Gene loci information

Transcript annotation

  • This transcript has been annotated as Alpha-amylase.

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.t4 TSS g6053.t4 13890242 13890242
chr_2 g6053 g6053.t4 isoform g6053.t4 13890291 13891362
chr_2 g6053 g6053.t4 exon g6053.t4.exon1 13890291 13890343
chr_2 g6053 g6053.t4 cds g6053.t4.CDS1 13890291 13890343
chr_2 g6053 g6053.t4 exon g6053.t4.exon2 13890409 13890509
chr_2 g6053 g6053.t4 cds g6053.t4.CDS2 13890409 13890509
chr_2 g6053 g6053.t4 exon g6053.t4.exon3 13890563 13890632
chr_2 g6053 g6053.t4 cds g6053.t4.CDS3 13890563 13890632
chr_2 g6053 g6053.t4 exon g6053.t4.exon4 13890692 13890915
chr_2 g6053 g6053.t4 cds g6053.t4.CDS4 13890692 13890915
chr_2 g6053 g6053.t4 exon g6053.t4.exon5 13890977 13891117
chr_2 g6053 g6053.t4 cds g6053.t4.CDS5 13890977 13891117
chr_2 g6053 g6053.t4 exon g6053.t4.exon6 13891234 13891362
chr_2 g6053 g6053.t4 cds g6053.t4.CDS6 13891234 13891262
chr_2 g6053 g6053.t4 TTS g6053.t4 13892345 13892345

Sequences

>g6053.t4 Gene=g6053 Length=718
ATGAAACTTTTAGTTGTAATTTTGAGCATTTTTGTAGCTGTCAATGCTCAATGGGACACT
CATTGGTGGAGTGGTCGAAGTGGAATTGTTCATTTATTTGAGTGGAAATGGAATGATATT
GCAAATGAATGTGAAACATTCTTAGCACCAAATGGTTACGCGGGAGTCCAAACTTCACCT
CCGTCAGAAAATTTAGTCATCGGAAATCGACCCTGGTGGGAAAGATATCAGCCAGTTTCA
TATCATTTGAATACACGATCAGGTGATAGAAATGCATTCGCTGATATGGTTAGACGATGC
AATGCTGTTGGTATTCGTATCTATCCTGATGTTGTAATTAATCATATGGCGGCTGGTGAT
GGTTATGGAACAGGCGGAAGTGAATCTAGAGTTAGCCAATTAAGCTTCCCAGCTGTTCCA
TATGGAAGTAATGACTTCAATCCAAGATGTGATATCACTAATTACAATGATCCATATCAA
GTTAGAAACTGCTGGCTTGTTGGTTTATCTGATCTTAAGACAGGAAGTGATTATGTCCGT
CAGAAAATTGCCGATTTCTTAAATGATTTGATTAGTCTTGGTGTTGCAGTTTTATTGCTA
AATCATCAAAATATTTAGCACATGTGGCCAGCAGATGTTCAGAATATTGTCTCACGCCTC
AACAATTTGAACACAAACCACGGTTTCCCAGCCAACGCCCGTCCATTTATCACACAGG

>g6053.t4 Gene=g6053 Length=205
MKLLVVILSIFVAVNAQWDTHWWSGRSGIVHLFEWKWNDIANECETFLAPNGYAGVQTSP
PSENLVIGNRPWWERYQPVSYHLNTRSGDRNAFADMVRRCNAVGIRIYPDVVINHMAAGD
GYGTGGSESRVSQLSFPAVPYGSNDFNPRCDITNYNDPYQVRNCWLVGLSDLKTGSDYVR
QKIADFLNDLISLGVAVLLLNHQNI

Protein features from InterProScan

Transcript Database ID Name Start End E.value
8 g6053.t4 Gene3D G3DSA:3.20.20.80 Glycosidases 18 198 1.1E-83
2 g6053.t4 PANTHER PTHR43447 ALPHA-AMYLASE 16 196 4.0E-66
3 g6053.t4 PANTHER PTHR43447:SF7 ALPHA-AMYLASE 16 196 4.0E-66
5 g6053.t4 PRINTS PR00110 Alpha-amylase signature 72 89 1.5E-9
4 g6053.t4 PRINTS PR00110 Alpha-amylase signature 104 115 1.5E-9
1 g6053.t4 Pfam PF00128 Alpha amylase, catalytic domain 82 188 1.6E-4
10 g6053.t4 Phobius SIGNAL_PEPTIDE Signal peptide region 1 16 -
11 g6053.t4 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 2 -
12 g6053.t4 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 3 11 -
13 g6053.t4 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 12 16 -
9 g6053.t4 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 17 205 -
15 g6053.t4 SMART SM00642 aamy 27 205 1.7E-6
6 g6053.t4 SUPERFAMILY SSF51445 (Trans)glycosidases 19 195 2.8E-50
7 g6053.t4 SignalP_EUK SignalP-noTM SignalP-noTM 1 16 -
14 g6053.t4 SignalP_GRAM_NEGATIVE SignalP-noTM SignalP-noTM 1 18 -

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