General information for g5992.t9
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Alpha-glucosidase.
Parent gene
- The parent gene g5992 is located on chr_2: 13217206..13217627 (+ 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 | g5992 | g5992.t9 | TSS | g5992.t9 | 13215415 | 13215415 |
| chr_2 | g5992 | g5992.t9 | isoform | g5992.t9 | 13216236 | 13217627 |
| chr_2 | g5992 | g5992.t9 | exon | g5992.t9.exon1 | 13216236 | 13216305 |
| chr_2 | g5992 | g5992.t9 | cds | g5992.t9.CDS1 | 13216246 | 13216305 |
| chr_2 | g5992 | g5992.t9 | exon | g5992.t9.exon2 | 13216365 | 13216868 |
| chr_2 | g5992 | g5992.t9 | cds | g5992.t9.CDS2 | 13216365 | 13216868 |
| chr_2 | g5992 | g5992.t9 | exon | g5992.t9.exon3 | 13216931 | 13217232 |
| chr_2 | g5992 | g5992.t9 | cds | g5992.t9.CDS3 | 13216931 | 13217232 |
| chr_2 | g5992 | g5992.t9 | exon | g5992.t9.exon4 | 13217288 | 13217431 |
| chr_2 | g5992 | g5992.t9 | cds | g5992.t9.CDS4 | 13217288 | 13217431 |
| chr_2 | g5992 | g5992.t9 | exon | g5992.t9.exon5 | 13217492 | 13217627 |
| chr_2 | g5992 | g5992.t9 | cds | g5992.t9.CDS5 | 13217492 | 13217627 |
| chr_2 | g5992 | g5992.t9 | TTS | g5992.t9 | 13217695 | 13217695 |
Sequences
>g5992.t9 Gene=g5992 Length=1156
TGTTAAGGCAATGTCAGATATGTTGATTTATTACATTGATATGGGCGTTGCAGGTTTTCG
ATTGGACGCTATTAATCATCTTTTTGAAGACGCGCTATTCAGAAATGAAACTCAATGGAA
TCCAGAAGAAGAAATAGAAAACTATGATGATTTAAATCATGAACATACAAAGGACCTCAA
TGAAACATTCCTTTTTGTTTACTCATGGCGAAAAATGATTGATGACTATATCGTACAGAA
AAATATCTCATCCGATATTTTGGTTATGACTGAAGCTTATGCAAGTACAAGTGATACCAT
GCGTTATTATCATGATCCAACAAATCCAAATGTACGAGGCGCTCATATGCCATTTAACTT
TCAATTAATTTTCAATTTTCAAGCAAATGCAAAATCTGAAGACATTCAAAGAGGCATTTT
TGAATGGCTCAACAATATGCCAGAAGGTGAAACAGCTAATTGGGTTGCAGGTAGTCATGA
TCATAGCAGAGTTGCATCACGTATTATGCCAGAGAAAATTCACATGGTCAATACAGTTGT
ACTTACGCTTCCGGGTTCTAGTATAACCTATATGGGCGAGGAAATTGGTATGCACGATAA
CAAAGATGTGCCAAATTGGGATAATCGAAACAAAAATAGAACGCCTATGCAATGGAATGG
TGGTGTAGGTGCCGGTTTTACAACAAGAAATGCCAACGAAACGTGGCTACCAATTCATCC
AAATTATTTAACTGTGAACTTGCAAGCAGAAACGGAACGACCTCGAAGTACATACAAATA
TTTCCAAAGCTTAACTGCACTCAGAAAAACAAATGCACTTCGCAAAGGAGATTTTGACTT
TAAGATTATTAATGAAGATGTTTTTGGTTACACAAGAAATTACAATAAAGAGGAAGGTTA
TTTGATTCTCATCAACCTTTCTGGTTCAAGTCATCATTTGGATTTGAAAGCTTTTGATAC
TTTTGGAAAAAATAAATTGCGTGTTGTAACAGCAGCACCAAATTCTCGATTTGATGTTGG
TGATATTGTAGAAAAAGAACATGTCACGGTTGGTTTATATGATGCTGTAGTTTTTGATTA
TGTATCATCAGCATCGAGTGTGGTTCTTAGCATTGCTCTTTTCTTTACAACGATTTTTGT
TTATCTTTTTAATTAA
>g5992.t9 Gene=g5992 Length=381
MSDMLIYYIDMGVAGFRLDAINHLFEDALFRNETQWNPEEEIENYDDLNHEHTKDLNETF
LFVYSWRKMIDDYIVQKNISSDILVMTEAYASTSDTMRYYHDPTNPNVRGAHMPFNFQLI
FNFQANAKSEDIQRGIFEWLNNMPEGETANWVAGSHDHSRVASRIMPEKIHMVNTVVLTL
PGSSITYMGEEIGMHDNKDVPNWDNRNKNRTPMQWNGGVGAGFTTRNANETWLPIHPNYL
TVNLQAETERPRSTYKYFQSLTALRKTNALRKGDFDFKIINEDVFGYTRNYNKEEGYLIL
INLSGSSHHLDLKAFDTFGKNKLRVVTAAPNSRFDVGDIVEKEHVTVGLYDAVVFDYVSS
ASSVVLSIALFFTTIFVYLFN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g5992.t9 | Gene3D | G3DSA:3.20.20.80 | Glycosidases | 1 | 273 | 8.0E-60 |
| 2 | g5992.t9 | PANTHER | PTHR10357 | ALPHA-AMYLASE FAMILY MEMBER | 1 | 366 | 8.9E-109 |
| 3 | g5992.t9 | PANTHER | PTHR10357:SF177 | FI17312P1-RELATED | 1 | 366 | 8.9E-109 |
| 1 | g5992.t9 | Pfam | PF00128 | Alpha amylase, catalytic domain | 1 | 199 | 4.1E-22 |
| 8 | g5992.t9 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 356 | - |
| 9 | g5992.t9 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 357 | 380 | - |
| 7 | g5992.t9 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 381 | 381 | - |
| 5 | g5992.t9 | SUPERFAMILY | SSF51445 | (Trans)glycosidases | 2 | 268 | 6.29E-41 |
| 4 | g5992.t9 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 358 | 380 | - |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5992/g5992.t9; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5992.t9.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