General information for g598.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 g598 is located on chr_3: 4401358..4403092 (+ 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 | g598 | g598.t1 | TSS | g598.t1 | 4401342 | 4401342 |
| chr_3 | g598 | g598.t1 | isoform | g598.t1 | 4401358 | 4403092 |
| chr_3 | g598 | g598.t1 | exon | g598.t1.exon1 | 4401358 | 4401958 |
| chr_3 | g598 | g598.t1 | cds | g598.t1.CDS1 | 4401358 | 4401958 |
| chr_3 | g598 | g598.t1 | exon | g598.t1.exon2 | 4402011 | 4402038 |
| chr_3 | g598 | g598.t1 | cds | g598.t1.CDS2 | 4402011 | 4402038 |
| chr_3 | g598 | g598.t1 | exon | g598.t1.exon3 | 4402100 | 4402346 |
| chr_3 | g598 | g598.t1 | cds | g598.t1.CDS3 | 4402100 | 4402346 |
| chr_3 | g598 | g598.t1 | exon | g598.t1.exon4 | 4402411 | 4402453 |
| chr_3 | g598 | g598.t1 | cds | g598.t1.CDS4 | 4402411 | 4402453 |
| chr_3 | g598 | g598.t1 | exon | g598.t1.exon5 | 4402524 | 4403092 |
| chr_3 | g598 | g598.t1 | cds | g598.t1.CDS5 | 4402524 | 4403092 |
| chr_3 | g598 | g598.t1 | TTS | g598.t1 | 4403179 | 4403179 |
Sequences
>g598.t1 Gene=g598 Length=1488
ATGAAGGAATTAACATTATTAAGTTTCATTCTATTTTCAAGTACTACTTTTGCAGCTTAT
ACTGATCCACATTGGTGGACAGGTAGAAGTGCTATGGTTCATTTAATGGATTGGAGATGG
CAAGATATTGCAAGAGAATGTGAAGAATTTCTTGCACCAAATGGATATGCCGGAGTTCAA
GTTTCCCCAGCTAATGAGCACAATATTTTTGATGATCAAAGGTCATGGATGGAAAGATAT
GGCCCAATTAGCTATAATATAACTACACGCTCAGGCAATGAAGCAGCTTTTGCTGACATG
ACTCGTCGATGTAATGCTGTTGGTGTTAGAATTTATGTAGATGTAGTGTTTAATCATATG
ACTGGCAGTGGCACTTTAGGATCTGCTGGAAACACTGCTGATCCTGCTAACCTTTACTAT
CCAGCTGTGCCATATACAAGTGAACATTTTAATCCTTATTGTACAGTCACTGATTGGAGC
AATATTTATCAAATACGCAATTGTCAATTTCCTGGATTGCCTGACCTAAATCAAGGTCAT
GAACATGTACGAGCAAAAATAGCAGATTATCTTAATAATTTAATTAGACTTGGTGTCGCA
GGATTTCGTGTGGATATAATGAAGCACATGTGGCCACAGGATCTTGAAGTAATTTGGTCA
AGAATGAATAATCTCAATACTTTACATGGCTTTGCATCAAATTCACGACCATTTGTTGTT
GGTGAAGTTACTGATGGTCATGATTTAGAAAAACATGGATTTTTAGGAAGTGAATATTTT
CCACTTGGAACAATTACAGAATTTAGATTTTCTGAGGAAATTTCAAGAGTTTTTAGTGGA
AGAGATCAATTGAAATGGCTTCAATCTTTTGGTGAGGGGTGGGGATTTTGGCCGTCAAAA
TATTCTTTAACATTTGTTGATAATCACGACAATCAACGCGACGATCCAAATGTGTTAACA
TACAAAGATGGAAGATTGTATAAAATGGCAACTGCTTTCCATTTGGCTTGGCCATATGGT
GTTCCACGTATTATGAGTTCATTCAATTTTACAAATCGCGATCAAGGACCACCAAGAGAT
GCTGTAGGCAATATTGTTGCACCACAATTTAATGCAAATGGACAATGTACAAATGGTTGG
GTTTGCGAGCATAGATGGCATCAAATCAAAGAAATGGTCAAGTTCAGAAATGTCGTAGGT
TCAGCTGCTGTTGCAAATTGGTGGGATAATGGTGGAAATCAAATTGCTTTTTCAAGAGGA
AATCGCGGTTTTATTGCATTTAATGGTCAATATGGAATTGATTTAAGTCAAAATCTACAA
ACTGGCTTGCCTGCAGGAACTTATTGTGATATTGCCACAGGAATAAAATCAGGAGCATCA
TGCACAGGAGGTTCAGTTGTAATTGGAAGTGATGGTAGAGCAAATATCTTTTTAAGTGCT
ACTGTACCTGAAGGATTTTTAGCTATACATGCAGAATCGAGATTGTAA
>g598.t1 Gene=g598 Length=495
MKELTLLSFILFSSTTFAAYTDPHWWTGRSAMVHLMDWRWQDIARECEEFLAPNGYAGVQ
VSPANEHNIFDDQRSWMERYGPISYNITTRSGNEAAFADMTRRCNAVGVRIYVDVVFNHM
TGSGTLGSAGNTADPANLYYPAVPYTSEHFNPYCTVTDWSNIYQIRNCQFPGLPDLNQGH
EHVRAKIADYLNNLIRLGVAGFRVDIMKHMWPQDLEVIWSRMNNLNTLHGFASNSRPFVV
GEVTDGHDLEKHGFLGSEYFPLGTITEFRFSEEISRVFSGRDQLKWLQSFGEGWGFWPSK
YSLTFVDNHDNQRDDPNVLTYKDGRLYKMATAFHLAWPYGVPRIMSSFNFTNRDQGPPRD
AVGNIVAPQFNANGQCTNGWVCEHRWHQIKEMVKFRNVVGSAAVANWWDNGGNQIAFSRG
NRGFIAFNGQYGIDLSQNLQTGLPAGTYCDIATGIKSGASCTGGSVVIGSDGRANIFLSA
TVPEGFLAIHAESRL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 19 | g598.t1 | CDD | cd11317 | AmyAc_bac_euk_AmyA | 29 | 399 | 4.22313E-168 |
| 13 | g598.t1 | Gene3D | G3DSA:3.20.20.80 | Glycosidases | 20 | 400 | 8.4E-159 |
| 12 | g598.t1 | Gene3D | G3DSA:2.60.40.1180 | - | 402 | 495 | 7.6E-32 |
| 3 | g598.t1 | PANTHER | PTHR43447 | ALPHA-AMYLASE | 17 | 494 | 6.8E-150 |
| 4 | g598.t1 | PANTHER | PTHR43447:SF7 | ALPHA-AMYLASE | 17 | 494 | 6.8E-150 |
| 6 | g598.t1 | PRINTS | PR00110 | Alpha-amylase signature | 76 | 93 | 4.7E-20 |
| 7 | g598.t1 | PRINTS | PR00110 | Alpha-amylase signature | 108 | 119 | 4.7E-20 |
| 5 | g598.t1 | PRINTS | PR00110 | Alpha-amylase signature | 199 | 210 | 4.7E-20 |
| 8 | g598.t1 | PRINTS | PR00110 | Alpha-amylase signature | 300 | 312 | 4.7E-20 |
| 2 | g598.t1 | Pfam | PF00128 | Alpha amylase, catalytic domain | 85 | 314 | 9.7E-18 |
| 1 | g598.t1 | Pfam | PF02806 | Alpha amylase, C-terminal all-beta domain | 408 | 491 | 3.1E-11 |
| 15 | g598.t1 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 18 | - |
| 16 | g598.t1 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 3 | - |
| 17 | g598.t1 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 4 | 12 | - |
| 18 | g598.t1 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 13 | 18 | - |
| 14 | g598.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 19 | 495 | - |
| 21 | g598.t1 | SMART | SM00642 | aamy | 30 | 396 | 4.0E-77 |
| 22 | g598.t1 | SMART | SM00632 | Aamy_c | 405 | 494 | 2.8E-36 |
| 10 | g598.t1 | SUPERFAMILY | SSF51445 | (Trans)glycosidases | 22 | 397 | 1.65E-89 |
| 9 | g598.t1 | SUPERFAMILY | SSF51011 | Glycosyl hydrolase domain | 403 | 494 | 1.77E-31 |
| 11 | g598.t1 | SignalP_EUK | SignalP-noTM | SignalP-noTM | 1 | 18 | - |
| 20 | g598.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 g598/g598.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g598.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