General information for g5273.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative 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.t2 | TSS | g5273.t2 | 8343787 | 8343787 |
| chr_2 | g5273 | g5273.t2 | isoform | g5273.t2 | 8343840 | 8346069 |
| chr_2 | g5273 | g5273.t2 | exon | g5273.t2.exon1 | 8343840 | 8343877 |
| chr_2 | g5273 | g5273.t2 | exon | g5273.t2.exon2 | 8344670 | 8345154 |
| chr_2 | g5273 | g5273.t2 | cds | g5273.t2.CDS1 | 8344960 | 8345154 |
| chr_2 | g5273 | g5273.t2 | exon | g5273.t2.exon3 | 8345209 | 8346069 |
| chr_2 | g5273 | g5273.t2 | cds | g5273.t2.CDS2 | 8345209 | 8346069 |
| chr_2 | g5273 | g5273.t2 | TTS | g5273.t2 | NA | NA |
Sequences
>g5273.t2 Gene=g5273 Length=1384
ATGAAAGACCAAAATAAAACATTTTTTAGAAAATATAAAATTTTTAAGAGATGAGACTTT
AAAATATACACAAGGAAATGCTGTCCTCTTCACTGTTGATTGGCCTTATGATGAGGAAAT
TCAATGTGGAAGTGTAAAGGATGTTTTTATTACAGTTGACTTTGGTCGATCGTCATTCAA
CGAAGTAATAGAAAAATTTGCAAAATTGAGAGAATATCAGCCAACAGGACCATTGGTCAA
TACTGAATTTTATTCTGGTTGGTTTACTTTATGGCAAGGTTCACATTCAGTGACTAATAC
ATCTGAATTAGCAAAAACACTTGACCATATGTTAGTACTTGGAGCAAATGTTGACTTTTA
TGTATATTTTGGTGGAACAAATTTTGGTTTTTGGTCTGGTGCTGATGGGAGAGGCATTGG
AAATTATATGCCTGATATCACAAGTTATGATTATGATGCACCAATGGATGAAGCAGGAAA
TCCCACAGAAAAAGTTTATGCTTTTAAAGAAGTCATTCAGAAGTATTTGAGTTTAGATGA
TTTAGAAATTCCTGAGAAAATAAAAACAATGGCTCCCGGATCTCTCACAATGACACCAGT
CAATTCACTTTTATCAGCAGAAGGCAGAAATATTTTAGGATCACGTCCGATTGAATCAAA
TACATTATTGACTTTTGAACAATTGAAACAATTTTCTGGCTTTGTGCTTTATGAGACAGA
ATTGCCAAAACTCACTCGAGATCCAGCAAATTTATTTATTACTGATTTGAGAGATCGAGC
ATTAGTTTATGTCGATGAAGAATATGTTGGTTTACTATCACGTGAAAATGTCATCAATAC
TCTTCCTATTAATGCTGATTATGGTTCAAAGCTTTCGATTCTTGTTGAAAATCAGGGAAG
ATTAAATTTTGGTGTCACTGATGATTACAAAGGAATCAGAGGAACAGTCGCAGTTCAAAC
TTTTGATGCCTCTTCTAACAATTTATATGAATTCAATAATTGGACAATAACAGGATTTCC
TTTTGATAAATCAGTAGATTTAGAAAGTTTAGCAAGAGCTTCAAATGACTATCAAATTGA
TTCAAGTGGACTAGCATCAAATGGACCAATAATTTTCCATGCAACACTCACAATAAATGA
CAATGAAGAAATATTTGACACTTATTGGGATACAAGTGATTGGAATAAAGGATTTTTATT
TGTCAATGGTTTTAATTTAGGTCGTTATTGGTCAGTTGGTCCTCAAATTACTTTGTACAT
ACCAAAAGACATTTTACAACATGGCAAAAATGCAATTTTCTTAGTTGAACTTCAACAAGC
TTCAAATGATTTAAAAATGCATTTTGTAAAAGGTCCAATTTTCATTAATGATACTCCTGC
TTAA
>g5273.t2 Gene=g5273 Length=351
MLVLGANVDFYVYFGGTNFGFWSGADGRGIGNYMPDITSYDYDAPMDEAGNPTEKVYAFK
EVIQKYLSLDDLEIPEKIKTMAPGSLTMTPVNSLLSAEGRNILGSRPIESNTLLTFEQLK
QFSGFVLYETELPKLTRDPANLFITDLRDRALVYVDEEYVGLLSRENVINTLPINADYGS
KLSILVENQGRLNFGVTDDYKGIRGTVAVQTFDASSNNLYEFNNWTITGFPFDKSVDLES
LARASNDYQIDSSGLASNGPIIFHATLTINDNEEIFDTYWDTSDWNKGFLFVNGFNLGRY
WSVGPQITLYIPKDILQHGKNAIFLVELQQASNDLKMHFVKGPIFINDTPA
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g5273.t2 | Gene3D | G3DSA:2.60.120.260 | - | 11 | 329 | 0e+00 |
| 8 | g5273.t2 | Gene3D | G3DSA:2.60.120.260 | - | 88 | 231 | 0e+00 |
| 2 | g5273.t2 | PANTHER | PTHR23421:SF65 | BETA GALACTOSIDASE, ISOFORM A | 1 | 331 | 0e+00 |
| 3 | g5273.t2 | PANTHER | PTHR23421 | BETA-GALACTOSIDASE RELATED | 1 | 331 | 0e+00 |
| 5 | g5273.t2 | PRINTS | PR00742 | Glycosyl hydrolase family 35 signature | 6 | 21 | 2e-07 |
| 4 | g5273.t2 | PRINTS | PR00742 | Glycosyl hydrolase family 35 signature | 287 | 303 | 2e-07 |
| 1 | g5273.t2 | Pfam | PF01301 | Glycosyl hydrolases family 35 | 6 | 65 | 0e+00 |
| 7 | g5273.t2 | SUPERFAMILY | SSF51445 | (Trans)glycosidases | 6 | 68 | 0e+00 |
| 6 | g5273.t2 | SUPERFAMILY | SSF49785 | Galactose-binding domain-like | 185 | 334 | 0e+00 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5273/g5273.t2; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5273.t2.fa.iupred3.txt does not exist
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. There were no conditions that were differentially expressed