General information for g597.t1
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.t1 | TSS | g597.t1 | 4399335 | 4399335 |
| chr_3 | g597 | g597.t1 | isoform | g597.t1 | 4399353 | 4400977 |
| chr_3 | g597 | g597.t1 | exon | g597.t1.exon1 | 4399353 | 4399981 |
| chr_3 | g597 | g597.t1 | cds | g597.t1.CDS1 | 4399353 | 4399981 |
| chr_3 | g597 | g597.t1 | exon | g597.t1.exon2 | 4400041 | 4400330 |
| chr_3 | g597 | g597.t1 | cds | g597.t1.CDS2 | 4400041 | 4400330 |
| chr_3 | g597 | g597.t1 | exon | g597.t1.exon3 | 4400412 | 4400977 |
| chr_3 | g597 | g597.t1 | cds | g597.t1.CDS3 | 4400412 | 4400977 |
| chr_3 | g597 | g597.t1 | TTS | g597.t1 | 4401030 | 4401030 |
Sequences
>g597.t1 Gene=g597 Length=1485
ATGAAGGAATTAACATTATTGAGTTTCATTCTATTTTCAAGTGCTGTTTTTGCAGCTTAT
ACTGATCCACATTGGTGGACAGGTAGAAGTGCTATGGTTCATTTAATGGATTGGAGATGG
CAAGATATTGCAAGAGAATGTGAAGAATTTCTTGCACCAAATGGATATGCCGGAGTTCAA
GTTTCCCCAGCTAATGAGCACAATATTTTTGATGATCAAAGGTCATGGATGGAAAGATAT
GGCCCAATCAGTTATATTTTAACTACAAGATCGGGAAATCAAGCAGCTTTTGCTGACATG
ACTCGTCGATGTAATGCAGTTGGTGTTAGAATTTATGTAGATGTAGTGTTTAATCATATG
ACTGGCAGTGGCACTTTAGGATCTGCTGGAAACACTGCTGACTTAGTAAATCGAAACTAT
CCAGCAGTTCCTTATACTAGAGAACATTTCAATCCAAGCTGCAACATTTACAATTGGAAT
AATCCATATGAAATTCGTAATTGTGAACTTCTTGGATTGCCCGACCTAAATCAAGGAAAC
GAACATGTTCGCACAAAAATTGTTGAGTTTTTGAACAATTTGATTGATCTTGGTGTTGCA
GGTTTTAGAGTTGATGCAATGAAACACATGTGGCCTGGGGATCTTGAAGTTATTTGGTCT
AGACTAAAAAATTTGAATACAGCTCACGGATTTCCAGCGAATGCAAGACCTTTTGTTGTT
GGTGAAGTTATTGCCGGTTATAGCATTGAAAATGATGGATTTTTAGGAAGTGAATATTTC
CCATTGGGAACAATTACAGAATTCAGATATTCACAAGAAATTTCAAGAGTTTTTAGTGGA
AACGACTTGCTTAAGTGGTTATCAAGCTTCGGTGAAGGATGGGGATTTTGGCCATCGAAA
TATGCTCTTACTTTTGTCGATAATCACGACAATCAACGTGATGGACACGTGTTAACTTAT
AAGAATGGAAGAACTTATAAAATGGCAACTGCTTTCCATTTGGCTTGGCCATATGGTGTT
CCTCGTCTTATGAGTTCATTTAATTTTACAAATCGTGACCAAGGGCCACCAAGAGATGCT
GTAGGCAATATTGTTGCACCAGAATTTAATGCAAATGGACAATGTACAAATGGTTGGGTT
TGCGAGCATAGATGGCATCAAATTAAAGAAATGGTCAAGTTCAGAAATGTTGTAGGTTCA
GCTGCTGTTGCAAATTGGTGGGATAATGGTGGAAATCAAATTGCTTTTTCAAGAGGAAAT
CGTGGGTTTATAGCATTCAATGGTCAATATGGAATAGATTTAAGTCAAAATCTACAAACT
GGCTTGCCTGCAGGAACTTATTGTGATATTGCCACAGGAATAAAATCAGGCTCATCATGC
ACAGGAGGTTCAGTTGTAGTTGGAAGTGATGGTAGAGCAAATATCTTTTTAAGTGCTACT
GTACCTGAAGGATTTTTAGCTATACACGCAGAATCGAGGTTATAA
>g597.t1 Gene=g597 Length=494
MKELTLLSFILFSSAVFAAYTDPHWWTGRSAMVHLMDWRWQDIARECEEFLAPNGYAGVQ
VSPANEHNIFDDQRSWMERYGPISYILTTRSGNQAAFADMTRRCNAVGVRIYVDVVFNHM
TGSGTLGSAGNTADLVNRNYPAVPYTREHFNPSCNIYNWNNPYEIRNCELLGLPDLNQGN
EHVRTKIVEFLNNLIDLGVAGFRVDAMKHMWPGDLEVIWSRLKNLNTAHGFPANARPFVV
GEVIAGYSIENDGFLGSEYFPLGTITEFRYSQEISRVFSGNDLLKWLSSFGEGWGFWPSK
YALTFVDNHDNQRDGHVLTYKNGRTYKMATAFHLAWPYGVPRLMSSFNFTNRDQGPPRDA
VGNIVAPEFNANGQCTNGWVCEHRWHQIKEMVKFRNVVGSAAVANWWDNGGNQIAFSRGN
RGFIAFNGQYGIDLSQNLQTGLPAGTYCDIATGIKSGSSCTGGSVVVGSDGRANIFLSAT
VPEGFLAIHAESRL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 19 | g597.t1 | CDD | cd11317 | AmyAc_bac_euk_AmyA | 29 | 398 | 6.06281E-177 |
| 13 | g597.t1 | Gene3D | G3DSA:3.20.20.80 | Glycosidases | 20 | 399 | 3.5E-162 |
| 12 | g597.t1 | Gene3D | G3DSA:2.60.40.1180 | - | 401 | 494 | 1.5E-32 |
| 3 | g597.t1 | PANTHER | PTHR43447 | ALPHA-AMYLASE | 18 | 493 | 2.4E-155 |
| 4 | g597.t1 | PANTHER | PTHR43447:SF7 | ALPHA-AMYLASE | 18 | 493 | 2.4E-155 |
| 6 | g597.t1 | PRINTS | PR00110 | Alpha-amylase signature | 76 | 93 | 1.2E-20 |
| 7 | g597.t1 | PRINTS | PR00110 | Alpha-amylase signature | 108 | 119 | 1.2E-20 |
| 5 | g597.t1 | PRINTS | PR00110 | Alpha-amylase signature | 199 | 210 | 1.2E-20 |
| 8 | g597.t1 | PRINTS | PR00110 | Alpha-amylase signature | 300 | 312 | 1.2E-20 |
| 2 | g597.t1 | Pfam | PF00128 | Alpha amylase, catalytic domain | 91 | 334 | 3.3E-17 |
| 1 | g597.t1 | Pfam | PF02806 | Alpha amylase, C-terminal all-beta domain | 407 | 490 | 1.1E-11 |
| 15 | g597.t1 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 18 | - |
| 16 | g597.t1 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 3 | - |
| 17 | g597.t1 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 4 | 12 | - |
| 18 | g597.t1 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 13 | 18 | - |
| 14 | g597.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 19 | 494 | - |
| 21 | g597.t1 | SMART | SM00642 | aamy | 30 | 395 | 6.3E-79 |
| 22 | g597.t1 | SMART | SM00632 | Aamy_c | 404 | 493 | 2.3E-38 |
| 10 | g597.t1 | SUPERFAMILY | SSF51445 | (Trans)glycosidases | 22 | 396 | 1.06E-91 |
| 9 | g597.t1 | SUPERFAMILY | SSF51011 | Glycosyl hydrolase domain | 402 | 493 | 1.96E-32 |
| 11 | g597.t1 | SignalP_EUK | SignalP-noTM | SignalP-noTM | 1 | 18 | - |
| 20 | g597.t1 | 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.
Data is missing for g597/g597.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g597.t1.fa.iupred3.txt does not exist
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