General information for g7793.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 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.t1 | TSS | g7793.t1 | 26139344 | 26139344 |
| chr_2 | g7793 | g7793.t1 | isoform | g7793.t1 | 26139360 | 26141476 |
| chr_2 | g7793 | g7793.t1 | exon | g7793.t1.exon1 | 26139360 | 26139422 |
| chr_2 | g7793 | g7793.t1 | cds | g7793.t1.CDS1 | 26139360 | 26139422 |
| chr_2 | g7793 | g7793.t1 | exon | g7793.t1.exon2 | 26139519 | 26139684 |
| chr_2 | g7793 | g7793.t1 | cds | g7793.t1.CDS2 | 26139519 | 26139684 |
| chr_2 | g7793 | g7793.t1 | exon | g7793.t1.exon3 | 26139759 | 26139929 |
| chr_2 | g7793 | g7793.t1 | cds | g7793.t1.CDS3 | 26139759 | 26139929 |
| chr_2 | g7793 | g7793.t1 | exon | g7793.t1.exon4 | 26139995 | 26140079 |
| chr_2 | g7793 | g7793.t1 | cds | g7793.t1.CDS4 | 26139995 | 26140079 |
| chr_2 | g7793 | g7793.t1 | exon | g7793.t1.exon5 | 26140131 | 26140264 |
| chr_2 | g7793 | g7793.t1 | cds | g7793.t1.CDS5 | 26140131 | 26140264 |
| chr_2 | g7793 | g7793.t1 | exon | g7793.t1.exon6 | 26140354 | 26140376 |
| chr_2 | g7793 | g7793.t1 | cds | g7793.t1.CDS6 | 26140354 | 26140376 |
| chr_2 | g7793 | g7793.t1 | exon | g7793.t1.exon7 | 26140441 | 26140568 |
| chr_2 | g7793 | g7793.t1 | cds | g7793.t1.CDS7 | 26140441 | 26140568 |
| chr_2 | g7793 | g7793.t1 | exon | g7793.t1.exon8 | 26140633 | 26140680 |
| chr_2 | g7793 | g7793.t1 | cds | g7793.t1.CDS8 | 26140633 | 26140680 |
| chr_2 | g7793 | g7793.t1 | exon | g7793.t1.exon9 | 26140742 | 26140850 |
| chr_2 | g7793 | g7793.t1 | cds | g7793.t1.CDS9 | 26140742 | 26140850 |
| chr_2 | g7793 | g7793.t1 | exon | g7793.t1.exon10 | 26140907 | 26141476 |
| chr_2 | g7793 | g7793.t1 | cds | g7793.t1.CDS10 | 26140907 | 26141476 |
| chr_2 | g7793 | g7793.t1 | TTS | g7793.t1 | 26141539 | 26141539 |
Sequences
>g7793.t1 Gene=g7793 Length=1497
ATGAAAGTGTTTTTAGTTTTTCTTTCCATTGTGCTGACTATTACATTTTCTAGTGCACAA
TGGGATCCTCATTATGCATCTAATAGAAATGTTATGGTTCATCTATTTGAATGGAAATGG
AAAGATATTGCTGAAGAATGTGAAACATTTCTTGCACCAAATGGATTTGCAGGGGTGCAA
GTGAGTCCACCAACTGAAAATACTGCAATTCATCTTGACTGGCTATCAACTATTCGCCCA
TGGTGGGAACGTTACCAGCCGATAAGCTATAAATTAGAAACACGCTCAGGAAATGAAGCT
GCTTTTGCTGATATGGTTCGACGATGCAATGCTGTTGGTGTTCGTATTTACGTTGATATT
TTACTAAATCATATGAGTGCGACTAATGGTACAGGAACTGGTGGAAGTAGTGGAACTGTA
TCAACAACTTATTTGAATTTTCCTTCTGTACCATTCACAACAGAAGATTTTAATCCATAC
TGCAGTCTTGATTGGAATTCACAACAGAGTATTCGAAATTGTTGGCTTGTTGGTTTACCT
GATTTAAATCAAAAGCGAGCGCACGTTAGAGACATGCAAATTAACTTACTAAATCATCTC
ATTGATCTCGGAGTTGCTGGCTTTAGGGTTGATGCTGCTAAGCACATGTGGGCTGAAGAC
CTTGAGTATATTTTCAGTAGAATGCATAATTTAAACACAAATCATGGTTTCCATGCCAAC
AGTCGTCCTTTCGTTGTGCAAGAAGTCATCGTAGGTGATGGCATTTATATGGATCATTAT
ACACATTTGGGTGCTGTCACTGTTTTTGAAGCAAGCAGAATTATGGGACAAGTTTTGCGT
GGACATGCTGACATCAATGATTTAAGATATTTCAGTTCACGTTTTGGAATTGAATCTAAA
GAAGCTTTAATTTTTGTTGATAACCATGACAATCAACGTGATGGTGGACTTCCATTAACA
AACCATAGAGAACCAAGAATTTACAAAATAGCAACTGCATACAATTTAGCTCAAGATTTC
GGTCATCAAAGAATTATGAGTTCATTCTATTTTTCACATAGAGATCAAGGACCTCCACAG
GATGCATCACAAAATATTCTCTCACCAACATTCGATGCTAATGGACAATGCACAAATGGT
TGGGTTTGTGAGCATCGATGGCCTGCAATTAGAAATATGGTACAATTTAGTGCAGCAGTA
AAGGGAACAAAAGCAGAAAACTGGTGGACAGGATGGAATGAAATTGCATTTTCACGCGGC
AATCGAGGATTTATTGCAATAAATGCAAAAGATAATGGTGATTCTACCAATGTACGGTTA
TACACTTCACTACCAGCCGGTATTTACTGCGATATGTCGAGTGGAAATAAAGTTGGCAAC
AGCTGCACAAGAAAAACTGTTACAGTAGGTTCTGATGGCTATGCTGATATTTATATTCCA
GGCGCATATAGTAACGAGGAAGGATTCATCGCAATTCATGTCGATGCGAAACTGTAA
>g7793.t1 Gene=g7793 Length=498
MKVFLVFLSIVLTITFSSAQWDPHYASNRNVMVHLFEWKWKDIAEECETFLAPNGFAGVQ
VSPPTENTAIHLDWLSTIRPWWERYQPISYKLETRSGNEAAFADMVRRCNAVGVRIYVDI
LLNHMSATNGTGTGGSSGTVSTTYLNFPSVPFTTEDFNPYCSLDWNSQQSIRNCWLVGLP
DLNQKRAHVRDMQINLLNHLIDLGVAGFRVDAAKHMWAEDLEYIFSRMHNLNTNHGFHAN
SRPFVVQEVIVGDGIYMDHYTHLGAVTVFEASRIMGQVLRGHADINDLRYFSSRFGIESK
EALIFVDNHDNQRDGGLPLTNHREPRIYKIATAYNLAQDFGHQRIMSSFYFSHRDQGPPQ
DASQNILSPTFDANGQCTNGWVCEHRWPAIRNMVQFSAAVKGTKAENWWTGWNEIAFSRG
NRGFIAINAKDNGDSTNVRLYTSLPAGIYCDMSSGNKVGNSCTRKTVTVGSDGYADIYIP
GAYSNEEGFIAIHVDAKL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 21 | g7793.t1 | CDD | cd11317 | AmyAc_bac_euk_AmyA | 29 | 400 | 1.03473E-162 |
| 15 | g7793.t1 | Gene3D | G3DSA:3.20.20.80 | Glycosidases | 21 | 402 | 1.1E-150 |
| 14 | g7793.t1 | Gene3D | G3DSA:2.60.40.1180 | - | 404 | 498 | 5.0E-29 |
| 3 | g7793.t1 | PANTHER | PTHR43447 | ALPHA-AMYLASE | 14 | 498 | 9.2E-140 |
| 4 | g7793.t1 | PANTHER | PTHR43447:SF7 | ALPHA-AMYLASE | 14 | 498 | 9.2E-140 |
| 5 | g7793.t1 | PRINTS | PR00110 | Alpha-amylase signature | 81 | 98 | 3.5E-26 |
| 8 | g7793.t1 | PRINTS | PR00110 | Alpha-amylase signature | 113 | 124 | 3.5E-26 |
| 7 | g7793.t1 | PRINTS | PR00110 | Alpha-amylase signature | 205 | 216 | 3.5E-26 |
| 9 | g7793.t1 | PRINTS | PR00110 | Alpha-amylase signature | 244 | 262 | 3.5E-26 |
| 6 | g7793.t1 | PRINTS | PR00110 | Alpha-amylase signature | 300 | 312 | 3.5E-26 |
| 2 | g7793.t1 | Pfam | PF00128 | Alpha amylase, catalytic domain | 91 | 313 | 5.4E-15 |
| 1 | g7793.t1 | Pfam | PF02806 | Alpha amylase, C-terminal all-beta domain | 415 | 481 | 1.5E-8 |
| 17 | g7793.t1 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 19 | - |
| 18 | g7793.t1 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 2 | - |
| 19 | g7793.t1 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 3 | 14 | - |
| 20 | g7793.t1 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 15 | 19 | - |
| 16 | g7793.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 20 | 498 | - |
| 23 | g7793.t1 | SMART | SM00642 | aamy | 30 | 397 | 4.0E-72 |
| 24 | g7793.t1 | SMART | SM00632 | Aamy_c | 406 | 497 | 9.1E-28 |
| 11 | g7793.t1 | SUPERFAMILY | SSF51445 | (Trans)glycosidases | 22 | 396 | 3.56E-83 |
| 10 | g7793.t1 | SUPERFAMILY | SSF51011 | Glycosyl hydrolase domain | 402 | 498 | 4.98E-26 |
| 13 | g7793.t1 | SignalP_EUK | SignalP-noTM | SignalP-noTM | 1 | 19 | - |
| 22 | g7793.t1 | SignalP_GRAM_NEGATIVE | SignalP-noTM | SignalP-noTM | 1 | 19 | - |
| 12 | g7793.t1 | SignalP_GRAM_POSITIVE | SignalP-TM | SignalP-TM | 1 | 19 | - |
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