General information for g5273.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Beta-galactosidase.
Parent gene
- The parent gene g5273 is located on chr_2: 8343840..8346069 (+ 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 | g5273 | g5273.t1 | TSS | g5273.t1 | 8343787 | 8343787 |
| chr_2 | g5273 | g5273.t1 | isoform | g5273.t1 | 8343840 | 8346069 |
| chr_2 | g5273 | g5273.t1 | exon | g5273.t1.exon1 | 8343840 | 8343933 |
| chr_2 | g5273 | g5273.t1 | cds | g5273.t1.CDS1 | 8343840 | 8343933 |
| chr_2 | g5273 | g5273.t1 | exon | g5273.t1.exon2 | 8343991 | 8344040 |
| chr_2 | g5273 | g5273.t1 | cds | g5273.t1.CDS2 | 8343991 | 8344040 |
| chr_2 | g5273 | g5273.t1 | exon | g5273.t1.exon3 | 8344098 | 8344388 |
| chr_2 | g5273 | g5273.t1 | cds | g5273.t1.CDS3 | 8344098 | 8344388 |
| chr_2 | g5273 | g5273.t1 | exon | g5273.t1.exon4 | 8344441 | 8345154 |
| chr_2 | g5273 | g5273.t1 | cds | g5273.t1.CDS4 | 8344441 | 8345154 |
| chr_2 | g5273 | g5273.t1 | exon | g5273.t1.exon5 | 8345209 | 8346069 |
| chr_2 | g5273 | g5273.t1 | cds | g5273.t1.CDS5 | 8345209 | 8346069 |
| chr_2 | g5273 | g5273.t1 | TTS | g5273.t1 | NA | NA |
Sequences
>g5273.t1 Gene=g5273 Length=2010
ATGAAAGACCAAAATAAAACATTTTTTAGAAAATATAAATTTTTCATTATCGCTGCTGTT
GTTCTTATCTTAATTTGTGCAATCGTTGGAATTGTGCTTGGGATTTATTTCAGTCGTTCT
TCTGACAATAATCATGAAGCATCGGTGAGAAACTTTACAATAGATCATAAGCATGATACA
TTTTTGATGGATGGAAAACCATTTCGATATGTTGCTGGTGCATTTCATTATTTTCGTGCA
TTACCACAAGTTTGGCGAGAAAGATTGAGAACAATGAAAGCTGGTGGTCTTAATGCAGTT
GATTTGTATGTTCATTGGGCTTTACACAATCCAGAAGATGGAGTTTATAATTGGGAAGGA
ATTGCTGATGTTGAGAGAATTATTGAAATTGCAACTGAAGAAAATTTCTATATCATTTTA
AGGCCTGGTCCATATATCTGTGCAGAAATTGACAATGGTGGACTACCTTATTGGCTTGCA
ACAAAATATCCAGGAATAAAATTGAGAACGAGTGATAAAAATTATCTTTTTGAAGTCGAA
AGATGGTACTCAAAGCTTATGCCAAAATTTGTCAAACATTTTTATGGAAATGGCGGCAAT
ATCATTATGGTGCAAGTTGAAAATGAATATGGAGCTTATAGTGCATGTGATAATGAATAT
AAAGAATTTTTAAGAGATGAGACTTTAAAATATACACAAGGAAATGCTGTCCTCTTCACT
GTTGATTGGCCTTATGATGAGGAAATTCAATGTGGAAGTGTAAAGGATGTTTTTATTACA
GTTGACTTTGGTCGATCGTCATTCAACGAAGTAATAGAAAAATTTGCAAAATTGAGAGAA
TATCAGCCAACAGGACCATTGGTCAATACTGAATTTTATTCTGGTTGGTTTACTTTATGG
CAAGGTTCACATTCAGTGACTAATACATCTGAATTAGCAAAAACACTTGACCATATGTTA
GTACTTGGAGCAAATGTTGACTTTTATGTATATTTTGGTGGAACAAATTTTGGTTTTTGG
TCTGGTGCTGATGGGAGAGGCATTGGAAATTATATGCCTGATATCACAAGTTATGATTAT
GATGCACCAATGGATGAAGCAGGAAATCCCACAGAAAAAGTTTATGCTTTTAAAGAAGTC
ATTCAGAAGTATTTGAGTTTAGATGATTTAGAAATTCCTGAGAAAATAAAAACAATGGCT
CCCGGATCTCTCACAATGACACCAGTCAATTCACTTTTATCAGCAGAAGGCAGAAATATT
TTAGGATCACGTCCGATTGAATCAAATACATTATTGACTTTTGAACAATTGAAACAATTT
TCTGGCTTTGTGCTTTATGAGACAGAATTGCCAAAACTCACTCGAGATCCAGCAAATTTA
TTTATTACTGATTTGAGAGATCGAGCATTAGTTTATGTCGATGAAGAATATGTTGGTTTA
CTATCACGTGAAAATGTCATCAATACTCTTCCTATTAATGCTGATTATGGTTCAAAGCTT
TCGATTCTTGTTGAAAATCAGGGAAGATTAAATTTTGGTGTCACTGATGATTACAAAGGA
ATCAGAGGAACAGTCGCAGTTCAAACTTTTGATGCCTCTTCTAACAATTTATATGAATTC
AATAATTGGACAATAACAGGATTTCCTTTTGATAAATCAGTAGATTTAGAAAGTTTAGCA
AGAGCTTCAAATGACTATCAAATTGATTCAAGTGGACTAGCATCAAATGGACCAATAATT
TTCCATGCAACACTCACAATAAATGACAATGAAGAAATATTTGACACTTATTGGGATACA
AGTGATTGGAATAAAGGATTTTTATTTGTCAATGGTTTTAATTTAGGTCGTTATTGGTCA
GTTGGTCCTCAAATTACTTTGTACATACCAAAAGACATTTTACAACATGGCAAAAATGCA
ATTTTCTTAGTTGAACTTCAACAAGCTTCAAATGATTTAAAAATGCATTTTGTAAAAGGT
CCAATTTTCATTAATGATACTCCTGCTTAA
>g5273.t1 Gene=g5273 Length=669
MKDQNKTFFRKYKFFIIAAVVLILICAIVGIVLGIYFSRSSDNNHEASVRNFTIDHKHDT
FLMDGKPFRYVAGAFHYFRALPQVWRERLRTMKAGGLNAVDLYVHWALHNPEDGVYNWEG
IADVERIIEIATEENFYIILRPGPYICAEIDNGGLPYWLATKYPGIKLRTSDKNYLFEVE
RWYSKLMPKFVKHFYGNGGNIIMVQVENEYGAYSACDNEYKEFLRDETLKYTQGNAVLFT
VDWPYDEEIQCGSVKDVFITVDFGRSSFNEVIEKFAKLREYQPTGPLVNTEFYSGWFTLW
QGSHSVTNTSELAKTLDHMLVLGANVDFYVYFGGTNFGFWSGADGRGIGNYMPDITSYDY
DAPMDEAGNPTEKVYAFKEVIQKYLSLDDLEIPEKIKTMAPGSLTMTPVNSLLSAEGRNI
LGSRPIESNTLLTFEQLKQFSGFVLYETELPKLTRDPANLFITDLRDRALVYVDEEYVGL
LSRENVINTLPINADYGSKLSILVENQGRLNFGVTDDYKGIRGTVAVQTFDASSNNLYEF
NNWTITGFPFDKSVDLESLARASNDYQIDSSGLASNGPIIFHATLTINDNEEIFDTYWDT
SDWNKGFLFVNGFNLGRYWSVGPQITLYIPKDILQHGKNAIFLVELQQASNDLKMHFVKG
PIFINDTPA
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 15 | g5273.t1 | Gene3D | G3DSA:3.20.20.80 | Glycosidases | 45 | 328 | 8.8E-98 |
| 14 | g5273.t1 | Gene3D | G3DSA:2.60.120.260 | - | 329 | 647 | 1.0E-93 |
| 13 | g5273.t1 | Gene3D | G3DSA:2.60.120.260 | - | 406 | 549 | 1.0E-93 |
| 2 | g5273.t1 | PANTHER | PTHR23421:SF65 | BETA GALACTOSIDASE, ISOFORM A | 19 | 649 | 1.5E-238 |
| 3 | g5273.t1 | PANTHER | PTHR23421 | BETA-GALACTOSIDASE RELATED | 19 | 649 | 1.5E-238 |
| 19 | g5273.t1 | PIRSF | PIRSF006336 | B-gal | 20 | 664 | 5.2E-221 |
| 4 | g5273.t1 | PRINTS | PR00742 | Glycosyl hydrolase family 35 signature | 64 | 81 | 7.7E-40 |
| 10 | g5273.t1 | PRINTS | PR00742 | Glycosyl hydrolase family 35 signature | 85 | 103 | 7.7E-40 |
| 6 | g5273.t1 | PRINTS | PR00742 | Glycosyl hydrolase family 35 signature | 140 | 159 | 7.7E-40 |
| 7 | g5273.t1 | PRINTS | PR00742 | Glycosyl hydrolase family 35 signature | 196 | 211 | 7.7E-40 |
| 9 | g5273.t1 | PRINTS | PR00742 | Glycosyl hydrolase family 35 signature | 288 | 303 | 7.7E-40 |
| 8 | g5273.t1 | PRINTS | PR00742 | Glycosyl hydrolase family 35 signature | 352 | 368 | 7.7E-40 |
| 5 | g5273.t1 | PRINTS | PR00742 | Glycosyl hydrolase family 35 signature | 605 | 621 | 7.7E-40 |
| 1 | g5273.t1 | Pfam | PF01301 | Glycosyl hydrolases family 35 | 61 | 383 | 3.1E-108 |
| 16 | g5273.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 11 | - |
| 18 | g5273.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 12 | 37 | - |
| 17 | g5273.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 38 | 669 | - |
| 12 | g5273.t1 | SUPERFAMILY | SSF51445 | (Trans)glycosidases | 51 | 386 | 4.01E-95 |
| 11 | g5273.t1 | SUPERFAMILY | SSF49785 | Galactose-binding domain-like | 503 | 652 | 1.73E-25 |
| 20 | g5273.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 13 | 35 | - |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5273/g5273.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5273.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.
