATTTAGAAAGTTTGGCAAGAACTTCAAAT
GGCTATCAAATTGATTCAAGTGGACTAGCATTAAATGGACCAATAATTTTCCATGCAACA
CTCACAATTAATGACAATGAAGAAATATTTGACACTTATTGGGATACAAGTGATTGGAAT
AAAGGATTTTTGTTTGTCAATGGTTTTAATTTAGGTCGTTATTGGTCAGTTGGTCCTCAA
ATTACTATGTACATACCAAAAGACATTTTACAACATGGCAAAAATGCAATTTTCTTAGTT
GAACTTCAACAAGCCCCGACCAACCTCAAGATGCATTTTGTAAAAGGTCCAATCTTTATA
AATGATGAAAAAGTTTAA
>g5272.t4 Gene=g5272 Length=401
MVMYNFNKLREVQPKGPLVNTEFYTGWLTHWQEANARRGGEDLAKTLEYMLVLGANVDFY
MYFGGTNFGFWAGANDWGIGKYMADITSYDYDAPMDEAGNPTEKYMIFRDVIKKYIDVVD
ESEIPEKIKTMAPGSLTMTPVNSLLSAEGRNILGSRSIESNTLLTFEQLKQFSGFVLYET
ELPKLTRDPANLLITDLRDRALVYVDEEYVGLLSRENVINTLPINADYGSKLSILVENQG
RINFQIADDYKGIRGTVAVQTFDASSNNLYEFNNWTITGFPFDKSVDLESLARTSNGYQI
DSSGLALNGPIIFHATLTINDNEEIFDTYWDTSDWNKGFLFVNGFNLGRYWSVGPQITMY
IPKDILQHGKNAIFLVELQQAPTNLKMHFVKGPIFINDEKV
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 11 | g5272.t4 | Gene3D | G3DSA:3.20.20.80 | Glycosidases | 2 | 59 | 0 |
| 9 | g5272.t4 | Gene3D | G3DSA:2.60.120.260 | - | 60 | 379 | 0 |
| 10 | g5272.t4 | Gene3D | G3DSA:2.60.120.260 | - | 138 | 281 | 0 |
| 2 | g5272.t4 | PANTHER | PTHR23421:SF65 | BETA GALACTOSIDASE, ISOFORM A | 7 | 380 | 0 |
| 3 | g5272.t4 | PANTHER | PTHR23421 | BETA-GALACTOSIDASE RELATED | 7 | 380 | 0 |
| 5 | g5272.t4 | PRINTS | PR00742 | Glycosyl hydrolase family 35 signature | 19 | 34 | 0 |
| 4 | g5272.t4 | PRINTS | PR00742 | Glycosyl hydrolase family 35 signature | 55 | 70 | 0 |
| 6 | g5272.t4 | PRINTS | PR00742 | Glycosyl hydrolase family 35 signature | 337 | 353 | 0 |
| 1 | g5272.t4 | Pfam | PF01301 | Glycosyl hydrolases family 35 | 5 | 114 | 0 |
| 8 | g5272.t4 | SUPERFAMILY | SSF51445 | (Trans)glycosidases | 4 | 117 | 0 |
| 7 | g5272.t4 | SUPERFAMILY | SSF49785 | Galactose-binding domain-like | 235 | 384 | 0 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5272/g5272.t4; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5272.t4.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.
