General information for g5992.t8
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.t8 | TSS | g5992.t8 | 13215415 | 13215415 |
| chr_2 | g5992 | g5992.t8 | isoform | g5992.t8 | 13215667 | 13217627 |
| chr_2 | g5992 | g5992.t8 | exon | g5992.t8.exon1 | 13215667 | 13215888 |
| chr_2 | g5992 | g5992.t8 | cds | g5992.t8.CDS1 | 13215671 | 13215888 |
| chr_2 | g5992 | g5992.t8 | exon | g5992.t8.exon2 | 13215943 | 13216143 |
| chr_2 | g5992 | g5992.t8 | cds | g5992.t8.CDS2 | 13215943 | 13216143 |
| chr_2 | g5992 | g5992.t8 | exon | g5992.t8.exon3 | 13216206 | 13216305 |
| chr_2 | g5992 | g5992.t8 | cds | g5992.t8.CDS3 | 13216206 | 13216305 |
| chr_2 | g5992 | g5992.t8 | exon | g5992.t8.exon4 | 13216365 | 13216868 |
| chr_2 | g5992 | g5992.t8 | cds | g5992.t8.CDS4 | 13216365 | 13216868 |
| chr_2 | g5992 | g5992.t8 | exon | g5992.t8.exon5 | 13216931 | 13217232 |
| chr_2 | g5992 | g5992.t8 | cds | g5992.t8.CDS5 | 13216931 | 13217232 |
| chr_2 | g5992 | g5992.t8 | exon | g5992.t8.exon6 | 13217288 | 13217431 |
| chr_2 | g5992 | g5992.t8 | cds | g5992.t8.CDS6 | 13217288 | 13217431 |
| chr_2 | g5992 | g5992.t8 | exon | g5992.t8.exon7 | 13217492 | 13217627 |
| chr_2 | g5992 | g5992.t8 | cds | g5992.t8.CDS7 | 13217492 | 13217627 |
| chr_2 | g5992 | g5992.t8 | TTS | g5992.t8 | 13217695 | 13217695 |
Sequences
>g5992.t8 Gene=g5992 Length=1609
AGGTATGATTCAGAGATTAGATCACTTGAAAGATGCAGGTTTCGACACGTTCTGGTTAAG
TCCTATTTTTAAAAGCCCTCAAAAAGATACTGGTTATGATGTTTCCGATTATTATACAAT
TGAACCTGATTATGGAACTATGGATGATTTCAAAGCATTGATTGCAAAAGCAAAATCACT
TGGCATTCGAGTAATGCTTGATTTTATTCCAAACCACACTAGTGATGAACACGAATGGTT
TATAAAATCATGTGCAAATGAATCAGAATTTCGTGATTATTATGTTTGGCATGATGGTCA
ACCTAATCCTGAAGGTGGTCGCCCATTTCTACCAAACAATTGGATCAGTGTTTTTGGCGG
TCCTGCTTGGACGTGGGTAGAGTCACGTCAGCAATATTATCTTCATCAATTCTTACCTGG
ACAACCAGATTTGAATTATCGTAGTGATAACGTTGTTAAGGCAATGTCAGATATGTTGAT
TTATTACATTGATATGGGCGTTGCAGGTTTTCGATTGGACGCTATTAATCATCTTTTTGA
AGACGCGCTATTCAGAAATGAAACTCAATGGAATCCAGAAGAAGAAATAGAAAACTATGA
TGATTTAAATCATGAACATACAAAGGACCTCAATGAAACATTCCTTTTTGTTTACTCATG
GCGAAAAATGATTGATGACTATATCGTACAGAAAAATATCTCATCCGATATTTTGGTTAT
GACTGAAGCTTATGCAAGTACAAGTGATACCATGCGTTATTATCATGATCCAACAAATCC
AAATGTACGAGGCGCTCATATGCCATTTAACTTTCAATTAATTTTCAATTTTCAAGCAAA
TGCAAAATCTGAAGACATTCAAAGAGGCATTTTTGAATGGCTCAACAATATGCCAGAAGG
TGAAACAGCTAATTGGGTTGCAGGTAGTCATGATCATAGCAGAGTTGCATCACGTATTAT
GCCAGAGAAAATTCACATGGTCAATACAGTTGTACTTACGCTTCCGGGTTCTAGTATAAC
CTATATGGGCGAGGAAATTGGTATGCACGATAACAAAGATGTGCCAAATTGGGATAATCG
AAACAAAAATAGAACGCCTATGCAATGGAATGGTGGTGTAGGTGCCGGTTTTACAACAAG
AAATGCCAACGAAACGTGGCTACCAATTCATCCAAATTATTTAACTGTGAACTTGCAAGC
AGAAACGGAACGACCTCGAAGTACATACAAATATTTCCAAAGCTTAACTGCACTCAGAAA
AACAAATGCACTTCGCAAAGGAGATTTTGACTTTAAGATTATTAATGAAGATGTTTTTGG
TTACACAAGAAATTACAATAAAGAGGAAGGTTATTTGATTCTCATCAACCTTTCTGGTTC
AAGTCATCATTTGGATTTGAAAGCTTTTGATACTTTTGGAAAAAATAAATTGCGTGTTGT
AACAGCAGCACCAAATTCTCGATTTGATGTTGGTGATATTGTAGAAAAAGAACATGTCAC
GGTTGGTTTATATGATGCTGTAGTTTTTGATTATGTATCATCAGCATCGAGTGTGGTTCT
TAGCATTGCTCTTTTCTTTACAACGATTTTTGTTTATCTTTTTAATTAA
>g5992.t8 Gene=g5992 Length=534
MIQRLDHLKDAGFDTFWLSPIFKSPQKDTGYDVSDYYTIEPDYGTMDDFKALIAKAKSLG
IRVMLDFIPNHTSDEHEWFIKSCANESEFRDYYVWHDGQPNPEGGRPFLPNNWISVFGGP
AWTWVESRQQYYLHQFLPGQPDLNYRSDNVVKAMSDMLIYYIDMGVAGFRLDAINHLFED
ALFRNETQWNPEEEIENYDDLNHEHTKDLNETFLFVYSWRKMIDDYIVQKNISSDILVMT
EAYASTSDTMRYYHDPTNPNVRGAHMPFNFQLIFNFQANAKSEDIQRGIFEWLNNMPEGE
TANWVAGSHDHSRVASRIMPEKIHMVNTVVLTLPGSSITYMGEEIGMHDNKDVPNWDNRN
KNRTPMQWNGGVGAGFTTRNANETWLPIHPNYLTVNLQAETERPRSTYKYFQSLTALRKT
NALRKGDFDFKIINEDVFGYTRNYNKEEGYLILINLSGSSHHLDLKAFDTFGKNKLRVVT
AAPNSRFDVGDIVEKEHVTVGLYDAVVFDYVSSASSVVLSIALFFTTIFVYLFN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g5992.t8 | Gene3D | G3DSA:3.20.20.80 | Glycosidases | 2 | 419 | 3.3E-130 |
| 8 | g5992.t8 | Gene3D | G3DSA:3.90.400.10 | - | 73 | 147 | 3.3E-130 |
| 2 | g5992.t8 | PANTHER | PTHR10357 | ALPHA-AMYLASE FAMILY MEMBER | 3 | 518 | 1.2E-186 |
| 3 | g5992.t8 | PANTHER | PTHR10357:SF177 | FI17312P1-RELATED | 3 | 518 | 1.2E-186 |
| 1 | g5992.t8 | Pfam | PF00128 | Alpha amylase, catalytic domain | 2 | 352 | 6.5E-88 |
| 10 | g5992.t8 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 509 | - |
| 11 | g5992.t8 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 510 | 533 | - |
| 9 | g5992.t8 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 534 | 534 | - |
| 6 | g5992.t8 | SMART | SM00642 | aamy | 1 | 398 | 4.8E-92 |
| 5 | g5992.t8 | SUPERFAMILY | SSF51445 | (Trans)glycosidases | 2 | 421 | 1.72E-102 |
| 4 | g5992.t8 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 511 | 533 | - |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5992/g5992.t8; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5992.t8.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