Gene loci information

Transcript annotation

  • This transcript has been annotated as Alpha-amylase A.

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 g6053 g6053.t55 TSS g6053.t55 13890242 13890242
chr_2 g6053 g6053.t55 isoform g6053.t55 13890985 13892251
chr_2 g6053 g6053.t55 exon g6053.t55.exon1 13890985 13891117
chr_2 g6053 g6053.t55 exon g6053.t55.exon2 13891263 13891506
chr_2 g6053 g6053.t55 cds g6053.t55.CDS1 13891266 13891506
chr_2 g6053 g6053.t55 exon g6053.t55.exon3 13891629 13892251
chr_2 g6053 g6053.t55 cds g6053.t55.CDS2 13891629 13892251
chr_2 g6053 g6053.t55 TTS g6053.t55 13892345 13892345

Sequences

>g6053.t55 Gene=g6053 Length=1000
ACTAATTACAATGATCCATATCAAGTTAGAAACTGCTGGCTTGTTGGTTTATCTGATCTT
AAGACAGGAAGTGATTATGTCCGTCAGAAAATTGCCGATTTCTTAAATGATTTGATTAGT
CTTGGTGTTGCAGCACATGTGGCCAGCAGATGTTCAGAATATTGTCTCACGCCTCAACAA
TTTGAACACAAACCACGGTTTCCCAGCCAACGCCCGTCCATTTATCACACAGGAAGTTAT
TGATTTGGGTGGTGAAGCAATTAAAAAAGACGAATATTTGCACATTGGAACAATCACAGA
GTTTAGATACAGTGCTGAAATTGGACGAGTTTTCCGTGGTTATGATTTATTGAAATATCT
TAAGAACTTTGGTGAAGGATGGGGTTTTATGGCATCAGCATCAGCTCTTACTTTTGTTGA
CAATCACGACAACCAGAGAGGACATGGAGCGGGAGGTGCCAATGTTCTCACATATAAAGT
CTCAAAGAATTACAAAATGGCAACAGCTTTCCATCTCGCATGGAATTACGGAATTCCTCG
TATCATGAGTAGCTTTGCTTTCAATGATGGCGATCAAGGTCCACCAGCTGATGGCTATGG
TAATTTGAAATCACCAGAATTTAATTCAGAAGGAGCTTGCACTAATGGATGGGTTTGCGA
ACATCGTTGGAGACAAATTTACAACATGGTTAAATTCCGTAATGCAGCTGGTGGTGCAGC
TGTACAAAATTGGTGGGAAAATGGAAGCGGAAAACAGATTGCTTTCTCACGTGGCAACAG
AGCTTTCATTGCCTTTAATTTGGACTCATATGGCATCAATCAAAATTTGTACACAGGATT
ACCAGCTGGAACTTATTGTGAAATTGCATCAGGAAGCAAGAGCGGTTCAAGTTGCACAGG
AAAAACAATTACAGTCGATGGCAGTGGAAATGCCTACATTGATTTACCACACAATGCTGA
CGACGGTTTTGTTGCAATTCATGTTGATGCGAAATTGTAA

>g6053.t55 Gene=g6053 Length=287
MWPADVQNIVSRLNNLNTNHGFPANARPFITQEVIDLGGEAIKKDEYLHIGTITEFRYSA
EIGRVFRGYDLLKYLKNFGEGWGFMASASALTFVDNHDNQRGHGAGGANVLTYKVSKNYK
MATAFHLAWNYGIPRIMSSFAFNDGDQGPPADGYGNLKSPEFNSEGACTNGWVCEHRWRQ
IYNMVKFRNAAGGAAVQNWWENGSGKQIAFSRGNRAFIAFNLDSYGINQNLYTGLPAGTY
CEIASGSKSGSSCTGKTITVDGSGNAYIDLPHNADDGFVAIHVDAKL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
10 g6053.t55 Gene3D G3DSA:3.20.20.80 Glycosidases 1 193 0
9 g6053.t55 Gene3D G3DSA:2.60.40.1180 - 194 287 0
2 g6053.t55 PANTHER PTHR43447 ALPHA-AMYLASE 1 287 0
3 g6053.t55 PANTHER PTHR43447:SF7 ALPHA-AMYLASE 1 287 0
5 g6053.t55 PRINTS PR00110 Alpha-amylase signature 29 47 0
4 g6053.t55 PRINTS PR00110 Alpha-amylase signature 88 100 0
1 g6053.t55 Pfam PF02806 Alpha amylase, C-terminal all-beta domain 202 272 0
8 g6053.t55 SMART SM00632 Aamy_c 197 286 0
7 g6053.t55 SUPERFAMILY SSF51445 (Trans)glycosidases 1 190 0
6 g6053.t55 SUPERFAMILY SSF51011 Glycosyl hydrolase domain 195 286 0

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

GO terms from InterProScan

GOID TERM ONTOLOGY
GO:0043169 cation binding MF
GO:0004556 alpha-amylase activity MF
GO:0005975 carbohydrate metabolic process BP
GO:0003824 catalytic activity MF

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