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_4 g14591 g14591.t2 TSS g14591.t2 1429090 1429090
chr_4 g14591 g14591.t2 isoform g14591.t2 1429126 1431522
chr_4 g14591 g14591.t2 exon g14591.t2.exon1 1429126 1429349
chr_4 g14591 g14591.t2 cds g14591.t2.CDS1 1429126 1429349
chr_4 g14591 g14591.t2 exon g14591.t2.exon2 1429408 1429631
chr_4 g14591 g14591.t2 cds g14591.t2.CDS2 1429408 1429631
chr_4 g14591 g14591.t2 exon g14591.t2.exon3 1429734 1429882
chr_4 g14591 g14591.t2 cds g14591.t2.CDS3 1429734 1429882
chr_4 g14591 g14591.t2 exon g14591.t2.exon4 1430179 1430414
chr_4 g14591 g14591.t2 cds g14591.t2.CDS4 1430179 1430414
chr_4 g14591 g14591.t2 exon g14591.t2.exon5 1430474 1430542
chr_4 g14591 g14591.t2 cds g14591.t2.CDS5 1430474 1430542
chr_4 g14591 g14591.t2 exon g14591.t2.exon6 1430603 1430676
chr_4 g14591 g14591.t2 cds g14591.t2.CDS6 1430603 1430676
chr_4 g14591 g14591.t2 exon g14591.t2.exon7 1431029 1431522
chr_4 g14591 g14591.t2 cds g14591.t2.CDS7 1431029 1431522
chr_4 g14591 g14591.t2 TTS g14591.t2 1431566 1431566

Sequences

>g14591.t2 Gene=g14591 Length=1470
ATGAAAATTTTCCTAGCACTTCTAAGTGCATTAGTAATTGTTAGTGCACAAAGAAATCCA
CATTGGTGGAGTGGTAGAAGTGCTTTTGTTCATCTTTTTGAATGGAAATGGAACGACATT
GCGAATGAGTGTGAAAATTTTCTTGCACCACGTGGATATGCCGGAGTTCAAATTTCTCCA
CCAAATGAAAATCTCGTAATTTCAAATCGACCATGGTGGGAGAGATATCAACCTGTCAGC
TATATTTTGACAACAAGATCAGGTTCAAGAGCAGAGTTGGCAAATATGATTTCACGTTGT
AATGCTGTTGGTATTAGAATTATTGCTGATGTTGTTATCAACCATATGGGAGCTGCAAAT
GGAATCGGAACAGGTGGATCAACAAGTGATTACAATAATTTAAATTTCCCAGCAGTTCCT
TATAGCAATAATGATTTTAATCCCAATTGCGCTATTAATAACTACAATGATCCTTATCAA
GTAAGAAATTGCCGTCTTGTTGGTCTCCCTGATTTGAAACTTGATTCAGCTTGGGTTCGT
GATAAAATTGTTAATTACATGAATGATTTGATTAGTCTTGGTGTCGCTGGATTTAGAGTC
AAACATATGTGGCCTGCAGATTTGCAACATATTTTCAACCGATTAAACAACCTCAACACA
GCTCATGGTTTTCCTGCCAATTCACGTCCATTCATCACGCAAGAAGTTATTGATTTGGGT
GGTGAAGCCATTTCTAAAAATGAATACACTCATCTTGGAACTGTAACTGAATTTAGATAC
TCAGCTGAAATTGGTCGTGTTTTTAATGGTAGAGATTTATTGAAATATCTTTATAATTTC
GGAACAGCTTGGGGTTTCTTGCAAAGTGATTATGCTTTGACTTTTGTTGACAACCACGAT
AACCAACGTGGTCATGGTGCCGGAGGTGACAATGTTTTAACATATAAGAATGCAAAAAGG
TACAAGATGGCAACTGCGTTCCACCTTGCTTGGCCATTCGGTATTCCACGTGTCATGAGC
AGTTTTGCTTTTAACGATGGCGATCAAGGTCCACCAGCTGATGGAAATGGAAATCTTATA
TCACCTGGATTTAATGCTGATGGCTCATGCACTAATGGTTGGGTTTGTGAACACCGATGG
CGTCAAATTTATAACATGATTGGATTCAGAAATGTCGCTGGTACAGCAGCTGTTGCAAAT
TGGTGGGAAAATGGCAGTGGTCAACAAATCGCATTTTCACGTGGAAATCGTGCTTTCATC
GCCTTTAATCAAGATTCAAGTGCTTTGAATTCTAACATTTATACTGGTCTTGCTGCTGGA
ACTTATTGTGACATTGCATCAGGAGCTAAAAGTGGATCATCATGCACAGGAAAATCAATT
GTTGTAGGAAGCAATGGCTATGCCCAAATTAACTTAGGAGCAGGTGAAACAGAAGGCTAT
GTCGCTATTCATGTTGATGCAAAATTGTAA

>g14591.t2 Gene=g14591 Length=489
MKIFLALLSALVIVSAQRNPHWWSGRSAFVHLFEWKWNDIANECENFLAPRGYAGVQISP
PNENLVISNRPWWERYQPVSYILTTRSGSRAELANMISRCNAVGIRIIADVVINHMGAAN
GIGTGGSTSDYNNLNFPAVPYSNNDFNPNCAINNYNDPYQVRNCRLVGLPDLKLDSAWVR
DKIVNYMNDLISLGVAGFRVKHMWPADLQHIFNRLNNLNTAHGFPANSRPFITQEVIDLG
GEAISKNEYTHLGTVTEFRYSAEIGRVFNGRDLLKYLYNFGTAWGFLQSDYALTFVDNHD
NQRGHGAGGDNVLTYKNAKRYKMATAFHLAWPFGIPRVMSSFAFNDGDQGPPADGNGNLI
SPGFNADGSCTNGWVCEHRWRQIYNMIGFRNVAGTAAVANWWENGSGQQIAFSRGNRAFI
AFNQDSSALNSNIYTGLAAGTYCDIASGAKSGSSCTGKSIVVGSNGYAQINLGAGETEGY
VAIHVDAKL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
20 g14591.t2 CDD cd11317 AmyAc_bac_euk_AmyA 26 393 0.0
14 g14591.t2 Gene3D G3DSA:3.20.20.80 Glycosidases 17 394 1.7E-172
13 g14591.t2 Gene3D G3DSA:2.60.40.1180 - 396 489 7.2E-33
3 g14591.t2 PANTHER PTHR43447 ALPHA-AMYLASE 15 489 8.9E-166
4 g14591.t2 PANTHER PTHR43447:SF7 ALPHA-AMYLASE 15 489 8.9E-166
7 g14591.t2 PRINTS PR00110 Alpha-amylase signature 72 89 4.9E-26
5 g14591.t2 PRINTS PR00110 Alpha-amylase signature 104 115 4.9E-26
6 g14591.t2 PRINTS PR00110 Alpha-amylase signature 231 249 4.9E-26
8 g14591.t2 PRINTS PR00110 Alpha-amylase signature 290 302 4.9E-26
2 g14591.t2 Pfam PF00128 Alpha amylase, catalytic domain 88 332 6.5E-13
1 g14591.t2 Pfam PF02806 Alpha amylase, C-terminal all-beta domain 404 474 2.1E-11
16 g14591.t2 Phobius SIGNAL_PEPTIDE Signal peptide region 1 18 -
17 g14591.t2 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 2 -
18 g14591.t2 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 3 14 -
19 g14591.t2 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 15 18 -
15 g14591.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 19 489 -
21 g14591.t2 SMART SM00642 aamy 27 390 2.1E-96
22 g14591.t2 SMART SM00632 Aamy_c 399 488 2.3E-39
10 g14591.t2 SUPERFAMILY SSF51445 (Trans)glycosidases 19 391 2.11E-102
9 g14591.t2 SUPERFAMILY SSF51011 Glycosyl hydrolase domain 398 489 1.38E-29
12 g14591.t2 SignalP_EUK SignalP-noTM SignalP-noTM 1 16 -
11 g14591.t2 SignalP_GRAM_POSITIVE SignalP-TM SignalP-TM 1 16 -

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

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