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.t3 TSS g6053.t3 13890242 13890242
chr_2 g6053 g6053.t3 isoform g6053.t3 13890291 13891085
chr_2 g6053 g6053.t3 exon g6053.t3.exon1 13890291 13890343
chr_2 g6053 g6053.t3 cds g6053.t3.CDS1 13890291 13890343
chr_2 g6053 g6053.t3 exon g6053.t3.exon2 13890409 13890509
chr_2 g6053 g6053.t3 cds g6053.t3.CDS2 13890409 13890509
chr_2 g6053 g6053.t3 exon g6053.t3.exon3 13890563 13890632
chr_2 g6053 g6053.t3 cds g6053.t3.CDS3 13890563 13890632
chr_2 g6053 g6053.t3 exon g6053.t3.exon4 13890692 13890915
chr_2 g6053 g6053.t3 cds g6053.t3.CDS4 13890692 13890915
chr_2 g6053 g6053.t3 exon g6053.t3.exon5 13890977 13891085
chr_2 g6053 g6053.t3 cds g6053.t3.CDS5 13890977 13891083
chr_2 g6053 g6053.t3 TTS g6053.t3 NA NA

Sequences

>g6053.t3 Gene=g6053 Length=557
ATGAAACTTTTAGTTGTAATTTTGAGCATTTTTGTAGCTGTCAATGCTCAATGGGACACT
CATTGGTGGAGTGGTCGAAGTGGAATTGTTCATTTATTTGAGTGGAAATGGAATGATATT
GCAAATGAATGTGAAACATTCTTAGCACCAAATGGTTACGCGGGAGTCCAAACTTCACCT
CCGTCAGAAAATTTAGTCATCGGAAATCGACCCTGGTGGGAAAGATATCAGCCAGTTTCA
TATCATTTGAATACACGATCAGGTGATAGAAATGCATTCGCTGATATGGTTAGACGATGC
AATGCTGTTGGTATTCGTATCTATCCTGATGTTGTAATTAATCATATGGCGGCTGGTGAT
GGTTATGGAACAGGCGGAAGTGAATCTAGAGTTAGCCAATTAAGCTTCCCAGCTGTTCCA
TATGGAAGTAATGACTTCAATCCAAGATGTGATATCACTAATTACAATGATCCATATCAA
GTTAGAAACTGCTGGCTTGTTGGTTTATCTGATCTTAAGACAGGAAGTGATTATGTCCGT
CAGAAAATTGCCGATTT

>g6053.t3 Gene=g6053 Length=185
MKLLVVILSIFVAVNAQWDTHWWSGRSGIVHLFEWKWNDIANECETFLAPNGYAGVQTSP
PSENLVIGNRPWWERYQPVSYHLNTRSGDRNAFADMVRRCNAVGIRIYPDVVINHMAAGD
GYGTGGSESRVSQLSFPAVPYGSNDFNPRCDITNYNDPYQVRNCWLVGLSDLKTGSDYVR
QKIAD

Protein features from InterProScan

Transcript Database ID Name Start End E.value
7 g6053.t3 Gene3D G3DSA:3.20.20.80 Glycosidases 18 185 1.3E-77
1 g6053.t3 PANTHER PTHR43447 ALPHA-AMYLASE 16 184 6.6E-62
2 g6053.t3 PANTHER PTHR43447:SF7 ALPHA-AMYLASE 16 184 6.6E-62
4 g6053.t3 PRINTS PR00110 Alpha-amylase signature 72 89 1.3E-9
3 g6053.t3 PRINTS PR00110 Alpha-amylase signature 104 115 1.3E-9
9 g6053.t3 Phobius SIGNAL_PEPTIDE Signal peptide region 1 16 -
10 g6053.t3 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 2 -
11 g6053.t3 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 3 11 -
12 g6053.t3 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 12 16 -
8 g6053.t3 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 17 185 -
14 g6053.t3 SMART SM00642 aamy 27 185 0.0019
5 g6053.t3 SUPERFAMILY SSF51445 (Trans)glycosidases 19 185 4.6E-47
6 g6053.t3 SignalP_EUK SignalP-noTM SignalP-noTM 1 16 -
13 g6053.t3 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