Gene loci information

Transcript annotation

  • This transcript has been annotated as Beta-galactosidase.

Parent gene

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 g5274 g5274.t1 TSS g5274.t1 8346444 8346444
chr_2 g5274 g5274.t1 isoform g5274.t1 8346701 8348862
chr_2 g5274 g5274.t1 exon g5274.t1.exon1 8346701 8346703
chr_2 g5274 g5274.t1 cds g5274.t1.CDS1 8346701 8346703
chr_2 g5274 g5274.t1 exon g5274.t1.exon2 8346759 8346922
chr_2 g5274 g5274.t1 cds g5274.t1.CDS2 8346759 8346922
chr_2 g5274 g5274.t1 exon g5274.t1.exon3 8346980 8347109
chr_2 g5274 g5274.t1 cds g5274.t1.CDS3 8346980 8347109
chr_2 g5274 g5274.t1 exon g5274.t1.exon4 8347161 8347755
chr_2 g5274 g5274.t1 cds g5274.t1.CDS4 8347161 8347755
chr_2 g5274 g5274.t1 exon g5274.t1.exon5 8347821 8347945
chr_2 g5274 g5274.t1 cds g5274.t1.CDS5 8347821 8347945
chr_2 g5274 g5274.t1 exon g5274.t1.exon6 8347999 8348862
chr_2 g5274 g5274.t1 cds g5274.t1.CDS6 8347999 8348862
chr_2 g5274 g5274.t1 TTS g5274.t1 8348940 8348940

Sequences

>g5274.t1 Gene=g5274 Length=1881
ATGGTGACAAGAAAATTTGACATTGACTATGTAAATAATACTTTTTTGATGGATGGAGAG
CCATTTCGATATGTCGCTGGTTCATTTCACTACTTTCGTGCGCATCAAGATACATGGAGA
GATAAATTACAGAAAATGAGAGCAAGTGGTTTGAATGCTGTTGATATTTATGTTCAATGG
TCGCTTCATAATCCAAAAGATGGAATTTATAATTGGGAAGGAATTGCTGATGTTGAAAGA
TTTATTCAAATTGCAACTGAAGAAGATCTCTATATCATTTTAAGGCCTGGTCCATATATC
TGTGCAGAAATTGACAATGGTGGTCTTCCTTATTGGCTTGAAACAAAATATCCAGGAATT
CAAGTACGTACAAGTGATCAAAATTATTTGAATGAAATTGAAAAATGGTATGATGTGCTC
ATGCCAAAATTTGTTAATTATCTTTATGGAAATGGTGGCAATATCATTATGGTGCAAGTT
GAGAATGAATATGGAGCTTATCAAGTTTGCGATGAAGAATATAAAGAATTTTTAAAAGTT
TTGACATTAAAGCACACGGAAGATAAAGCTGTTCTTTTTACAACTGATCGTCCTATCGGC
AATGAATTAGCATGTGGTCAAGTTAAAGATGTTTTCGTTACGACCGATTTTGGTATTGCG
AATGAATCAGAAGTTGCTTTTAATTTTAATAAATTACGAGAAGTTCAACCAAATGGTCCA
TTTGTTAATTCTGAATTTTATACTGGATGGTTAACGCATTGGCAAGAACCAAATGCAAGA
CGTGATGCAGCTGAATTAGCAGCAACTTTAAGAATCATGTTGAGTGAACCATATAATGCT
AATGTCAACTTTTACATGTTTTTTGGAGGCACAAATTTTGGTTTTTGGGCAGGAGCAAAT
GATTGGGGTATTGGAAAATATATGGCTGATATCACAAGTTATGATTATGATGCACCATTA
AGTGAGCCAGGAGACATCACTCCGAAGTATTTAATTCTTAGATCAGTTATTGCACAGTAC
TTACAACTGCCTCCTTTGAATCTGCCGGATCCATCTACAAAGAAAATTTATCCATCAATT
AATGTCACTGCAGTAAATACAATGTTTTCACAAGTTGGAAGACAAAATTTAGGATCAAAT
GCAATTGACGCTGGTGGAAGATTGAAAACTTTTGAAGAACTTGATCAATTTTCAGGCTTT
GTTCTCTATGAGACACATTTGCCTAAAACTTTCTCAAGAGATCCATCAAATTTAGTGATT
GAAAAATTAAGAGACCGTGCTTTAATTTATATTGATGAGAGATTTGTTGGTATTTTATCA
AGAGAGAATGGAATCAAATCTATGCCAATACAAAAAGGATATGCTGGCAAGAAGCTGCAA
ATTCTTGTTGAGAATCAGGGACGTATAAATTTCCAAGAGAATTTTGATTTGAAAGGCATT
GTTGGAAATGTAACATTGCAGAAATTTGAGGAGCCTTATTATGAGGAATTAGGTGACTGG
ATAATAACTGGTTATCCGTTTGAAGAATACTCAGGTATTTCATCATTTTTGTCTAGTAGC
AGTGCAGAATGTACTACTTGTTCACCTGCTAAAAATGGTTGGTTAAAAAATGGACCAGTT
ATTTTTAAAGGCACTCTAACAATTGATGAGGAACCAGCAGATACTTGGTGGAATATTAGA
AATGGATGGGGAAAGGGAAATTTGTTTGTTAATGGCGTAAATTTGGGTCGTTATTGGTCT
ATTGGACCTCAAATGACTATGTATATTGCGAAGGAATTTTTGAAGACTGGAGACAATGAA
ATTGTTATTCTTGAGTTACAAAAAGCACCTCTCGACTTCCAGATTAATTTTGCTGATCAA
GCCGACTATAATGAAAATTGA

>g5274.t1 Gene=g5274 Length=626
MVTRKFDIDYVNNTFLMDGEPFRYVAGSFHYFRAHQDTWRDKLQKMRASGLNAVDIYVQW
SLHNPKDGIYNWEGIADVERFIQIATEEDLYIILRPGPYICAEIDNGGLPYWLETKYPGI
QVRTSDQNYLNEIEKWYDVLMPKFVNYLYGNGGNIIMVQVENEYGAYQVCDEEYKEFLKV
LTLKHTEDKAVLFTTDRPIGNELACGQVKDVFVTTDFGIANESEVAFNFNKLREVQPNGP
FVNSEFYTGWLTHWQEPNARRDAAELAATLRIMLSEPYNANVNFYMFFGGTNFGFWAGAN
DWGIGKYMADITSYDYDAPLSEPGDITPKYLILRSVIAQYLQLPPLNLPDPSTKKIYPSI
NVTAVNTMFSQVGRQNLGSNAIDAGGRLKTFEELDQFSGFVLYETHLPKTFSRDPSNLVI
EKLRDRALIYIDERFVGILSRENGIKSMPIQKGYAGKKLQILVENQGRINFQENFDLKGI
VGNVTLQKFEEPYYEELGDWIITGYPFEEYSGISSFLSSSSAECTTCSPAKNGWLKNGPV
IFKGTLTIDEEPADTWWNIRNGWGKGNLFVNGVNLGRYWSIGPQMTMYIAKEFLKTGDNE
IVILELQKAPLDFQINFADQADYNEN

Protein features from InterProScan

Transcript Database ID Name Start End E.value
15 g5274.t1 Gene3D G3DSA:3.20.20.80 Glycosidases 1 283 0
13 g5274.t1 Gene3D G3DSA:2.60.120.260 - 285 607 0
14 g5274.t1 Gene3D G3DSA:2.60.120.260 - 362 506 0
2 g5274.t1 PANTHER PTHR23421:SF65 BETA GALACTOSIDASE, ISOFORM A 4 608 0
3 g5274.t1 PANTHER PTHR23421 BETA-GALACTOSIDASE RELATED 4 608 0
16 g5274.t1 PIRSF PIRSF006336 B-gal 1 624 0
10 g5274.t1 PRINTS PR00742 Glycosyl hydrolase family 35 signature 18 35 0
4 g5274.t1 PRINTS PR00742 Glycosyl hydrolase family 35 signature 39 57 0
7 g5274.t1 PRINTS PR00742 Glycosyl hydrolase family 35 signature 94 113 0
9 g5274.t1 PRINTS PR00742 Glycosyl hydrolase family 35 signature 150 165 0
6 g5274.t1 PRINTS PR00742 Glycosyl hydrolase family 35 signature 242 257 0
5 g5274.t1 PRINTS PR00742 Glycosyl hydrolase family 35 signature 280 295 0
8 g5274.t1 PRINTS PR00742 Glycosyl hydrolase family 35 signature 565 581 0
1 g5274.t1 Pfam PF01301 Glycosyl hydrolases family 35 15 339 0
12 g5274.t1 SUPERFAMILY SSF51445 (Trans)glycosidases 7 343 0
11 g5274.t1 SUPERFAMILY SSF49785 Galactose-binding domain-like 462 610 0

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g5274/g5274.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5274.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

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.

Raw TPM values