General information for g17506.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 g17506 is located on chr_4: 13695826..13697516 (- 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_4 | g17506 | g17506.t1 | isoform | g17506.t1 | 13695826 | 13697516 |
| chr_4 | g17506 | g17506.t1 | exon | g17506.t1.exon1 | 13695826 | 13696103 |
| chr_4 | g17506 | g17506.t1 | cds | g17506.t1.CDS1 | 13695826 | 13696103 |
| chr_4 | g17506 | g17506.t1 | exon | g17506.t1.exon2 | 13696216 | 13696401 |
| chr_4 | g17506 | g17506.t1 | cds | g17506.t1.CDS2 | 13696216 | 13696401 |
| chr_4 | g17506 | g17506.t1 | exon | g17506.t1.exon3 | 13696690 | 13696950 |
| chr_4 | g17506 | g17506.t1 | cds | g17506.t1.CDS3 | 13696690 | 13696950 |
| chr_4 | g17506 | g17506.t1 | exon | g17506.t1.exon4 | 13697018 | 13697118 |
| chr_4 | g17506 | g17506.t1 | cds | g17506.t1.CDS4 | 13697018 | 13697118 |
| chr_4 | g17506 | g17506.t1 | exon | g17506.t1.exon5 | 13697179 | 13697248 |
| chr_4 | g17506 | g17506.t1 | cds | g17506.t1.CDS5 | 13697179 | 13697248 |
| chr_4 | g17506 | g17506.t1 | exon | g17506.t1.exon6 | 13697303 | 13697403 |
| chr_4 | g17506 | g17506.t1 | cds | g17506.t1.CDS6 | 13697303 | 13697403 |
| chr_4 | g17506 | g17506.t1 | exon | g17506.t1.exon7 | 13697464 | 13697516 |
| chr_4 | g17506 | g17506.t1 | cds | g17506.t1.CDS7 | 13697464 | 13697516 |
| chr_4 | g17506 | g17506.t1 | TSS | g17506.t1 | NA | NA |
| chr_4 | g17506 | g17506.t1 | TTS | g17506.t1 | NA | NA |
Sequences
>g17506.t1 Gene=g17506 Length=1050
ATGAAGGCATTGGTTTTATTTTTTGCTTTCTTGGCACTTGTAAACGCTCAATGGGATACG
CATTGGTGGAGTGGTCGAAGTGGAATTGTACATCTCTTTGAATGGAAATGGAATGATATT
GCAAATGAATGTGAAACATTTTTAGCTCCTAATGGTTTTGCTGGTGTACAAACATCTGTT
CCAATTGAAAATGTCATAGCACAAGGAAGACCATGGTGGGAAAGATATCAACCAGTTTCA
TACAAACTTGAAACTCGTTCAGGAAATAGACAACAATTTGCTGACATGGTACGTCGTTGC
AATGCTGGAGTTCGAATTTATCCTGACGTAATTATCAACCACATGGCAGCCATGGATGGA
GTTGGAACTGGTGGAAGTATTTCACAAGTTAGTAATTATAATTTCCCAGCTGTGCCTTAT
TCAAGTTATGATTTTAATCCACGATGTGGTATTTACAATTATGGTAATGTTAATGAAGTA
AGAAATTGTTGGTTGCAAGGATTGTCAGATTTGGCAGCACATACTGAATATGTAAGAATA
AAAACTTCAGAATATTTAAATGATTTGATTGATCTTGGTGTTGCTGCTCATGGATTTCCA
GCTAATGCTCGTCCTTTCATTGCTCAAGAAGTTATTGATCTTGGTGGTGAAGCAATCAGT
CGTGATGAATATTTACACATTGGAACAATCACAGAATTCAAATTTAGTGCTGAAATTGGT
CGAGTTTTTAGAGGCTATGATCAATTGAAACATTTGAGTAATTTTGGTGAAGGAGTTCAA
AATTGGTGGGATAATGGTGGAAATGAAATTGCTTTTTCACATGGAAATCGTGGATTTATT
GCATTCAATTTGAATAATCATGACATTAATAGAACATTCTACACTGGACTTTCTGCTGGC
ACTTATTGTGATGTTGCATCAGGCAGTAAAGTTGGATCTTCATGCAGTGGAAAATCAGTT
ACAGTTGATGGAAGTGGAAATGCTTTCATTAATTTACCTTATAATGTTGAAGATGGTTTT
CTTGCCATTCATGTTGATGCTAAATTGTAA
>g17506.t1 Gene=g17506 Length=349
MKALVLFFAFLALVNAQWDTHWWSGRSGIVHLFEWKWNDIANECETFLAPNGFAGVQTSV
PIENVIAQGRPWWERYQPVSYKLETRSGNRQQFADMVRRCNAGVRIYPDVIINHMAAMDG
VGTGGSISQVSNYNFPAVPYSSYDFNPRCGIYNYGNVNEVRNCWLQGLSDLAAHTEYVRI
KTSEYLNDLIDLGVAAHGFPANARPFIAQEVIDLGGEAISRDEYLHIGTITEFKFSAEIG
RVFRGYDQLKHLSNFGEGVQNWWDNGGNEIAFSHGNRGFIAFNLNNHDINRTFYTGLSAG
TYCDVASGSKVGSSCSGKSVTVDGSGNAFINLPYNVEDGFLAIHVDAKL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 15 | g17506.t1 | Gene3D | G3DSA:3.20.20.80 | Glycosidases | 18 | 199 | 8.6E-74 |
| 14 | g17506.t1 | Gene3D | G3DSA:2.60.40.1180 | - | 257 | 349 | 4.9E-34 |
| 3 | g17506.t1 | PANTHER | PTHR43447 | ALPHA-AMYLASE | 4 | 197 | 3.6E-100 |
| 6 | g17506.t1 | PANTHER | PTHR43447:SF5 | PANCREATIC ALPHA-AMYLASE | 4 | 197 | 3.6E-100 |
| 4 | g17506.t1 | PANTHER | PTHR43447 | ALPHA-AMYLASE | 199 | 258 | 3.6E-100 |
| 7 | g17506.t1 | PANTHER | PTHR43447:SF5 | PANCREATIC ALPHA-AMYLASE | 199 | 258 | 3.6E-100 |
| 2 | g17506.t1 | PANTHER | PTHR43447 | ALPHA-AMYLASE | 256 | 349 | 3.6E-100 |
| 5 | g17506.t1 | PANTHER | PTHR43447:SF5 | PANCREATIC ALPHA-AMYLASE | 256 | 349 | 3.6E-100 |
| 9 | g17506.t1 | PRINTS | PR00110 | Alpha-amylase signature | 72 | 89 | 1.9E-21 |
| 10 | g17506.t1 | PRINTS | PR00110 | Alpha-amylase signature | 103 | 114 | 1.9E-21 |
| 8 | g17506.t1 | PRINTS | PR00110 | Alpha-amylase signature | 206 | 224 | 1.9E-21 |
| 1 | g17506.t1 | Pfam | PF02806 | Alpha amylase, C-terminal all-beta domain | 263 | 334 | 7.7E-10 |
| 17 | g17506.t1 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 16 | - |
| 18 | g17506.t1 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 2 | - |
| 19 | g17506.t1 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 3 | 11 | - |
| 20 | g17506.t1 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 12 | 16 | - |
| 16 | g17506.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 17 | 349 | - |
| 22 | g17506.t1 | SMART | SM00642 | aamy | 27 | 346 | 1.6E-19 |
| 23 | g17506.t1 | SMART | SM00632 | Aamy_c | 260 | 348 | 1.1E-39 |
| 12 | g17506.t1 | SUPERFAMILY | SSF51445 | (Trans)glycosidases | 19 | 293 | 2.61E-49 |
| 11 | g17506.t1 | SUPERFAMILY | SSF51011 | Glycosyl hydrolase domain | 258 | 348 | 2.09E-32 |
| 13 | g17506.t1 | SignalP_EUK | SignalP-noTM | SignalP-noTM | 1 | 16 | - |
| 21 | g17506.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 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