General information for g597.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Alpha-amylase A.
Parent gene
- The parent gene g597 is located on chr_3: 4400306..4400977 (+ 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_3 | g597 | g597.t2 | TSS | g597.t2 | 4399335 | 4399335 |
| chr_3 | g597 | g597.t2 | isoform | g597.t2 | 4400306 | 4400977 |
| chr_3 | g597 | g597.t2 | exon | g597.t2.exon1 | 4400306 | 4400334 |
| chr_3 | g597 | g597.t2 | cds | g597.t2.CDS1 | 4400313 | 4400334 |
| chr_3 | g597 | g597.t2 | exon | g597.t2.exon2 | 4400412 | 4400977 |
| chr_3 | g597 | g597.t2 | cds | g597.t2.CDS2 | 4400412 | 4400977 |
| chr_3 | g597 | g597.t2 | TTS | g597.t2 | 4401030 | 4401030 |
Sequences
>g597.t2 Gene=g597 Length=595
TCGAAATATGCTCTTACTTTTGTCGGTAAATAATCACGACAATCAACGTGATGGACACGT
GTTAACTTATAAGAATGGAAGAACTTATAAAATGGCAACTGCTTTCCATTTGGCTTGGCC
ATATGGTGTTCCTCGTCTTATGAGTTCATTTAATTTTACAAATCGTGACCAAGGGCCACC
AAGAGATGCTGTAGGCAATATTGTTGCACCAGAATTTAATGCAAATGGACAATGTACAAA
TGGTTGGGTTTGCGAGCATAGATGGCATCAAATTAAAGAAATGGTCAAGTTCAGAAATGT
TGTAGGTTCAGCTGCTGTTGCAAATTGGTGGGATAATGGTGGAAATCAAATTGCTTTTTC
AAGAGGAAATCGTGGGTTTATAGCATTCAATGGTCAATATGGAATAGATTTAAGTCAAAA
TCTACAAACTGGCTTGCCTGCAGGAACTTATTGTGATATTGCCACAGGAATAAAATCAGG
CTCATCATGCACAGGAGGTTCAGTTGTAGTTGGAAGTGATGGTAGAGCAAATATCTTTTT
AAGTGCTACTGTACCTGAAGGATTTTTAGCTATACACGCAGAATCGAGGTTATAA
>g597.t2 Gene=g597 Length=195
MLLLLSVNNHDNQRDGHVLTYKNGRTYKMATAFHLAWPYGVPRLMSSFNFTNRDQGPPRD
AVGNIVAPEFNANGQCTNGWVCEHRWHQIKEMVKFRNVVGSAAVANWWDNGGNQIAFSRG
NRGFIAFNGQYGIDLSQNLQTGLPAGTYCDIATGIKSGSSCTGGSVVVGSDGRANIFLSA
TVPEGFLAIHAESRL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g597.t2 | Gene3D | G3DSA:3.20.20.80 | Glycosidases | 3 | 100 | 0 |
| 7 | g597.t2 | Gene3D | G3DSA:2.60.40.1180 | - | 102 | 195 | 0 |
| 2 | g597.t2 | PANTHER | PTHR43447 | ALPHA-AMYLASE | 7 | 194 | 0 |
| 3 | g597.t2 | PANTHER | PTHR43447:SF7 | ALPHA-AMYLASE | 7 | 194 | 0 |
| 1 | g597.t2 | Pfam | PF02806 | Alpha amylase, C-terminal all-beta domain | 108 | 191 | 0 |
| 6 | g597.t2 | SMART | SM00632 | Aamy_c | 105 | 194 | 0 |
| 5 | g597.t2 | SUPERFAMILY | SSF51445 | (Trans)glycosidases | 4 | 97 | 0 |
| 4 | g597.t2 | SUPERFAMILY | SSF51011 | Glycosyl hydrolase domain | 103 | 194 | 0 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g597/g597.t2; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g597.t2.fa.iupred3.txt does not exist
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