General information for g2575.t2
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.t2 | isoform | g2575.t2 | 18818413 | 18820410 |
| chr_3 | g2575 | g2575.t2 | TSS | g2575.t2 | 18818413 | 18818413 |
| chr_3 | g2575 | g2575.t2 | exon | g2575.t2.exon1 | 18818413 | 18818578 |
| chr_3 | g2575 | g2575.t2 | exon | g2575.t2.exon2 | 18819127 | 18819248 |
| chr_3 | g2575 | g2575.t2 | cds | g2575.t2.CDS1 | 18819141 | 18819248 |
| chr_3 | g2575 | g2575.t2 | exon | g2575.t2.exon3 | 18819311 | 18819607 |
| chr_3 | g2575 | g2575.t2 | cds | g2575.t2.CDS2 | 18819311 | 18819607 |
| chr_3 | g2575 | g2575.t2 | exon | g2575.t2.exon4 | 18819660 | 18819744 |
| chr_3 | g2575 | g2575.t2 | cds | g2575.t2.CDS3 | 18819660 | 18819744 |
| chr_3 | g2575 | g2575.t2 | exon | g2575.t2.exon5 | 18819808 | 18819902 |
| chr_3 | g2575 | g2575.t2 | cds | g2575.t2.CDS4 | 18819808 | 18819902 |
| chr_3 | g2575 | g2575.t2 | exon | g2575.t2.exon6 | 18819962 | 18820410 |
| chr_3 | g2575 | g2575.t2 | cds | g2575.t2.CDS5 | 18819962 | 18820408 |
| chr_3 | g2575 | g2575.t2 | TTS | g2575.t2 | NA | NA |
Sequences
>g2575.t2 Gene=g2575 Length=1214
CAGTTTAATTTGAGAAGTGTAACAGAAACAGTCAGAAGAATATTTGCTTAGTGATTGAGA
ACAGAAAGAATATAAAATTGCATTTTCGATTACTAATTTTCTTCTTTTTTATATGAGTAA
GAGAGATAATTTACATTAACATTTTTACGTACATTTTTTCAAACAAGTAATCGCACTTAA
ATGAAAGTAAGCATGAGAAAATTATCAAGTGTTTTATTGACGCTGACCTACATAGCATTG
TCTTCATCGCTTGCAGAGAGTCAGCACACCTTATCAGTCGATAATTTTGTCTCAGAGAGA
ACATTTGAAATTGATTACGAAAATAATACATTTGTGCGGGATGGAAAGCCATTTCAATTT
GTTGGTGGATCATTTCACTACTTTCGAGCAATGCCACAAACGTGGCAAAGAAAGTTGAGA
ACAATGAGAGCTGCTGGATTGCAAGTTGTGACAACTTATGTTGAATGGAGTTTGCATGCT
CCAAAAGACGGCGTGTATGACTTCACTGGCATTGCAGATATTGAAGAGTTCATTAAACTT
GCAGCACAAGAAGATTTACTTGTGATTCTACGGCCTGGTCCATATATTTGTGCAGAACGT
GATAATGGTGGCCTACCATATTGGCTTTTACACAAATATCCTAATATTCTTCTTCGTACT
GATGATGAGGATTATAAAAGAGAAGTTGCAAAATGGTATTCAGTACTGATGCCAAAAATG
CAGAAATTTTTTTATGCAAACGGTGGGCCAATAATTATGGTTCAGGTTGAAAATGAATAT
GGAAGTTTTTATGCATGTGATGAAAATTATAAATTGTGGATTCGTGATGAAACATTAAAA
TACACACAATCACATGCTGTTCTTTTTACAAATGATGGGCCAGGAATGTTAAGATGTGGA
AAAATTCCTAATGTGCTTGCAACTTTAGATTTTGGTGCAGCAGATGATAGCTCAATCGAT
CAATATTGGAAAACGTTAAGAAAATTTGAAAAAAAAGGTCCTTTAATGAATTCTGAATAT
TATCCTGGATGGCTTTCTCACTGGCAAGAGCAATTTCAAAAAGTTGATACAAAATTACTT
TTACGTCCATTAGAAAAAATGCTTGAAGACAAAGCATCTGTCAATTTATATATGTTTTAC
GGAGGCACAAATTTCGGATTTACAGCTGGTGCAAATGATGGAGGCCCTGGAAATTATAAT
AGTGATATAACAAG
>g2575.t2 Gene=g2575 Length=344
MKVSMRKLSSVLLTLTYIALSSSLAESQHTLSVDNFVSERTFEIDYENNTFVRDGKPFQF
VGGSFHYFRAMPQTWQRKLRTMRAAGLQVVTTYVEWSLHAPKDGVYDFTGIADIEEFIKL
AAQEDLLVILRPGPYICAERDNGGLPYWLLHKYPNILLRTDDEDYKREVAKWYSVLMPKM
QKFFYANGGPIIMVQVENEYGSFYACDENYKLWIRDETLKYTQSHAVLFTNDGPGMLRCG
KIPNVLATLDFGAADDSSIDQYWKTLRKFEKKGPLMNSEYYPGWLSHWQEQFQKVDTKLL
LRPLEKMLEDKASVNLYMFYGGTNFGFTAGANDGGPGNYNSDIT
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 13 | g2575.t2 | Gene3D | G3DSA:3.20.20.80 | Glycosidases | 35 | 316 | 4.8E-101 |
| 2 | g2575.t2 | PANTHER | PTHR23421:SF65 | BETA GALACTOSIDASE, ISOFORM A | 17 | 343 | 1.2E-127 |
| 3 | g2575.t2 | PANTHER | PTHR23421 | BETA-GALACTOSIDASE RELATED | 17 | 343 | 1.2E-127 |
| 5 | g2575.t2 | PRINTS | PR00742 | Glycosyl hydrolase family 35 signature | 54 | 71 | 9.7E-36 |
| 6 | g2575.t2 | PRINTS | PR00742 | Glycosyl hydrolase family 35 signature | 75 | 93 | 9.7E-36 |
| 7 | g2575.t2 | PRINTS | PR00742 | Glycosyl hydrolase family 35 signature | 130 | 149 | 9.7E-36 |
| 4 | g2575.t2 | PRINTS | PR00742 | Glycosyl hydrolase family 35 signature | 186 | 201 | 9.7E-36 |
| 9 | g2575.t2 | PRINTS | PR00742 | Glycosyl hydrolase family 35 signature | 276 | 291 | 9.7E-36 |
| 8 | g2575.t2 | PRINTS | PR00742 | Glycosyl hydrolase family 35 signature | 312 | 327 | 9.7E-36 |
| 1 | g2575.t2 | Pfam | PF01301 | Glycosyl hydrolases family 35 | 51 | 335 | 3.9E-101 |
| 15 | g2575.t2 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 25 | - |
| 16 | g2575.t2 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 7 | - |
| 17 | g2575.t2 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 8 | 20 | - |
| 18 | g2575.t2 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 21 | 25 | - |
| 14 | g2575.t2 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 26 | 344 | - |
| 20 | g2575.t2 | ProSitePatterns | PS01182 | Glycosyl hydrolases family 35 putative active site. | 188 | 200 | - |
| 10 | g2575.t2 | SUPERFAMILY | SSF51445 | (Trans)glycosidases | 41 | 341 | 8.78E-84 |
| 12 | g2575.t2 | SignalP_EUK | SignalP-noTM | SignalP-noTM | 1 | 27 | - |
| 19 | g2575.t2 | SignalP_GRAM_NEGATIVE | SignalP-noTM | SignalP-noTM | 1 | 25 | - |
| 11 | g2575.t2 | 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.
