General information for g5992.t1
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.t1 | TSS | g5992.t1 | 13215415 | 13215415 |
| chr_2 | g5992 | g5992.t1 | isoform | g5992.t1 | 13215455 | 13217627 |
| chr_2 | g5992 | g5992.t1 | exon | g5992.t1.exon1 | 13215455 | 13215611 |
| chr_2 | g5992 | g5992.t1 | cds | g5992.t1.CDS1 | 13215455 | 13215611 |
| chr_2 | g5992 | g5992.t1 | exon | g5992.t1.exon2 | 13215669 | 13215888 |
| chr_2 | g5992 | g5992.t1 | cds | g5992.t1.CDS2 | 13215669 | 13215888 |
| chr_2 | g5992 | g5992.t1 | exon | g5992.t1.exon3 | 13215943 | 13216143 |
| chr_2 | g5992 | g5992.t1 | cds | g5992.t1.CDS3 | 13215943 | 13216143 |
| chr_2 | g5992 | g5992.t1 | exon | g5992.t1.exon4 | 13216206 | 13216305 |
| chr_2 | g5992 | g5992.t1 | cds | g5992.t1.CDS4 | 13216206 | 13216305 |
| chr_2 | g5992 | g5992.t1 | exon | g5992.t1.exon5 | 13216365 | 13216868 |
| chr_2 | g5992 | g5992.t1 | cds | g5992.t1.CDS5 | 13216365 | 13216868 |
| chr_2 | g5992 | g5992.t1 | exon | g5992.t1.exon6 | 13216931 | 13217232 |
| chr_2 | g5992 | g5992.t1 | cds | g5992.t1.CDS6 | 13216931 | 13217232 |
| chr_2 | g5992 | g5992.t1 | exon | g5992.t1.exon7 | 13217288 | 13217431 |
| chr_2 | g5992 | g5992.t1 | cds | g5992.t1.CDS7 | 13217288 | 13217431 |
| chr_2 | g5992 | g5992.t1 | exon | g5992.t1.exon8 | 13217492 | 13217627 |
| chr_2 | g5992 | g5992.t1 | cds | g5992.t1.CDS8 | 13217492 | 13217627 |
| chr_2 | g5992 | g5992.t1 | TTS | g5992.t1 | 13217695 | 13217695 |
Sequences
>g5992.t1 Gene=g5992 Length=1764
ATGAAGTCAAAGATAACTTTTTTACTCTTTGTAATATTTATCATTGCAATTCATGGACAA
GATGATGAAAAAGAATGGTGGCGTACAGCTACTTTCTATCAAATCTATCCAAGAAGTTTC
ATGGATACAACTGGAAATGGAATTGGTGATTTAAAAGGTATGATTCAGAGATTAGATCAC
TTGAAAGATGCAGGTTTCGACACGTTCTGGTTAAGTCCTATTTTTAAAAGCCCTCAAAAA
GATACTGGTTATGATGTTTCCGATTATTATACAATTGAACCTGATTATGGAACTATGGAT
GATTTCAAAGCATTGATTGCAAAAGCAAAATCACTTGGCATTCGAGTAATGCTTGATTTT
ATTCCAAACCACACTAGTGATGAACACGAATGGTTTATAAAATCATGTGCAAATGAATCA
GAATTTCGTGATTATTATGTTTGGCATGATGGTCAACCTAATCCTGAAGGTGGTCGCCCA
TTTCTACCAAACAATTGGATCAGTGTTTTTGGCGGTCCTGCTTGGACGTGGGTAGAGTCA
CGTCAGCAATATTATCTTCATCAATTCTTACCTGGACAACCAGATTTGAATTATCGTAGT
GATAACGTTGTTAAGGCAATGTCAGATATGTTGATTTATTACATTGATATGGGCGTTGCA
GGTTTTCGATTGGACGCTATTAATCATCTTTTTGAAGACGCGCTATTCAGAAATGAAACT
CAATGGAATCCAGAAGAAGAAATAGAAAACTATGATGATTTAAATCATGAACATACAAAG
GACCTCAATGAAACATTCCTTTTTGTTTACTCATGGCGAAAAATGATTGATGACTATATC
GTACAGAAAAATATCTCATCCGATATTTTGGTTATGACTGAAGCTTATGCAAGTACAAGT
GATACCATGCGTTATTATCATGATCCAACAAATCCAAATGTACGAGGCGCTCATATGCCA
TTTAACTTTCAATTAATTTTCAATTTTCAAGCAAATGCAAAATCTGAAGACATTCAAAGA
GGCATTTTTGAATGGCTCAACAATATGCCAGAAGGTGAAACAGCTAATTGGGTTGCAGGT
AGTCATGATCATAGCAGAGTTGCATCACGTATTATGCCAGAGAAAATTCACATGGTCAAT
ACAGTTGTACTTACGCTTCCGGGTTCTAGTATAACCTATATGGGCGAGGAAATTGGTATG
CACGATAACAAAGATGTGCCAAATTGGGATAATCGAAACAAAAATAGAACGCCTATGCAA
TGGAATGGTGGTGTAGGTGCCGGTTTTACAACAAGAAATGCCAACGAAACGTGGCTACCA
ATTCATCCAAATTATTTAACTGTGAACTTGCAAGCAGAAACGGAACGACCTCGAAGTACA
TACAAATATTTCCAAAGCTTAACTGCACTCAGAAAAACAAATGCACTTCGCAAAGGAGAT
TTTGACTTTAAGATTATTAATGAAGATGTTTTTGGTTACACAAGAAATTACAATAAAGAG
GAAGGTTATTTGATTCTCATCAACCTTTCTGGTTCAAGTCATCATTTGGATTTGAAAGCT
TTTGATACTTTTGGAAAAAATAAATTGCGTGTTGTAACAGCAGCACCAAATTCTCGATTT
GATGTTGGTGATATTGTAGAAAAAGAACATGTCACGGTTGGTTTATATGATGCTGTAGTT
TTTGATTATGTATCATCAGCATCGAGTGTGGTTCTTAGCATTGCTCTTTTCTTTACAACG
ATTTTTGTTTATCTTTTTAATTAA
>g5992.t1 Gene=g5992 Length=587
MKSKITFLLFVIFIIAIHGQDDEKEWWRTATFYQIYPRSFMDTTGNGIGDLKGMIQRLDH
LKDAGFDTFWLSPIFKSPQKDTGYDVSDYYTIEPDYGTMDDFKALIAKAKSLGIRVMLDF
IPNHTSDEHEWFIKSCANESEFRDYYVWHDGQPNPEGGRPFLPNNWISVFGGPAWTWVES
RQQYYLHQFLPGQPDLNYRSDNVVKAMSDMLIYYIDMGVAGFRLDAINHLFEDALFRNET
QWNPEEEIENYDDLNHEHTKDLNETFLFVYSWRKMIDDYIVQKNISSDILVMTEAYASTS
DTMRYYHDPTNPNVRGAHMPFNFQLIFNFQANAKSEDIQRGIFEWLNNMPEGETANWVAG
SHDHSRVASRIMPEKIHMVNTVVLTLPGSSITYMGEEIGMHDNKDVPNWDNRNKNRTPMQ
WNGGVGAGFTTRNANETWLPIHPNYLTVNLQAETERPRSTYKYFQSLTALRKTNALRKGD
FDFKIINEDVFGYTRNYNKEEGYLILINLSGSSHHLDLKAFDTFGKNKLRVVTAAPNSRF
DVGDIVEKEHVTVGLYDAVVFDYVSSASSVVLSIALFFTTIFVYLFN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g5992.t1 | Gene3D | G3DSA:3.20.20.80 | Glycosidases | 26 | 472 | 1.0E-149 |
| 7 | g5992.t1 | Gene3D | G3DSA:3.90.400.10 | - | 126 | 200 | 1.0E-149 |
| 2 | g5992.t1 | PANTHER | PTHR10357 | ALPHA-AMYLASE FAMILY MEMBER | 12 | 571 | 1.9E-207 |
| 3 | g5992.t1 | PANTHER | PTHR10357:SF177 | FI17312P1-RELATED | 12 | 571 | 1.9E-207 |
| 1 | g5992.t1 | Pfam | PF00128 | Alpha amylase, catalytic domain | 49 | 405 | 7.0E-92 |
| 10 | g5992.t1 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 19 | - |
| 11 | g5992.t1 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 4 | - |
| 12 | g5992.t1 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 5 | 15 | - |
| 14 | g5992.t1 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 16 | 19 | - |
| 9 | g5992.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 20 | 562 | - |
| 13 | g5992.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 563 | 586 | - |
| 8 | g5992.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 587 | 587 | - |
| 16 | g5992.t1 | SMART | SM00642 | aamy | 34 | 451 | 5.1E-115 |
| 4 | g5992.t1 | SUPERFAMILY | SSF51445 | (Trans)glycosidases | 24 | 474 | 1.46E-116 |
| 5 | g5992.t1 | SignalP_EUK | SignalP-noTM | SignalP-noTM | 1 | 19 | - |
| 15 | g5992.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 564 | 586 | - |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5992/g5992.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5992.t1.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 transcript has been annotated with K01226 (trehalose-6-phosphate hydrolase)
Pathway
- This transcript belongs to the following pathways
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