General information for g7793.t3
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Alpha-amylase B.
Parent gene
- The parent gene g7793 is located on chr_2: 26140939..26141476 (+ 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 | g7793 | g7793.t3 | TSS | g7793.t3 | 26139344 | 26139344 |
| chr_2 | g7793 | g7793.t3 | isoform | g7793.t3 | 26139360 | 26141476 |
| chr_2 | g7793 | g7793.t3 | exon | g7793.t3.exon1 | 26139360 | 26139411 |
| chr_2 | g7793 | g7793.t3 | exon | g7793.t3.exon2 | 26139519 | 26139684 |
| chr_2 | g7793 | g7793.t3 | exon | g7793.t3.exon3 | 26139759 | 26139929 |
| chr_2 | g7793 | g7793.t3 | exon | g7793.t3.exon4 | 26140080 | 26140264 |
| chr_2 | g7793 | g7793.t3 | cds | g7793.t3.CDS1 | 26140219 | 26140264 |
| chr_2 | g7793 | g7793.t3 | exon | g7793.t3.exon5 | 26140354 | 26140376 |
| chr_2 | g7793 | g7793.t3 | cds | g7793.t3.CDS2 | 26140354 | 26140376 |
| chr_2 | g7793 | g7793.t3 | exon | g7793.t3.exon6 | 26140441 | 26140568 |
| chr_2 | g7793 | g7793.t3 | cds | g7793.t3.CDS3 | 26140441 | 26140568 |
| chr_2 | g7793 | g7793.t3 | exon | g7793.t3.exon7 | 26140633 | 26140680 |
| chr_2 | g7793 | g7793.t3 | cds | g7793.t3.CDS4 | 26140633 | 26140680 |
| chr_2 | g7793 | g7793.t3 | exon | g7793.t3.exon8 | 26140742 | 26140850 |
| chr_2 | g7793 | g7793.t3 | cds | g7793.t3.CDS5 | 26140742 | 26140850 |
| chr_2 | g7793 | g7793.t3 | exon | g7793.t3.exon9 | 26140907 | 26141476 |
| chr_2 | g7793 | g7793.t3 | cds | g7793.t3.CDS6 | 26140907 | 26141476 |
| chr_2 | g7793 | g7793.t3 | TTS | g7793.t3 | 26141539 | 26141539 |
Sequences
>g7793.t3 Gene=g7793 Length=1452
ATGAAAGTGTTTTTAGTTTTTCTTTCCATTGTGCTGACTATTACATTTTCTAGATCCTCA
TTATGCATCTAATAGAAATGTTATGGTTCATCTATTTGAATGGAAATGGAAAGATATTGC
TGAAGAATGTGAAACATTTCTTGCACCAAATGGATTTGCAGGGGTGCAAGTGAGTCCACC
AACTGAAAATACTGCAATTCATCTTGACTGGCTATCAACTATTCGCCCATGGTGGGAACG
TTACCAGCCGATAAGCTATAAATTAGAAACACGCTCAGGAAATGAAGCTGCTTTTGCTGA
TATGGTTCGACGATGCAATGCTGTTGGTGTTCGTATTTACGTTGATATTTTACTAAATCA
TATGAGTGCGACTAATGGTACAGGAACTGGTTGAATTTAAATTGTCATTAATTACTTTAA
ACTTAGTTTTCTAATTACAGTCTTGATTGGAATTCACAACAGAGTATTCGAAATTGTTGG
CTTGTTGGTTTACCTGATTTAAATCAAAAGCGAGCGCACGTTAGAGACATGCAAATTAAC
TTACTAAATCATCTCATTGATCTCGGAGTTGCTGGCTTTAGGGTTGATGCTGCTAAGCAC
ATGTGGGCTGAAGACCTTGAGTATATTTTCAGTAGAATGCATAATTTAAACACAAATCAT
GGTTTCCATGCCAACAGTCGTCCTTTCGTTGTGCAAGAAGTCATCGTAGGTGATGGCATT
TATATGGATCATTATACACATTTGGGTGCTGTCACTGTTTTTGAAGCAAGCAGAATTATG
GGACAAGTTTTGCGTGGACATGCTGACATCAATGATTTAAGATATTTCAGTTCACGTTTT
GGAATTGAATCTAAAGAAGCTTTAATTTTTGTTGATAACCATGACAATCAACGTGATGGT
GGACTTCCATTAACAAACCATAGAGAACCAAGAATTTACAAAATAGCAACTGCATACAAT
TTAGCTCAAGATTTCGGTCATCAAAGAATTATGAGTTCATTCTATTTTTCACATAGAGAT
CAAGGACCTCCACAGGATGCATCACAAAATATTCTCTCACCAACATTCGATGCTAATGGA
CAATGCACAAATGGTTGGGTTTGTGAGCATCGATGGCCTGCAATTAGAAATATGGTACAA
TTTAGTGCAGCAGTAAAGGGAACAAAAGCAGAAAACTGGTGGACAGGATGGAATGAAATT
GCATTTTCACGCGGCAATCGAGGATTTATTGCAATAAATGCAAAAGATAATGGTGATTCT
ACCAATGTACGGTTATACACTTCACTACCAGCCGGTATTTACTGCGATATGTCGAGTGGA
AATAAAGTTGGCAACAGCTGCACAAGAAAAACTGTTACAGTAGGTTCTGATGGCTATGCT
GATATTTATATTCCAGGCGCATATAGTAACGAGGAAGGATTCATCGCAATTCATGTCGAT
GCGAAACTGTAA
>g7793.t3 Gene=g7793 Length=307
MQINLLNHLIDLGVAGFRVDAAKHMWAEDLEYIFSRMHNLNTNHGFHANSRPFVVQEVIV
GDGIYMDHYTHLGAVTVFEASRIMGQVLRGHADINDLRYFSSRFGIESKEALIFVDNHDN
QRDGGLPLTNHREPRIYKIATAYNLAQDFGHQRIMSSFYFSHRDQGPPQDASQNILSPTF
DANGQCTNGWVCEHRWPAIRNMVQFSAAVKGTKAENWWTGWNEIAFSRGNRGFIAINAKD
NGDSTNVRLYTSLPAGIYCDMSSGNKVGNSCTRKTVTVGSDGYADIYIPGAYSNEEGFIA
IHVDAKL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 11 | g7793.t3 | Gene3D | G3DSA:3.20.20.80 | Glycosidases | 1 | 211 | 0 |
| 10 | g7793.t3 | Gene3D | G3DSA:2.60.40.1180 | - | 213 | 307 | 0 |
| 2 | g7793.t3 | PANTHER | PTHR43447 | ALPHA-AMYLASE | 3 | 307 | 0 |
| 3 | g7793.t3 | PANTHER | PTHR43447:SF7 | ALPHA-AMYLASE | 3 | 307 | 0 |
| 4 | g7793.t3 | PRINTS | PR00110 | Alpha-amylase signature | 14 | 25 | 0 |
| 6 | g7793.t3 | PRINTS | PR00110 | Alpha-amylase signature | 53 | 71 | 0 |
| 5 | g7793.t3 | PRINTS | PR00110 | Alpha-amylase signature | 109 | 121 | 0 |
| 1 | g7793.t3 | Pfam | PF02806 | Alpha amylase, C-terminal all-beta domain | 223 | 290 | 0 |
| 9 | g7793.t3 | SMART | SM00632 | Aamy_c | 215 | 306 | 0 |
| 8 | g7793.t3 | SUPERFAMILY | SSF51445 | (Trans)glycosidases | 2 | 205 | 0 |
| 7 | g7793.t3 | SUPERFAMILY | SSF51011 | Glycosyl hydrolase domain | 211 | 307 | 0 |
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