General information for g5272.t1
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.t1 | TSS | g5272.t1 | 8341436 | 8341436 |
| chr_2 | g5272 | g5272.t1 | isoform | g5272.t1 | 8341476 | 8343718 |
| chr_2 | g5272 | g5272.t1 | exon | g5272.t1.exon1 | 8341476 | 8341560 |
| chr_2 | g5272 | g5272.t1 | cds | g5272.t1.CDS1 | 8341476 | 8341560 |
| chr_2 | g5272 | g5272.t1 | exon | g5272.t1.exon2 | 8341620 | 8341957 |
| chr_2 | g5272 | g5272.t1 | cds | g5272.t1.CDS2 | 8341620 | 8341957 |
| chr_2 | g5272 | g5272.t1 | exon | g5272.t1.exon3 | 8342028 | 8342616 |
| chr_2 | g5272 | g5272.t1 | cds | g5272.t1.CDS3 | 8342028 | 8342616 |
| chr_2 | g5272 | g5272.t1 | exon | g5272.t1.exon4 | 8342673 | 8342797 |
| chr_2 | g5272 | g5272.t1 | cds | g5272.t1.CDS4 | 8342673 | 8342797 |
| chr_2 | g5272 | g5272.t1 | exon | g5272.t1.exon5 | 8342855 | 8343718 |
| chr_2 | g5272 | g5272.t1 | cds | g5272.t1.CDS5 | 8342855 | 8343718 |
| chr_2 | g5272 | g5272.t1 | TTS | g5272.t1 | 8343868 | 8343868 |
Sequences
>g5272.t1 Gene=g5272 Length=2001
ATGACACAAGGCTTCTGTGGTAGACATAAATGTCTTATCTCAATTGCTGCTGCAATCATT
GTAATCGCAGCAATTGTAGGAATCGTTCTTGGCGTGGTTCTAACACGTTCATCTAATGAT
GAAGAAAAACATGAACGTGGTTTTAGTATTGATTATGAACATGATACATTTTTGATGGAT
GGAAAACCTTTTAGATATGTCGCAGGATCTTTTCATTATTTTAGAGCTTTACCACAAACA
TGGCGTCAAAAATTAAAGACTTTAAAAGCTGGTGGACTTAATGCAGTTGACCTTTATATT
CAATGGTCACTTCATAATCCAGAAGATGGAATTTATAATTGGGATGGAATTGCTGATGTT
GAAAGAGTTGTAGAAATTGCAACTGAAGAAGGACTTTTCGTTATTTTAAGACCAGGACCA
TATATCTGTGCAGAAATTGACAATGGTGGACTGCCTTATTGGCTTGCAACGAAATATCCA
AACATTAAAGTTCGTACGAATGACACAAATTATCTTTTTGAAGTCGAAAGATGGTACTCA
AAGCTTATGCCAAAGTTTGAGAAACATCTTTATGGAAATGGCGGCAATATCATTATGGTG
CAAGTTGAAAATGAATATGGAGCATTTGGTGCATGCGATGAAGAATATAAAGAATTTTTG
AGAGATGAAACTTTAAAATATACACAAGACAAAGCCATTCTTTTCACAACTGATCGTCCA
ATTGATGATGAATTGAAATGTGGTCAAGTTAAAGATGTTTTCGTTACAACTGATTTTGGT
CTTTATAATTTCTCTATGGTCATGTATAATTTCAACAAATTAAGAGAAGTTCAACCTAAA
GGTCCACTTGTCAATACAGAATTTTACACAGGATGGCTGACACATTGGCAAGAAGCAAAT
GCAAGAAGAGGTGGTGAAGATTTGGCAAAAACACTTGAATATATGTTAGTTCTTGGCGCA
AATGTTGACTTTTACATGTACTTTGGTGGCACAAATTTCGGATTTTGGGCAGGAGCAAAT
GATTGGGGTATTGGAAAATATATGGCTGATATAACAAGTTATGATTATGATGCACCAATG
GATGAAGCAGGAAATCCCACTGAGAAGTACATGATCTTTCGTGATGTTATTAAAAAGTAC
ATTGATGTCGTCGATGAATCAGAAATTCCTGAGAAAATAAAAACGATGGCTCCCGGATCT
CTCACAATGACACCAGTAAATTCACTTTTATCAGCAGAAGGCAGAAATATTTTAGGATCA
CGTTCAATTGAATCAAATACATTATTGACTTTTGAACAATTGAAACAATTTTCTGGCTTT
GTTCTTTATGAGACAGAATTGCCAAAACTCACTCGAGATCCAGCAAATTTATTAATTACT
GATTTGAGAGATCGAGCATTAGTTTATGTCGATGAAGAATATGTTGGTTTATTGTCACGT
GAAAATGTCATCAATACTCTTCCTATTAATGCTGATTATGGTTCAAAGCTTTCAATACTT
GTTGAAAATCAGGGACGAATCAATTTCCAAATAGCAGATGATTACAAAGGAATCAGAGGA
ACAGTAGCAGTTCAAACTTTTGATGCTTCTTCTAACAATTTATATGAATTCAATAATTGG
ACAATAACAGGATTTCCTTTTGATAAGTCAGTAGATTTAGAAAGTTTGGCAAGAACTTCA
AATGGCTATCAAATTGATTCAAGTGGACTAGCATTAAATGGACCAATAATTTTCCATGCA
ACACTCACAATTAATGACAATGAAGAAATATTTGACACTTATTGGGATACAAGTGATTGG
AATAAAGGATTTTTGTTTGTCAATGGTTTTAATTTAGGTCGTTATTGGTCAGTTGGTCCT
CAAATTACTATGTACATACCAAAAGACATTTTACAACATGGCAAAAATGCAATTTTCTTA
GTTGAACTTCAACAAGCCCCGACCAACCTCAAGATGCATTTTGTAAAAGGTCCAATCTTT
ATAAATGATGAAAAAGTTTAA
>g5272.t1 Gene=g5272 Length=666
MTQGFCGRHKCLISIAAAIIVIAAIVGIVLGVVLTRSSNDEEKHERGFSIDYEHDTFLMD
GKPFRYVAGSFHYFRALPQTWRQKLKTLKAGGLNAVDLYIQWSLHNPEDGIYNWDGIADV
ERVVEIATEEGLFVILRPGPYICAEIDNGGLPYWLATKYPNIKVRTNDTNYLFEVERWYS
KLMPKFEKHLYGNGGNIIMVQVENEYGAFGACDEEYKEFLRDETLKYTQDKAILFTTDRP
IDDELKCGQVKDVFVTTDFGLYNFSMVMYNFNKLREVQPKGPLVNTEFYTGWLTHWQEAN
ARRGGEDLAKTLEYMLVLGANVDFYMYFGGTNFGFWAGANDWGIGKYMADITSYDYDAPM
DEAGNPTEKYMIFRDVIKKYIDVVDESEIPEKIKTMAPGSLTMTPVNSLLSAEGRNILGS
RSIESNTLLTFEQLKQFSGFVLYETELPKLTRDPANLLITDLRDRALVYVDEEYVGLLSR
ENVINTLPINADYGSKLSILVENQGRINFQIADDYKGIRGTVAVQTFDASSNNLYEFNNW
TITGFPFDKSVDLESLARTSNGYQIDSSGLALNGPIIFHATLTINDNEEIFDTYWDTSDW
NKGFLFVNGFNLGRYWSVGPQITMYIPKDILQHGKNAIFLVELQQAPTNLKMHFVKGPIF
INDEKV
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 15 | g5272.t1 | Gene3D | G3DSA:3.20.20.80 | Glycosidases | 41 | 324 | 3.3E-97 |
| 13 | g5272.t1 | Gene3D | G3DSA:2.60.120.260 | - | 325 | 644 | 4.0E-95 |
| 14 | g5272.t1 | Gene3D | G3DSA:2.60.120.260 | - | 403 | 546 | 4.0E-95 |
| 2 | g5272.t1 | PANTHER | PTHR23421:SF65 | BETA GALACTOSIDASE, ISOFORM A | 7 | 645 | 8.5E-248 |
| 3 | g5272.t1 | PANTHER | PTHR23421 | BETA-GALACTOSIDASE RELATED | 7 | 645 | 8.5E-248 |
| 19 | g5272.t1 | PIRSF | PIRSF006336 | B-gal | 16 | 660 | 5.2E-222 |
| 10 | g5272.t1 | PRINTS | PR00742 | Glycosyl hydrolase family 35 signature | 60 | 77 | 5.9E-40 |
| 9 | g5272.t1 | PRINTS | PR00742 | Glycosyl hydrolase family 35 signature | 81 | 99 | 5.9E-40 |
| 8 | g5272.t1 | PRINTS | PR00742 | Glycosyl hydrolase family 35 signature | 136 | 155 | 5.9E-40 |
| 7 | g5272.t1 | PRINTS | PR00742 | Glycosyl hydrolase family 35 signature | 192 | 207 | 5.9E-40 |
| 6 | g5272.t1 | PRINTS | PR00742 | Glycosyl hydrolase family 35 signature | 284 | 299 | 5.9E-40 |
| 5 | g5272.t1 | PRINTS | PR00742 | Glycosyl hydrolase family 35 signature | 320 | 335 | 5.9E-40 |
| 4 | g5272.t1 | PRINTS | PR00742 | Glycosyl hydrolase family 35 signature | 602 | 618 | 5.9E-40 |
| 1 | g5272.t1 | Pfam | PF01301 | Glycosyl hydrolases family 35 | 57 | 379 | 2.4E-110 |
| 16 | g5272.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 11 | - |
| 18 | g5272.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 12 | 34 | - |
| 17 | g5272.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 35 | 666 | - |
| 12 | g5272.t1 | SUPERFAMILY | SSF51445 | (Trans)glycosidases | 46 | 382 | 7.28E-96 |
| 11 | g5272.t1 | SUPERFAMILY | SSF49785 | Galactose-binding domain-like | 500 | 649 | 4.25E-24 |
| 20 | g5272.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 12 | 34 | - |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5272/g5272.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5272.t1.fa.iupred3.txt does not exist
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.
