General information for g2575.t4
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Beta-galactosidase.
Parent gene
- The parent gene g2575 is located on chr_3: 18819153..18821389 (+ 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 | g2575 | g2575.t4 | isoform | g2575.t4 | 18818413 | 18821027 |
| chr_3 | g2575 | g2575.t4 | TSS | g2575.t4 | 18818413 | 18818413 |
| chr_3 | g2575 | g2575.t4 | exon | g2575.t4.exon1 | 18818413 | 18818578 |
| chr_3 | g2575 | g2575.t4 | exon | g2575.t4.exon2 | 18819124 | 18819248 |
| chr_3 | g2575 | g2575.t4 | exon | g2575.t4.exon3 | 18819311 | 18819607 |
| chr_3 | g2575 | g2575.t4 | exon | g2575.t4.exon4 | 18819660 | 18819744 |
| chr_3 | g2575 | g2575.t4 | exon | g2575.t4.exon5 | 18819808 | 18819906 |
| chr_3 | g2575 | g2575.t4 | exon | g2575.t4.exon6 | 18819962 | 18820412 |
| chr_3 | g2575 | g2575.t4 | cds | g2575.t4.CDS1 | 18820082 | 18820412 |
| chr_3 | g2575 | g2575.t4 | exon | g2575.t4.exon7 | 18820470 | 18821027 |
| chr_3 | g2575 | g2575.t4 | cds | g2575.t4.CDS2 | 18820470 | 18821026 |
| chr_3 | g2575 | g2575.t4 | TTS | g2575.t4 | NA | NA |
Sequences
>g2575.t4 Gene=g2575 Length=1781
CAGTTTAATTTGAGAAGTGTAACAGAAACAGTCAGAAGAATATTTGCTTAGTGATTGAGA
ACAGAAAGAATATAAAATTGCATTTTCGATTACTAATTTTCTTCTTTTTTATATGAGTAA
GAGAGATAATTTACATTAACATTTTTACGTACATTTTTTCAAACAATAGGTAATCGCACT
TAAATGAAAGTAAGCATGAGAAAATTATCAAGTGTTTTATTGACGCTGACCTACATAGCA
TTGTCTTCATCGCTTGCAGAGAGTCAGCACACCTTATCAGTCGATAATTTTGTCTCAGAG
AGAACATTTGAAATTGATTACGAAAATAATACATTTGTGCGGGATGGAAAGCCATTTCAA
TTTGTTGGTGGATCATTTCACTACTTTCGAGCAATGCCACAAACGTGGCAAAGAAAGTTG
AGAACAATGAGAGCTGCTGGATTGCAAGTTGTGACAACTTATGTTGAATGGAGTTTGCAT
GCTCCAAAAGACGGCGTGTATGACTTCACTGGCATTGCAGATATTGAAGAGTTCATTAAA
CTTGCAGCACAAGAAGATTTACTTGTGATTCTACGGCCTGGTCCATATATTTGTGCAGAA
CGTGATAATGGTGGCCTACCATATTGGCTTTTACACAAATATCCTAATATTCTTCTTCGT
ACTGATGATGAGGATTATAAAAGAGAAGTTGCAAAATGGTATTCAGTACTGATGCCAAAA
ATGCAGAAATTTTTTTATGCAAACGGTGGGCCAATAATTATGGTTCAGGCAAGTTGAAAA
TGAATATGGAAGTTTTTATGCATGTGATGAAAATTATAAATTGTGGATTCGTGATGAAAC
ATTAAAATACACACAATCACATGCTGTTCTTTTTACAAATGATGGGCCAGGAATGTTAAG
ATGTGGAAAAATTCCTAATGTGCTTGCAACTTTAGATTTTGGTGCAGCAGATGATAGCTC
AATCGATCAATATTGGAAAACGTTAAGAAAATTTGAAAAAAAAGGTCCTTTAATGAATTC
TGAATATTATCCTGGATGGCTTTCTCACTGGCAAGAGCAATTTCAAAAAGTTGATACAAA
ATTACTTTTACGTCCATTAGAAAAAATGCTTGAAGACAAAGCATCTGTCAATTTATATAT
GTTTTACGGAGGCACAAATTTCGGATTTACAGCTGGTGCAAATGATGGAGGCCCTGGAAA
TTATAATAGTGATATAACAAGCTATGACTATGATGCACCAATGACAGAAAGTGGTGATAC
AACAGAAAAATATTTTGCATTGAGGGAACTTATAAGCAAATATTTCCCACTTCCTGATAT
TGAAGTACCTGAAAATTTAAGAAAAGTTAAACTTCCTGATGTTCACCTTAAACCATATTC
TGTGTTACTCGATTTAAACGGTCGAAGACATTTATCAAGTTTTACGGTAACATCATTAAA
TCCTATGACATTTGAAGCTCTAAATCAAAATTCAGGATTTATTCTTTATGAAACTAAATT
ACCAAATGTTAAAAGAGATCCTGTTTTGCTCAAAATCAATGAACTTAGAGATAGAGCATA
TATCTATGTCAATCGCCAATTTGTTGGAGTTCTTTCACGAGAAAATAAAATTGATTCACT
TCCTATAAGTTCAATGCTTGGTGAAGATTTGCAAATTATAGTTGAGAATGAAGGTCGCAT
TAATTATGGAATTGCAAATGATTTTAAAGGCATCATCGGAAATGTTCAATATAATTCAGT
GATACTTCTCAATTGGACTATGACAGGTTTTCCTTTAGAAA
>g2575.t4 Gene=g2575 Length=296
MLRCGKIPNVLATLDFGAADDSSIDQYWKTLRKFEKKGPLMNSEYYPGWLSHWQEQFQKV
DTKLLLRPLEKMLEDKASVNLYMFYGGTNFGFTAGANDGGPGNYNSDITSYDYDAPMTES
GDTTEKYFALRELISKYFPLPDIEVPENLRKVKLPDVHLKPYSVLLDLNGRRHLSSFTVT
SLNPMTFEALNQNSGFILYETKLPNVKRDPVLLKINELRDRAYIYVNRQFVGVLSRENKI
DSLPISSMLGEDLQIIVENEGRINYGIANDFKGIIGNVQYNSVILLNWTMTGFPLE
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g2575.t4 | Gene3D | G3DSA:3.20.20.80 | Glycosidases | 1 | 139 | 0.0e+00 |
| 7 | g2575.t4 | Gene3D | G3DSA:2.60.120.260 | - | 165 | 296 | 0.0e+00 |
| 2 | g2575.t4 | PANTHER | PTHR23421:SF172 | BETA-GALACTOSIDASE | 1 | 295 | 0.0e+00 |
| 3 | g2575.t4 | PANTHER | PTHR23421 | BETA-GALACTOSIDASE RELATED | 1 | 295 | 0.0e+00 |
| 5 | g2575.t4 | PRINTS | PR00742 | Glycosyl hydrolase family 35 signature | 41 | 56 | 3.2e-06 |
| 4 | g2575.t4 | PRINTS | PR00742 | Glycosyl hydrolase family 35 signature | 77 | 92 | 3.2e-06 |
| 1 | g2575.t4 | Pfam | PF01301 | Glycosyl hydrolases family 35 | 2 | 136 | 0.0e+00 |
| 6 | g2575.t4 | SUPERFAMILY | SSF51445 | (Trans)glycosidases | 18 | 140 | 0.0e+00 |
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.
