General information for g6053.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Alpha-amylase B.
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.t1 | TSS | g6053.t1 | 13890242 | 13890242 |
| chr_2 | g6053 | g6053.t1 | isoform | g6053.t1 | 13890291 | 13892251 |
| chr_2 | g6053 | g6053.t1 | exon | g6053.t1.exon1 | 13890291 | 13890343 |
| chr_2 | g6053 | g6053.t1 | cds | g6053.t1.CDS1 | 13890291 | 13890343 |
| chr_2 | g6053 | g6053.t1 | exon | g6053.t1.exon2 | 13890409 | 13890509 |
| chr_2 | g6053 | g6053.t1 | cds | g6053.t1.CDS2 | 13890409 | 13890509 |
| chr_2 | g6053 | g6053.t1 | exon | g6053.t1.exon3 | 13890563 | 13890632 |
| chr_2 | g6053 | g6053.t1 | cds | g6053.t1.CDS3 | 13890563 | 13890632 |
| chr_2 | g6053 | g6053.t1 | exon | g6053.t1.exon4 | 13890692 | 13890915 |
| chr_2 | g6053 | g6053.t1 | cds | g6053.t1.CDS4 | 13890692 | 13890915 |
| chr_2 | g6053 | g6053.t1 | exon | g6053.t1.exon5 | 13890977 | 13891117 |
| chr_2 | g6053 | g6053.t1 | cds | g6053.t1.CDS5 | 13890977 | 13891117 |
| chr_2 | g6053 | g6053.t1 | exon | g6053.t1.exon6 | 13891182 | 13891204 |
| chr_2 | g6053 | g6053.t1 | cds | g6053.t1.CDS6 | 13891182 | 13891204 |
| chr_2 | g6053 | g6053.t1 | exon | g6053.t1.exon7 | 13891263 | 13891506 |
| chr_2 | g6053 | g6053.t1 | cds | g6053.t1.CDS7 | 13891263 | 13891506 |
| chr_2 | g6053 | g6053.t1 | exon | g6053.t1.exon8 | 13891629 | 13892251 |
| chr_2 | g6053 | g6053.t1 | cds | g6053.t1.CDS8 | 13891629 | 13892251 |
| chr_2 | g6053 | g6053.t1 | TTS | g6053.t1 | 13892345 | 13892345 |
Sequences
>g6053.t1 Gene=g6053 Length=1479
ATGAAACTTTTAGTTGTAATTTTGAGCATTTTTGTAGCTGTCAATGCTCAATGGGACACT
CATTGGTGGAGTGGTCGAAGTGGAATTGTTCATTTATTTGAGTGGAAATGGAATGATATT
GCAAATGAATGTGAAACATTCTTAGCACCAAATGGTTACGCGGGAGTCCAAACTTCACCT
CCGTCAGAAAATTTAGTCATCGGAAATCGACCCTGGTGGGAAAGATATCAGCCAGTTTCA
TATCATTTGAATACACGATCAGGTGATAGAAATGCATTCGCTGATATGGTTAGACGATGC
AATGCTGTTGGTATTCGTATCTATCCTGATGTTGTAATTAATCATATGGCGGCTGGTGAT
GGTTATGGAACAGGCGGAAGTGAATCTAGAGTTAGCCAATTAAGCTTCCCAGCTGTTCCA
TATGGAAGTAATGACTTCAATCCAAGATGTGATATCACTAATTACAATGATCCATATCAA
GTTAGAAACTGCTGGCTTGTTGGTTTATCTGATCTTAAGACAGGAAGTGATTATGTCCGT
CAGAAAATTGCCGATTTCTTAAATGATTTGATTAGTCTTGGTGTTGCAGGTTTTCGTATT
GATGCCGTAAAGCACATGTGGCCAGCAGATGTTCAGAATATTGTCTCACGCCTCAACAAT
TTGAACACAAACCACGGTTTCCCAGCCAACGCCCGTCCATTTATCACACAGGAAGTTATT
GATTTGGGTGGTGAAGCAATTAAAAAAGACGAATATTTGCACATTGGAACAATCACAGAG
TTTAGATACAGTGCTGAAATTGGACGAGTTTTCCGTGGTTATGATTTATTGAAATATCTT
AAGAACTTTGGTGAAGGATGGGGTTTTATGGCATCAGCATCAGCTCTTACTTTTGTTGAC
AATCACGACAACCAGAGAGGACATGGAGCGGGAGGTGCCAATGTTCTCACATATAAAGTC
TCAAAGAATTACAAAATGGCAACAGCTTTCCATCTCGCATGGAATTACGGAATTCCTCGT
ATCATGAGTAGCTTTGCTTTCAATGATGGCGATCAAGGTCCACCAGCTGATGGCTATGGT
AATTTGAAATCACCAGAATTTAATTCAGAAGGAGCTTGCACTAATGGATGGGTTTGCGAA
CATCGTTGGAGACAAATTTACAACATGGTTAAATTCCGTAATGCAGCTGGTGGTGCAGCT
GTACAAAATTGGTGGGAAAATGGAAGCGGAAAACAGATTGCTTTCTCACGTGGCAACAGA
GCTTTCATTGCCTTTAATTTGGACTCATATGGCATCAATCAAAATTTGTACACAGGATTA
CCAGCTGGAACTTATTGTGAAATTGCATCAGGAAGCAAGAGCGGTTCAAGTTGCACAGGA
AAAACAATTACAGTCGATGGCAGTGGAAATGCCTACATTGATTTACCACACAATGCTGAC
GACGGTTTTGTTGCAATTCATGTTGATGCGAAATTGTAA
>g6053.t1 Gene=g6053 Length=492
MKLLVVILSIFVAVNAQWDTHWWSGRSGIVHLFEWKWNDIANECETFLAPNGYAGVQTSP
PSENLVIGNRPWWERYQPVSYHLNTRSGDRNAFADMVRRCNAVGIRIYPDVVINHMAAGD
GYGTGGSESRVSQLSFPAVPYGSNDFNPRCDITNYNDPYQVRNCWLVGLSDLKTGSDYVR
QKIADFLNDLISLGVAGFRIDAVKHMWPADVQNIVSRLNNLNTNHGFPANARPFITQEVI
DLGGEAIKKDEYLHIGTITEFRYSAEIGRVFRGYDLLKYLKNFGEGWGFMASASALTFVD
NHDNQRGHGAGGANVLTYKVSKNYKMATAFHLAWNYGIPRIMSSFAFNDGDQGPPADGYG
NLKSPEFNSEGACTNGWVCEHRWRQIYNMVKFRNAAGGAAVQNWWENGSGKQIAFSRGNR
AFIAFNLDSYGINQNLYTGLPAGTYCEIASGSKSGSSCTGKTITVDGSGNAYIDLPHNAD
DGFVAIHVDAKL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 20 | g6053.t1 | CDD | cd11317 | AmyAc_bac_euk_AmyA | 26 | 396 | 0.0 |
| 14 | g6053.t1 | Gene3D | G3DSA:3.20.20.80 | Glycosidases | 18 | 398 | 4.5E-176 |
| 13 | g6053.t1 | Gene3D | G3DSA:2.60.40.1180 | - | 399 | 492 | 2.0E-33 |
| 3 | g6053.t1 | PANTHER | PTHR43447 | ALPHA-AMYLASE | 16 | 492 | 1.4E-172 |
| 4 | g6053.t1 | PANTHER | PTHR43447:SF7 | ALPHA-AMYLASE | 16 | 492 | 1.4E-172 |
| 7 | g6053.t1 | PRINTS | PR00110 | Alpha-amylase signature | 72 | 89 | 4.9E-33 |
| 6 | g6053.t1 | PRINTS | PR00110 | Alpha-amylase signature | 104 | 115 | 4.9E-33 |
| 9 | g6053.t1 | PRINTS | PR00110 | Alpha-amylase signature | 195 | 206 | 4.9E-33 |
| 5 | g6053.t1 | PRINTS | PR00110 | Alpha-amylase signature | 234 | 252 | 4.9E-33 |
| 8 | g6053.t1 | PRINTS | PR00110 | Alpha-amylase signature | 293 | 305 | 4.9E-33 |
| 2 | g6053.t1 | Pfam | PF00128 | Alpha amylase, catalytic domain | 82 | 335 | 9.1E-15 |
| 1 | g6053.t1 | Pfam | PF02806 | Alpha amylase, C-terminal all-beta domain | 407 | 477 | 5.4E-13 |
| 16 | g6053.t1 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 16 | - |
| 17 | g6053.t1 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 2 | - |
| 18 | g6053.t1 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 3 | 11 | - |
| 19 | g6053.t1 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 12 | 16 | - |
| 15 | g6053.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 17 | 492 | - |
| 22 | g6053.t1 | SMART | SM00642 | aamy | 27 | 393 | 4.4E-98 |
| 23 | g6053.t1 | SMART | SM00632 | Aamy_c | 402 | 491 | 3.2E-43 |
| 11 | g6053.t1 | SUPERFAMILY | SSF51445 | (Trans)glycosidases | 19 | 395 | 1.38E-101 |
| 10 | g6053.t1 | SUPERFAMILY | SSF51011 | Glycosyl hydrolase domain | 401 | 491 | 9.16E-32 |
| 12 | g6053.t1 | SignalP_EUK | SignalP-noTM | SignalP-noTM | 1 | 16 | - |
| 21 | g6053.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.
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 transcript has been annotated with K01176 (alpha-amylase)
Pathway
- This transcript belongs to the following pathways
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