Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Alpha-amylase B.

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.t2 TSS g6053.t2 13890242 13890242
chr_2 g6053 g6053.t2 isoform g6053.t2 13890291 13890819
chr_2 g6053 g6053.t2 exon g6053.t2.exon1 13890291 13890343
chr_2 g6053 g6053.t2 cds g6053.t2.CDS1 13890291 13890343
chr_2 g6053 g6053.t2 exon g6053.t2.exon2 13890409 13890509
chr_2 g6053 g6053.t2 cds g6053.t2.CDS2 13890409 13890509
chr_2 g6053 g6053.t2 exon g6053.t2.exon3 13890563 13890632
chr_2 g6053 g6053.t2 cds g6053.t2.CDS3 13890563 13890632
chr_2 g6053 g6053.t2 exon g6053.t2.exon4 13890692 13890819
chr_2 g6053 g6053.t2 cds g6053.t2.CDS4 13890692 13890818
chr_2 g6053 g6053.t2 TTS g6053.t2 NA NA

Sequences

>g6053.t2 Gene=g6053 Length=352
ATGAAACTTTTAGTTGTAATTTTGAGCATTTTTGTAGCTGTCAATGCTCAATGGGACACT
CATTGGTGGAGTGGTCGAAGTGGAATTGTTCATTTATTTGAGTGGAAATGGAATGATATT
GCAAATGAATGTGAAACATTCTTAGCACCAAATGGTTACGCGGGAGTCCAAACTTCACCT
CCGTCAGAAAATTTAGTCATCGGAAATCGACCCTGGTGGGAAAGATATCAGCCAGTTTCA
TATCATTTGAATACACGATCAGGTGATAGAAATGCATTCGCTGATATGGTTAGACGATGC
AATGCTGTTGGTATTCGTATCTATCCTGATGTTGTAATTAATCATATGGCGG

>g6053.t2 Gene=g6053 Length=117
MKLLVVILSIFVAVNAQWDTHWWSGRSGIVHLFEWKWNDIANECETFLAPNGYAGVQTSP
PSENLVIGNRPWWERYQPVSYHLNTRSGDRNAFADMVRRCNAVGIRIYPDVVINHMA

Protein features from InterProScan

Transcript Database ID Name Start End E.value
8 g6053.t2 Gene3D G3DSA:3.20.20.80 Glycosidases 18 117 2.5E-50
2 g6053.t2 PANTHER PTHR43447 ALPHA-AMYLASE 4 116 1.7E-40
3 g6053.t2 PANTHER PTHR43447:SF5 PANCREATIC ALPHA-AMYLASE 4 116 1.7E-40
5 g6053.t2 PRINTS PR00110 Alpha-amylase signature 72 89 6.8E-10
4 g6053.t2 PRINTS PR00110 Alpha-amylase signature 104 115 6.8E-10
10 g6053.t2 Phobius SIGNAL_PEPTIDE Signal peptide region 1 16 -
11 g6053.t2 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 2 -
12 g6053.t2 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 3 11 -
13 g6053.t2 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 12 16 -
9 g6053.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 17 117 -
6 g6053.t2 SUPERFAMILY SSF51445 (Trans)glycosidases 19 117 2.91E-32
7 g6053.t2 SignalP_EUK SignalP-noTM SignalP-noTM 1 16 -
1 g6053.t2 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

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