Gene loci information

Transcript annotation

  • This transcript has been annotated as Beta-galactosidase-1-like protein.

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 g5272 g5272.t3 TSS g5272.t3 8341436 8341436
chr_2 g5272 g5272.t3 isoform g5272.t3 8341476 8342616
chr_2 g5272 g5272.t3 exon g5272.t3.exon1 8341476 8341560
chr_2 g5272 g5272.t3 cds g5272.t3.CDS1 8341476 8341560
chr_2 g5272 g5272.t3 exon g5272.t3.exon2 8341620 8341957
chr_2 g5272 g5272.t3 cds g5272.t3.CDS2 8341620 8341957
chr_2 g5272 g5272.t3 exon g5272.t3.exon3 8342028 8342616
chr_2 g5272 g5272.t3 cds g5272.t3.CDS3 8342028 8342615
chr_2 g5272 g5272.t3 TTS g5272.t3 NA NA

Sequences

>g5272.t3 Gene=g5272 Length=1012
ATGACACAAGGCTTCTGTGGTAGACATAAATGTCTTATCTCAATTGCTGCTGCAATCATT
GTAATCGCAGCAATTGTAGGAATCGTTCTTGGCGTGGTTCTAACACGTTCATCTAATGAT
GAAGAAAAACATGAACGTGGTTTTAGTATTGATTATGAACATGATACATTTTTGATGGAT
GGAAAACCTTTTAGATATGTCGCAGGATCTTTTCATTATTTTAGAGCTTTACCACAAACA
TGGCGTCAAAAATTAAAGACTTTAAAAGCTGGTGGACTTAATGCAGTTGACCTTTATATT
CAATGGTCACTTCATAATCCAGAAGATGGAATTTATAATTGGGATGGAATTGCTGATGTT
GAAAGAGTTGTAGAAATTGCAACTGAAGAAGGACTTTTCGTTATTTTAAGACCAGGACCA
TATATCTGTGCAGAAATTGACAATGGTGGACTGCCTTATTGGCTTGCAACGAAATATCCA
AACATTAAAGTTCGTACGAATGACACAAATTATCTTTTTGAAGTCGAAAGATGGTACTCA
AAGCTTATGCCAAAGTTTGAGAAACATCTTTATGGAAATGGCGGCAATATCATTATGGTG
CAAGTTGAAAATGAATATGGAGCATTTGGTGCATGCGATGAAGAATATAAAGAATTTTTG
AGAGATGAAACTTTAAAATATACACAAGACAAAGCCATTCTTTTCACAACTGATCGTCCA
ATTGATGATGAATTGAAATGTGGTCAAGTTAAAGATGTTTTCGTTACAACTGATTTTGGT
CTTTATAATTTCTCTATGGTCATGTATAATTTCAACAAATTAAGAGAAGTTCAACCTAAA
GGTCCACTTGTCAATACAGAATTTTACACAGGATGGCTGACACATTGGCAAGAAGCAAAT
GCAAGAAGAGGTGGTGAAGATTTGGCAAAAACACTTGAATATATGTTAGTTCTTGGCGCA
AATGTTGACTTTTACATGTACTTTGGTGGCACAAATTTCGGATTTTGGGCAG

>g5272.t3 Gene=g5272 Length=337
MTQGFCGRHKCLISIAAAIIVIAAIVGIVLGVVLTRSSNDEEKHERGFSIDYEHDTFLMD
GKPFRYVAGSFHYFRALPQTWRQKLKTLKAGGLNAVDLYIQWSLHNPEDGIYNWDGIADV
ERVVEIATEEGLFVILRPGPYICAEIDNGGLPYWLATKYPNIKVRTNDTNYLFEVERWYS
KLMPKFEKHLYGNGGNIIMVQVENEYGAFGACDEEYKEFLRDETLKYTQDKAILFTTDRP
IDDELKCGQVKDVFVTTDFGLYNFSMVMYNFNKLREVQPKGPLVNTEFYTGWLTHWQEAN
ARRGGEDLAKTLEYMLVLGANVDFYMYFGGTNFGFWA

Protein features from InterProScan

Transcript Database ID Name Start End E.value
12 g5272.t3 Gene3D G3DSA:3.20.20.80 Glycosidases 41 324 4.8E-98
2 g5272.t3 PANTHER PTHR23421:SF65 BETA GALACTOSIDASE, ISOFORM A 7 337 2.2E-146
3 g5272.t3 PANTHER PTHR23421 BETA-GALACTOSIDASE RELATED 7 337 2.2E-146
9 g5272.t3 PRINTS PR00742 Glycosyl hydrolase family 35 signature 60 77 8.6E-36
8 g5272.t3 PRINTS PR00742 Glycosyl hydrolase family 35 signature 81 99 8.6E-36
7 g5272.t3 PRINTS PR00742 Glycosyl hydrolase family 35 signature 136 155 8.6E-36
6 g5272.t3 PRINTS PR00742 Glycosyl hydrolase family 35 signature 192 207 8.6E-36
5 g5272.t3 PRINTS PR00742 Glycosyl hydrolase family 35 signature 284 299 8.6E-36
4 g5272.t3 PRINTS PR00742 Glycosyl hydrolase family 35 signature 320 335 8.6E-36
1 g5272.t3 Pfam PF01301 Glycosyl hydrolases family 35 56 337 6.3E-97
13 g5272.t3 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 11 -
15 g5272.t3 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 12 34 -
14 g5272.t3 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 35 337 -
11 g5272.t3 SUPERFAMILY SSF51445 (Trans)glycosidases 46 337 2.95E-84
10 g5272.t3 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.t3; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5272.t3.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