General information for g2575.t1
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.t1 | TSS | g2575.t1 | 18818413 | 18818413 |
| chr_3 | g2575 | g2575.t1 | isoform | g2575.t1 | 18819153 | 18821389 |
| chr_3 | g2575 | g2575.t1 | exon | g2575.t1.exon1 | 18819153 | 18819248 |
| chr_3 | g2575 | g2575.t1 | cds | g2575.t1.CDS1 | 18819153 | 18819248 |
| chr_3 | g2575 | g2575.t1 | exon | g2575.t1.exon2 | 18819311 | 18819607 |
| chr_3 | g2575 | g2575.t1 | cds | g2575.t1.CDS2 | 18819311 | 18819607 |
| chr_3 | g2575 | g2575.t1 | exon | g2575.t1.exon3 | 18819660 | 18819744 |
| chr_3 | g2575 | g2575.t1 | cds | g2575.t1.CDS3 | 18819660 | 18819744 |
| chr_3 | g2575 | g2575.t1 | exon | g2575.t1.exon4 | 18819808 | 18819902 |
| chr_3 | g2575 | g2575.t1 | cds | g2575.t1.CDS4 | 18819808 | 18819902 |
| chr_3 | g2575 | g2575.t1 | exon | g2575.t1.exon5 | 18819962 | 18820412 |
| chr_3 | g2575 | g2575.t1 | cds | g2575.t1.CDS5 | 18819962 | 18820412 |
| chr_3 | g2575 | g2575.t1 | exon | g2575.t1.exon6 | 18820470 | 18821389 |
| chr_3 | g2575 | g2575.t1 | cds | g2575.t1.CDS6 | 18820470 | 18821389 |
| chr_3 | g2575 | g2575.t1 | TTS | g2575.t1 | NA | NA |
Sequences
>g2575.t1 Gene=g2575 Length=1944
ATGAGAAAATTATCAAGTGTTTTATTGACGCTGACCTACATAGCATTGTCTTCATCGCTT
GCAGAGAGTCAGCACACCTTATCAGTCGATAATTTTGTCTCAGAGAGAACATTTGAAATT
GATTACGAAAATAATACATTTGTGCGGGATGGAAAGCCATTTCAATTTGTTGGTGGATCA
TTTCACTACTTTCGAGCAATGCCACAAACGTGGCAAAGAAAGTTGAGAACAATGAGAGCT
GCTGGATTGCAAGTTGTGACAACTTATGTTGAATGGAGTTTGCATGCTCCAAAAGACGGC
GTGTATGACTTCACTGGCATTGCAGATATTGAAGAGTTCATTAAACTTGCAGCACAAGAA
GATTTACTTGTGATTCTACGGCCTGGTCCATATATTTGTGCAGAACGTGATAATGGTGGC
CTACCATATTGGCTTTTACACAAATATCCTAATATTCTTCTTCGTACTGATGATGAGGAT
TATAAAAGAGAAGTTGCAAAATGGTATTCAGTACTGATGCCAAAAATGCAGAAATTTTTT
TATGCAAACGGTGGGCCAATAATTATGGTTCAGGTTGAAAATGAATATGGAAGTTTTTAT
GCATGTGATGAAAATTATAAATTGTGGATTCGTGATGAAACATTAAAATACACACAATCA
CATGCTGTTCTTTTTACAAATGATGGGCCAGGAATGTTAAGATGTGGAAAAATTCCTAAT
GTGCTTGCAACTTTAGATTTTGGTGCAGCAGATGATAGCTCAATCGATCAATATTGGAAA
ACGTTAAGAAAATTTGAAAAAAAAGGTCCTTTAATGAATTCTGAATATTATCCTGGATGG
CTTTCTCACTGGCAAGAGCAATTTCAAAAAGTTGATACAAAATTACTTTTACGTCCATTA
GAAAAAATGCTTGAAGACAAAGCATCTGTCAATTTATATATGTTTTACGGAGGCACAAAT
TTCGGATTTACAGCTGGTGCAAATGATGGAGGCCCTGGAAATTATAATAGTGATATAACA
AGCTATGACTATGATGCACCAATGACAGAAAGTGGTGATACAACAGAAAAATATTTTGCA
TTGAGGGAACTTATAAGCAAATATTTCCCACTTCCTGATATTGAAGTACCTGAAAATTTA
AGAAAAGTTAAACTTCCTGATGTTCACCTTAAACCATATTCTGTGTTACTCGATTTAAAC
GGTCGAAGACATTTATCAAGTTTTACGGTAACATCATTAAATCCTATGACATTTGAAGCT
CTAAATCAAAATTCAGGATTTATTCTTTATGAAACTAAATTACCAAATGTTAAAAGAGAT
CCTGTTTTGCTCAAAATCAATGAACTTAGAGATAGAGCATATATCTATGTCAATCGCCAA
TTTGTTGGAGTTCTTTCACGAGAAAATAAAATTGATTCACTTCCTATAAGTTCAATGCTT
GGTGAAGATTTGCAAATTATAGTTGAGAATGAAGGTCGCATTAATTATGGAATTGCAAAT
GATTTTAAAGGCATCATCGGAAATGTTCAATATAATTCAGTGATACTTCTCAATTGGACT
ATGACAGGTTTTCCTTTAGAAAATTATCGACAAATCGATGATCTCGTATCTGTTTTAAGA
AGAAAATATGGAAGTAATAGAACTGCATCTATAAAAAGTTATTTACGCTCAGGACCAACA
ATATTTCATGGAGAATTTATATTAAAGGAATCAGAAATTGCTGACACATATTTAGATCCA
ACTTTATGGGGCAAGGGTATTGCATTCATCAATGGTTTCAATTTAGGCAGATATTGGCCA
ATCGTTGGTCCACAAATTACATTATATGTACCAAAGGAAATTCTTAGAATTGGTACTAAC
AAAATTACCATGCTTGAACTGGAAAGAGCACCAGAGAACGGTTTAGTCAGTTTTACAGAT
ACACCTAACTTAGAAGGTTATTAA
>g2575.t1 Gene=g2575 Length=647
MRKLSSVLLTLTYIALSSSLAESQHTLSVDNFVSERTFEIDYENNTFVRDGKPFQFVGGS
FHYFRAMPQTWQRKLRTMRAAGLQVVTTYVEWSLHAPKDGVYDFTGIADIEEFIKLAAQE
DLLVILRPGPYICAERDNGGLPYWLLHKYPNILLRTDDEDYKREVAKWYSVLMPKMQKFF
YANGGPIIMVQVENEYGSFYACDENYKLWIRDETLKYTQSHAVLFTNDGPGMLRCGKIPN
VLATLDFGAADDSSIDQYWKTLRKFEKKGPLMNSEYYPGWLSHWQEQFQKVDTKLLLRPL
EKMLEDKASVNLYMFYGGTNFGFTAGANDGGPGNYNSDITSYDYDAPMTESGDTTEKYFA
LRELISKYFPLPDIEVPENLRKVKLPDVHLKPYSVLLDLNGRRHLSSFTVTSLNPMTFEA
LNQNSGFILYETKLPNVKRDPVLLKINELRDRAYIYVNRQFVGVLSRENKIDSLPISSML
GEDLQIIVENEGRINYGIANDFKGIIGNVQYNSVILLNWTMTGFPLENYRQIDDLVSVLR
RKYGSNRTASIKSYLRSGPTIFHGEFILKESEIADTYLDPTLWGKGIAFINGFNLGRYWP
IVGPQITLYVPKEILRIGTNKITMLELERAPENGLVSFTDTPNLEGY
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 18 | g2575.t1 | Gene3D | G3DSA:3.20.20.80 | Glycosidases | 31 | 312 | 2.9E-100 |
| 17 | g2575.t1 | Gene3D | G3DSA:2.60.120.260 | - | 313 | 628 | 3.7E-103 |
| 16 | g2575.t1 | Gene3D | G3DSA:2.60.120.260 | - | 390 | 525 | 3.7E-103 |
| 3 | g2575.t1 | PANTHER | PTHR23421:SF172 | BETA-GALACTOSIDASE | 26 | 645 | 6.8E-222 |
| 4 | g2575.t1 | PANTHER | PTHR23421 | BETA-GALACTOSIDASE RELATED | 26 | 645 | 6.8E-222 |
| 24 | g2575.t1 | PIRSF | PIRSF006336 | B-gal | 4 | 645 | 2.1E-240 |
| 8 | g2575.t1 | PRINTS | PR00742 | Glycosyl hydrolase family 35 signature | 50 | 67 | 2.2E-40 |
| 11 | g2575.t1 | PRINTS | PR00742 | Glycosyl hydrolase family 35 signature | 71 | 89 | 2.2E-40 |
| 10 | g2575.t1 | PRINTS | PR00742 | Glycosyl hydrolase family 35 signature | 126 | 145 | 2.2E-40 |
| 6 | g2575.t1 | PRINTS | PR00742 | Glycosyl hydrolase family 35 signature | 182 | 197 | 2.2E-40 |
| 9 | g2575.t1 | PRINTS | PR00742 | Glycosyl hydrolase family 35 signature | 272 | 287 | 2.2E-40 |
| 5 | g2575.t1 | PRINTS | PR00742 | Glycosyl hydrolase family 35 signature | 308 | 323 | 2.2E-40 |
| 7 | g2575.t1 | PRINTS | PR00742 | Glycosyl hydrolase family 35 signature | 585 | 601 | 2.2E-40 |
| 2 | g2575.t1 | Pfam | PF01301 | Glycosyl hydrolases family 35 | 47 | 367 | 3.2E-113 |
| 1 | g2575.t1 | Pfam | PF13364 | Beta-galactosidase jelly roll domain | 556 | 624 | 2.2E-4 |
| 20 | g2575.t1 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 21 | - |
| 21 | g2575.t1 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 3 | - |
| 22 | g2575.t1 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 4 | 16 | - |
| 23 | g2575.t1 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 17 | 21 | - |
| 19 | g2575.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 22 | 647 | - |
| 26 | g2575.t1 | ProSitePatterns | PS01182 | Glycosyl hydrolases family 35 putative active site. | 184 | 196 | - |
| 13 | g2575.t1 | SUPERFAMILY | SSF51445 | (Trans)glycosidases | 37 | 371 | 1.66E-93 |
| 12 | g2575.t1 | SUPERFAMILY | SSF49785 | Galactose-binding domain-like | 487 | 635 | 6.23E-28 |
| 15 | g2575.t1 | SignalP_EUK | SignalP-noTM | SignalP-noTM | 1 | 23 | - |
| 25 | g2575.t1 | SignalP_GRAM_NEGATIVE | SignalP-noTM | SignalP-noTM | 1 | 21 | - |
| 14 | g2575.t1 | SignalP_GRAM_POSITIVE | SignalP-TM | SignalP-TM | 1 | 23 | - |
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:0004565 | beta-galactosidase activity | MF |
| GO:0005975 | carbohydrate metabolic process | BP |
KEGG
Orthology
- This transcript has been annotated with K12309 (beta-galactosidase)
Pathway
- This transcript belongs to the following pathways
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.
