General information for g2575.t3
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative 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.t3 | isoform | g2575.t3 | 18818413 | 18820412 |
| chr_3 | g2575 | g2575.t3 | TSS | g2575.t3 | 18818413 | 18818413 |
| chr_3 | g2575 | g2575.t3 | exon | g2575.t3.exon1 | 18818413 | 18818578 |
| chr_3 | g2575 | g2575.t3 | exon | g2575.t3.exon2 | 18819124 | 18819248 |
| chr_3 | g2575 | g2575.t3 | cds | g2575.t3.CDS1 | 18819141 | 18819248 |
| chr_3 | g2575 | g2575.t3 | exon | g2575.t3.exon3 | 18819311 | 18819607 |
| chr_3 | g2575 | g2575.t3 | cds | g2575.t3.CDS2 | 18819311 | 18819607 |
| chr_3 | g2575 | g2575.t3 | exon | g2575.t3.exon4 | 18819660 | 18819744 |
| chr_3 | g2575 | g2575.t3 | cds | g2575.t3.CDS3 | 18819660 | 18819744 |
| chr_3 | g2575 | g2575.t3 | exon | g2575.t3.exon5 | 18819808 | 18819906 |
| chr_3 | g2575 | g2575.t3 | cds | g2575.t3.CDS4 | 18819808 | 18819906 |
| chr_3 | g2575 | g2575.t3 | exon | g2575.t3.exon6 | 18819962 | 18820412 |
| chr_3 | g2575 | g2575.t3 | cds | g2575.t3.CDS5 | 18819962 | 18819966 |
| chr_3 | g2575 | g2575.t3 | TTS | g2575.t3 | NA | NA |
Sequences
>g2575.t3 Gene=g2575 Length=1223
CAGTTTAATTTGAGAAGTGTAACAGAAACAGTCAGAAGAATATTTGCTTAGTGATTGAGA
ACAGAAAGAATATAAAATTGCATTTTCGATTACTAATTTTCTTCTTTTTTATATGAGTAA
GAGAGATAATTTACATTAACATTTTTACGTACATTTTTTCAAACAATAGGTAATCGCACT
TAAATGAAAGTAAGCATGAGAAAATTATCAAGTGTTTTATTGACGCTGACCTACATAGCA
TTGTCTTCATCGCTTGCAGAGAGTCAGCACACCTTATCAGTCGATAATTTTGTCTCAGAG
AGAACATTTGAAATTGATTACGAAAATAATACATTTGTGCGGGATGGAAAGCCATTTCAA
TTTGTTGGTGGATCATTTCACTACTTTCGAGCAATGCCACAAACGTGGCAAAGAAAGTTG
AGAACAATGAGAGCTGCTGGATTGCAAGTTGTGACAACTTATGTTGAATGGAGTTTGCAT
GCTCCAAAAGACGGCGTGTATGACTTCACTGGCATTGCAGATATTGAAGAGTTCATTAAA
CTTGCAGCACAAGAAGATTTACTTGTGATTCTACGGCCTGGTCCATATATTTGTGCAGAA
CGTGATAATGGTGGCCTACCATATTGGCTTTTACACAAATATCCTAATATTCTTCTTCGT
ACTGATGATGAGGATTATAAAAGAGAAGTTGCAAAATGGTATTCAGTACTGATGCCAAAA
ATGCAGAAATTTTTTTATGCAAACGGTGGGCCAATAATTATGGTTCAGGCAAGTTGAAAA
TGAATATGGAAGTTTTTATGCATGTGATGAAAATTATAAATTGTGGATTCGTGATGAAAC
ATTAAAATACACACAATCACATGCTGTTCTTTTTACAAATGATGGGCCAGGAATGTTAAG
ATGTGGAAAAATTCCTAATGTGCTTGCAACTTTAGATTTTGGTGCAGCAGATGATAGCTC
AATCGATCAATATTGGAAAACGTTAAGAAAATTTGAAAAAAAAGGTCCTTTAATGAATTC
TGAATATTATCCTGGATGGCTTTCTCACTGGCAAGAGCAATTTCAAAAAGTTGATACAAA
ATTACTTTTACGTCCATTAGAAAAAATGCTTGAAGACAAAGCATCTGTCAATTTATATAT
GTTTTACGGAGGCACAAATTTCGGATTTACAGCTGGTGCAAATGATGGAGGCCCTGGAAA
TTATAATAGTGATATAACAAGCT
>g2575.t3 Gene=g2575 Length=197
MKVSMRKLSSVLLTLTYIALSSSLAESQHTLSVDNFVSERTFEIDYENNTFVRDGKPFQF
VGGSFHYFRAMPQTWQRKLRTMRAAGLQVVTTYVEWSLHAPKDGVYDFTGIADIEEFIKL
AAQEDLLVILRPGPYICAERDNGGLPYWLLHKYPNILLRTDDEDYKREVAKWYSVLMPKM
QKFFYANGGPIIMVQAS
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 11 | g2575.t3 | Gene3D | G3DSA:3.20.20.80 | Glycosidases | 35 | 197 | 1.6E-66 |
| 2 | g2575.t3 | PANTHER | PTHR23421:SF65 | BETA GALACTOSIDASE, ISOFORM A | 16 | 195 | 1.0E-76 |
| 3 | g2575.t3 | PANTHER | PTHR23421 | BETA-GALACTOSIDASE RELATED | 16 | 195 | 1.0E-76 |
| 5 | g2575.t3 | PRINTS | PR00742 | Glycosyl hydrolase family 35 signature | 54 | 71 | 2.5E-19 |
| 6 | g2575.t3 | PRINTS | PR00742 | Glycosyl hydrolase family 35 signature | 75 | 93 | 2.5E-19 |
| 7 | g2575.t3 | PRINTS | PR00742 | Glycosyl hydrolase family 35 signature | 130 | 149 | 2.5E-19 |
| 4 | g2575.t3 | PRINTS | PR00742 | Glycosyl hydrolase family 35 signature | 186 | 197 | 2.5E-19 |
| 1 | g2575.t3 | Pfam | PF01301 | Glycosyl hydrolases family 35 | 51 | 195 | 5.8E-62 |
| 13 | g2575.t3 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 25 | - |
| 14 | g2575.t3 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 7 | - |
| 15 | g2575.t3 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 8 | 20 | - |
| 16 | g2575.t3 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 21 | 25 | - |
| 12 | g2575.t3 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 26 | 197 | - |
| 8 | g2575.t3 | SUPERFAMILY | SSF51445 | (Trans)glycosidases | 41 | 195 | 2.56E-57 |
| 10 | g2575.t3 | SignalP_EUK | SignalP-noTM | SignalP-noTM | 1 | 27 | - |
| 17 | g2575.t3 | SignalP_GRAM_NEGATIVE | SignalP-noTM | SignalP-noTM | 1 | 25 | - |
| 9 | g2575.t3 | SignalP_GRAM_POSITIVE | SignalP-TM | SignalP-TM | 1 | 27 | - |
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.
