General information for g5993.t4
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Alpha-glucosidase.
Parent gene
- The parent gene g5993 is located on chr_2: 13219931..13220650 (+ 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 | g5993 | g5993.t4 | TSS | g5993.t4 | 13218283 | 13218283 |
| chr_2 | g5993 | g5993.t4 | isoform | g5993.t4 | 13218299 | 13219838 |
| chr_2 | g5993 | g5993.t4 | exon | g5993.t4.exon1 | 13218299 | 13218756 |
| chr_2 | g5993 | g5993.t4 | cds | g5993.t4.CDS1 | 13218631 | 13218756 |
| chr_2 | g5993 | g5993.t4 | exon | g5993.t4.exon2 | 13218819 | 13218959 |
| chr_2 | g5993 | g5993.t4 | cds | g5993.t4.CDS2 | 13218819 | 13218959 |
| chr_2 | g5993 | g5993.t4 | exon | g5993.t4.exon3 | 13219068 | 13219361 |
| chr_2 | g5993 | g5993.t4 | cds | g5993.t4.CDS3 | 13219068 | 13219361 |
| chr_2 | g5993 | g5993.t4 | exon | g5993.t4.exon4 | 13219431 | 13219507 |
| chr_2 | g5993 | g5993.t4 | cds | g5993.t4.CDS4 | 13219431 | 13219507 |
| chr_2 | g5993 | g5993.t4 | exon | g5993.t4.exon5 | 13219570 | 13219838 |
| chr_2 | g5993 | g5993.t4 | cds | g5993.t4.CDS5 | 13219570 | 13219837 |
| chr_2 | g5993 | g5993.t4 | TTS | g5993.t4 | 13220720 | 13220720 |
Sequences
>g5993.t4 Gene=g5993 Length=1239
ATGAAGTGGTTAGTATTAATAAATTTACTAATAGCAGTGATAACTGTAAAAGCAGGCTGG
CTGCCATTTTGGGTAGATGAAGAAGTAGAAGTTGAACTTTCTAACGAATTTGATTGGTGG
GAAAATGGAGTATTTTATCAAATTTATCCAAGATCATTTAAAGATGACAATAATGATGGA
ACTGGTGATATCAAGGGAATTATTTCGAAACTTGAACACTTGAAAGATTTGGGAGTAACA
GGTATGAAAAAAATTCACAACGTGATGAACTTTTATATAATTTTTTTAAAATTCACACAG
GAACTTGGCTTAGTCCAATTTTTAAAAGTCCTATGGTCGATGGAGGCTACGATATTTCAG
ATTATACTGATGTCAATGAAATTTATGGAACTAAAGAAGATTTAAAAGCATTATTTGATA
AAGCAAAAGAACTTGGACTTAAAATTATTCTTGACTTTGTGCCAAATCACTCAAGTGATC
AACACGAGTGGTTCCAAAAATCAGTAAATAATGTTTCAGAATATGCAAATTATTATACAT
GGCGTGAATGTGAATTAGTTAATGCAACAACTGGTGAAAGAAGATTAGTTAATAATTGGA
TTGCCGTGTTCAATACACCAATGTGGACTTACAATGCACAACGTAACATGTGTTATCATC
ATCAATTTACTCCCGAACAACCTGATATGAATTACAGGCATCCAGATAAAGTAATTCAAA
AAGAAATGTTCAACATTTTAGACTATTGGATGGATCAGGGTGCAGATGGTTTCCGAGTCG
ATGCTATCAATCATCTTTTTGAATCAGCTTCATTCACAAATCAACCACTTCTTTCTCCTG
ACCTTGATCCGACACTCTACAGCAGTTATAACCCTCTCTACACTAGAGACTTGCCCGAGT
CGTATCAATTCATTTATGATGTGCGCGAGCATATGGATGAATACTCGAGAAATCATGGCA
ATGTTACAAGGATTCTTATGACAGAAGCTTATGCGTCAGTTAAACAACAAACTTCCTGGT
ATGGTTCATATGCACGTCCTGGTTCACACGTACCATTCAACTTTGTTTTCATCGCTGATA
TTACGGCAGAATCGAATGCTACACATTATAAGGGCCTTGTTGATGAATGGATGGAAAATA
CTCCATCATTTGCAATGGGTCAAGCAAATTGGGTGCTCGGAAATCACGACAGACCAAGAC
TTCGTTCAAGATTTGGTGAGGAACGTTTTGAAAGCATGG
>g5993.t4 Gene=g5993 Length=302
MVDGGYDISDYTDVNEIYGTKEDLKALFDKAKELGLKIILDFVPNHSSDQHEWFQKSVNN
VSEYANYYTWRECELVNATTGERRLVNNWIAVFNTPMWTYNAQRNMCYHHQFTPEQPDMN
YRHPDKVIQKEMFNILDYWMDQGADGFRVDAINHLFESASFTNQPLLSPDLDPTLYSSYN
PLYTRDLPESYQFIYDVREHMDEYSRNHGNVTRILMTEAYASVKQQTSWYGSYARPGSHV
PFNFVFIADITAESNATHYKGLVDEWMENTPSFAMGQANWVLGNHDRPRLRSRFGEERFE
SM
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g5993.t4 | Gene3D | G3DSA:3.20.20.80 | Glycosidases | 1 | 298 | 0 |
| 7 | g5993.t4 | Gene3D | G3DSA:3.90.400.10 | - | 48 | 123 | 0 |
| 2 | g5993.t4 | PANTHER | PTHR10357 | ALPHA-AMYLASE FAMILY MEMBER | 1 | 302 | 0 |
| 3 | g5993.t4 | PANTHER | PTHR10357:SF177 | FI17312P1-RELATED | 1 | 302 | 0 |
| 1 | g5993.t4 | Pfam | PF00128 | Alpha amylase, catalytic domain | 2 | 298 | 0 |
| 5 | g5993.t4 | SMART | SM00642 | aamy | 2 | 302 | 0 |
| 4 | g5993.t4 | SUPERFAMILY | SSF51445 | (Trans)glycosidases | 2 | 293 | 0 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5993/g5993.t4; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5993.t4.fa.iupred3.txt does not exist
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| 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