General information for g4715.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 g4715 is located on chr_2: 4359278..4361336 (- 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 | g4715 | g4715.t1 | TTS | g4715.t1 | 4358730 | 4358730 |
| chr_2 | g4715 | g4715.t1 | isoform | g4715.t1 | 4358892 | 4361336 |
| chr_2 | g4715 | g4715.t1 | exon | g4715.t1.exon1 | 4358892 | 4359781 |
| chr_2 | g4715 | g4715.t1 | cds | g4715.t1.CDS1 | 4358892 | 4359781 |
| chr_2 | g4715 | g4715.t1 | exon | g4715.t1.exon2 | 4359843 | 4359853 |
| chr_2 | g4715 | g4715.t1 | cds | g4715.t1.CDS2 | 4359843 | 4359853 |
| chr_2 | g4715 | g4715.t1 | exon | g4715.t1.exon3 | 4360277 | 4360567 |
| chr_2 | g4715 | g4715.t1 | cds | g4715.t1.CDS3 | 4360277 | 4360567 |
| chr_2 | g4715 | g4715.t1 | exon | g4715.t1.exon4 | 4360966 | 4361336 |
| chr_2 | g4715 | g4715.t1 | cds | g4715.t1.CDS4 | 4360966 | 4361336 |
| chr_2 | g4715 | g4715.t1 | TSS | g4715.t1 | 4361363 | 4361363 |
Sequences
>g4715.t1 Gene=g4715 Length=1563
ATGCTTCGATCATTGCAATTGCTTCTCGGTGCAATTTGTTGTAGTGAATTTTTTATTCCT
CGTCCACAAGTTGCAGATTTACCAAAAGAAGTGAAGAGAAATTTTACTGATCCTCATTTT
TTAAGTGGTCATAATGGAATTGTGCAATTATTTGAATGGAAATGGTTAGATATAGCAAAA
GAATGTGAAGAATTTCTCGGTCCAAGGAAATTTGGTGGAGTTCAAATTTCTCCACCTAAT
GAAAATATTATTATTGAAAATAGACCGTGGTTCGAAAGATATCAACCAATTTCTTATAAA
ATTGCATCAAGATCTGGAAGTGAAAAAGAATTTTTAGAAATGACAAGACGATGCAATGCT
GTTGGTGTTAGAATTTATGCAGATATTGTCATAAATCATATGGCAGCTGATCAAGTAAAG
TACATAGCAAACGGCACAGGTGGATCACAAGCAATTCCTGCAGTTCGAAATTATCCAGCT
GTTCCTTATAGTATTTTTAATTTTCATCCAACTTGTGCAATTGTCAATTATCAGGATCCG
TATCAAGTCAGAAATTGTGAACTCGTTGGATTGCATGATCTTAATCAGACAATAGAAAAT
ACTAGAGATAGAATTGTTGAATATTTGAATCATTTGATTGATCTGGGAGTTGCTGGATTT
CGATATGATGCAGCTAAACACATGTGGCCAAAAGATCTTGAAATCATCACAAATCGAGTC
AAAAATTTAAATACAATCTTTGGTTTTGGACCAAATCTTGATCCATTTGTATATCAAGAA
GTGATTGATAATGGCAATGAGCCAATTAGTAAATATGAGTACACTTATGCTTGTGTCACA
GAATTTCGTTTCTCATCTGAAATTGGCAAAGCATTTACAGGCGGTGATGAGCTTAGATGG
CTGATTGGCTTTGGTGAAAAATGGGATTTATTGCCATCACATTTGGCAGTGACTTTTATT
GATAATCATGATTCACAAAGAAGTGGTAGCAATGATATTTTAACATACAAAAGAAGGAAA
AATTATATAATGGCTCAAGCATTTTCTTTAGCACATCCTTATGGCATTAAAAGAATTATG
AGTTCATTTTCATTCAATGACAATAATCAAGGACCACCAGCAGATGCCAATGGAACTATA
ATTTCACCAACAATAGATAAAAATGGAAATTGTACTAATGGTTGGGTTTGTGAACATCGA
TGGCGAGCTATTGCTTCTATGGTTGATTTTATTGATATTGTTGATGGTGAAAATGTTACA
TCATGGTGGGATAATGGAAAAAATCAAATTGCTTTTTCACGTGGATCAAAAGGCTTTATT
GTATTCAATCTTGATAGTGATGATATGTTCAATGTTCCAATTGAAACAACAATGAAAAGT
GGAATTTATTGTGACATAATTACAGGAGAGAAAATTTCAGATTTTGAATGTTCAGGAAAG
AAACTTGAAGTTGATGAAGATGGAATTGTAATTATTGATTTAGATTCTGATGATGAAAAT
GGAGTTATGGCGATTCATATCAATCAAGAGATAAAAAATATTAAAAATTTTGTAAATATT
TGA
>g4715.t1 Gene=g4715 Length=520
MLRSLQLLLGAICCSEFFIPRPQVADLPKEVKRNFTDPHFLSGHNGIVQLFEWKWLDIAK
ECEEFLGPRKFGGVQISPPNENIIIENRPWFERYQPISYKIASRSGSEKEFLEMTRRCNA
VGVRIYADIVINHMAADQVKYIANGTGGSQAIPAVRNYPAVPYSIFNFHPTCAIVNYQDP
YQVRNCELVGLHDLNQTIENTRDRIVEYLNHLIDLGVAGFRYDAAKHMWPKDLEIITNRV
KNLNTIFGFGPNLDPFVYQEVIDNGNEPISKYEYTYACVTEFRFSSEIGKAFTGGDELRW
LIGFGEKWDLLPSHLAVTFIDNHDSQRSGSNDILTYKRRKNYIMAQAFSLAHPYGIKRIM
SSFSFNDNNQGPPADANGTIISPTIDKNGNCTNGWVCEHRWRAIASMVDFIDIVDGENVT
SWWDNGKNQIAFSRGSKGFIVFNLDSDDMFNVPIETTMKSGIYCDIITGEKISDFECSGK
KLEVDEDGIVIIDLDSDDENGVMAIHINQEIKNIKNFVNI
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 21 | g4715.t1 | CDD | cd11317 | AmyAc_bac_euk_AmyA | 44 | 410 | 0.0 |
| 15 | g4715.t1 | Coils | Coil | Coil | 191 | 211 | - |
| 14 | g4715.t1 | Gene3D | G3DSA:3.20.20.80 | Glycosidases | 35 | 416 | 1.4E-159 |
| 13 | g4715.t1 | Gene3D | G3DSA:2.60.40.1180 | - | 417 | 518 | 1.5E-28 |
| 3 | g4715.t1 | PANTHER | PTHR43447 | ALPHA-AMYLASE | 32 | 509 | 2.0E-143 |
| 4 | g4715.t1 | PANTHER | PTHR43447:SF7 | ALPHA-AMYLASE | 32 | 509 | 2.0E-143 |
| 7 | g4715.t1 | PRINTS | PR00110 | Alpha-amylase signature | 90 | 107 | 2.8E-30 |
| 6 | g4715.t1 | PRINTS | PR00110 | Alpha-amylase signature | 122 | 133 | 2.8E-30 |
| 5 | g4715.t1 | PRINTS | PR00110 | Alpha-amylase signature | 217 | 228 | 2.8E-30 |
| 8 | g4715.t1 | PRINTS | PR00110 | Alpha-amylase signature | 256 | 274 | 2.8E-30 |
| 9 | g4715.t1 | PRINTS | PR00110 | Alpha-amylase signature | 314 | 326 | 2.8E-30 |
| 2 | g4715.t1 | Pfam | PF00128 | Alpha amylase, catalytic domain | 99 | 331 | 2.7E-12 |
| 1 | g4715.t1 | Pfam | PF02806 | Alpha amylase, C-terminal all-beta domain | 423 | 494 | 3.6E-9 |
| 17 | g4715.t1 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 25 | - |
| 18 | g4715.t1 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 3 | - |
| 19 | g4715.t1 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 4 | 14 | - |
| 20 | g4715.t1 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 15 | 25 | - |
| 16 | g4715.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 26 | 520 | - |
| 22 | g4715.t1 | SMART | SM00642 | aamy | 45 | 411 | 1.9E-76 |
| 23 | g4715.t1 | SMART | SM00632 | Aamy_c | 420 | 510 | 1.6E-24 |
| 11 | g4715.t1 | SUPERFAMILY | SSF51445 | (Trans)glycosidases | 42 | 410 | 1.17E-93 |
| 10 | g4715.t1 | SUPERFAMILY | SSF51011 | Glycosyl hydrolase domain | 418 | 510 | 9.6E-25 |
| 12 | g4715.t1 | SignalP_EUK | SignalP-noTM | SignalP-noTM | 1 | 16 | - |
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 |
| 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.
