General information for g6053.t39
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Alpha-amylase A.
Parent gene
- The parent gene g6053 is located on chr_2: 13891629..13893158 (+ strand)
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.t39 | TSS | g6053.t39 | 13890242 | 13890242 |
| chr_2 | g6053 | g6053.t39 | isoform | g6053.t39 | 13890291 | 13892251 |
| chr_2 | g6053 | g6053.t39 | exon | g6053.t39.exon1 | 13890291 | 13890343 |
| chr_2 | g6053 | g6053.t39 | exon | g6053.t39.exon2 | 13890409 | 13890509 |
| chr_2 | g6053 | g6053.t39 | exon | g6053.t39.exon3 | 13890581 | 13890632 |
| chr_2 | g6053 | g6053.t39 | exon | g6053.t39.exon4 | 13890692 | 13890915 |
| chr_2 | g6053 | g6053.t39 | exon | g6053.t39.exon5 | 13890977 | 13891138 |
| chr_2 | g6053 | g6053.t39 | exon | g6053.t39.exon6 | 13891263 | 13891506 |
| chr_2 | g6053 | g6053.t39 | exon | g6053.t39.exon7 | 13891629 | 13892251 |
| chr_2 | g6053 | g6053.t39 | cds | g6053.t39.CDS1 | 13891640 | 13892251 |
| chr_2 | g6053 | g6053.t39 | TTS | g6053.t39 | 13892345 | 13892345 |
Sequences
>g6053.t39 Gene=g6053 Length=1459
ATGAAACTTTTAGTTGTAATTTTGAGCATTTTTGTAGCTGTCAATGCTCAATGGGACACT
CATTGGTGGAGTGGTCGAAGTGGAATTGTTCATTTATTTGAGTGGAAATGGAATGATATT
GCAAATGAATGTGAAACATTCTTAGCACCAAATGCTTCACCTCCGTCAGAAAATTTAGTC
ATCGGAAATCGACCCTGGTGGGAAAGATATCAGCCAGTTTCATATCATTTGAATACACGA
TCAGGTGATAGAAATGCATTCGCTGATATGGTTAGACGATGCAATGCTGTTGGTATTCGT
ATCTATCCTGATGTTGTAATTAATCATATGGCGGCTGGTGATGGTTATGGAACAGGCGGA
AGTGAATCTAGAGTTAGCCAATTAAGCTTCCCAGCTGTTCCATATGGAAGTAATGACTTC
AATCCAAGATGTGATATCACTAATTACAATGATCCATATCAAGTTAGAAACTGCTGGCTT
GTTGGTTTATCTGATCTTAAGACAGGAAGTGATTATGTCCGTCAGAAAATTGCCGATTTC
TTAAATGATTTGATTAGTCTTGGTGTTGCAGGTAATTTCGTCTTAATTTTAACACATGTG
GCCAGCAGATGTTCAGAATATTGTCTCACGCCTCAACAATTTGAACACAAACCACGGTTT
CCCAGCCAACGCCCGTCCATTTATCACACAGGAAGTTATTGATTTGGGTGGTGAAGCAAT
TAAAAAAGACGAATATTTGCACATTGGAACAATCACAGAGTTTAGATACAGTGCTGAAAT
TGGACGAGTTTTCCGTGGTTATGATTTATTGAAATATCTTAAGAACTTTGGTGAAGGATG
GGGTTTTATGGCATCAGCATCAGCTCTTACTTTTGTTGACAATCACGACAACCAGAGAGG
ACATGGAGCGGGAGGTGCCAATGTTCTCACATATAAAGTCTCAAAGAATTACAAAATGGC
AACAGCTTTCCATCTCGCATGGAATTACGGAATTCCTCGTATCATGAGTAGCTTTGCTTT
CAATGATGGCGATCAAGGTCCACCAGCTGATGGCTATGGTAATTTGAAATCACCAGAATT
TAATTCAGAAGGAGCTTGCACTAATGGATGGGTTTGCGAACATCGTTGGAGACAAATTTA
CAACATGGTTAAATTCCGTAATGCAGCTGGTGGTGCAGCTGTACAAAATTGGTGGGAAAA
TGGAAGCGGAAAACAGATTGCTTTCTCACGTGGCAACAGAGCTTTCATTGCCTTTAATTT
GGACTCATATGGCATCAATCAAAATTTGTACACAGGATTACCAGCTGGAACTTATTGTGA
AATTGCATCAGGAAGCAAGAGCGGTTCAAGTTGCACAGGAAAAACAATTACAGTCGATGG
CAGTGGAAATGCCTACATTGATTTACCACACAATGCTGACGACGGTTTTGTTGCAATTCA
TGTTGATGCGAAATTGTAA
>g6053.t39 Gene=g6053 Length=203
MASASALTFVDNHDNQRGHGAGGANVLTYKVSKNYKMATAFHLAWNYGIPRIMSSFAFND
GDQGPPADGYGNLKSPEFNSEGACTNGWVCEHRWRQIYNMVKFRNAAGGAAVQNWWENGS
GKQIAFSRGNRAFIAFNLDSYGINQNLYTGLPAGTYCEIASGSKSGSSCTGKTITVDGSG
NAYIDLPHNADDGFVAIHVDAKL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g6053.t39 | Gene3D | G3DSA:3.20.20.80 | Glycosidases | 1 | 109 | 0 |
| 7 | g6053.t39 | Gene3D | G3DSA:2.60.40.1180 | - | 110 | 203 | 0 |
| 2 | g6053.t39 | PANTHER | PTHR43447 | ALPHA-AMYLASE | 2 | 203 | 0 |
| 3 | g6053.t39 | PANTHER | PTHR43447:SF7 | ALPHA-AMYLASE | 2 | 203 | 0 |
| 1 | g6053.t39 | Pfam | PF02806 | Alpha amylase, C-terminal all-beta domain | 118 | 188 | 0 |
| 6 | g6053.t39 | SMART | SM00632 | Aamy_c | 113 | 202 | 0 |
| 5 | g6053.t39 | SUPERFAMILY | SSF51445 | (Trans)glycosidases | 3 | 106 | 0 |
| 4 | g6053.t39 | SUPERFAMILY | SSF51011 | Glycosyl hydrolase domain | 111 | 202 | 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: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