General information for g5994.t6
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Maltase 1.
Parent gene
- The parent gene g5994 is located on chr_2: 13224141..13225689 (+ 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 | g5994 | g5994.t6 | TSS | g5994.t6 | 13223384 | 13223384 |
| chr_2 | g5994 | g5994.t6 | isoform | g5994.t6 | 13224141 | 13224771 |
| chr_2 | g5994 | g5994.t6 | exon | g5994.t6.exon1 | 13224141 | 13224145 |
| chr_2 | g5994 | g5994.t6 | exon | g5994.t6.exon2 | 13224216 | 13224323 |
| chr_2 | g5994 | g5994.t6 | exon | g5994.t6.exon3 | 13224385 | 13224771 |
| chr_2 | g5994 | g5994.t6 | cds | g5994.t6.CDS1 | 13224400 | 13224771 |
| chr_2 | g5994 | g5994.t6 | TTS | g5994.t6 | 13225782 | 13225782 |
Sequences
>g5994.t6 Gene=g5994 Length=500
ATGCGATAAACCACTTATTTGAAGTTGAAGACTTTAGAGACGAACCAGAAACTGGCTGGA
CAAATAACACAAACGATTATGGCTTTACTCACCATCATTACACTAAAGATTTGGATGAAA
CTTATGATATGGTTCGTGAATGGAGAAAATTAATTGATGATTTTAATGCCGCACATCCAG
GAAATACAAGAGTAATTTTCACAGAAGCTTATGCAAATGTATCATTCACAATGAAATACT
ATGGTTCAGAAGCTGAACCTATTGCACACTTTCCTTTCAACTTTCTACTTATTGAAAAAT
TAAATGAAGGCTCGAATGCAAATGATTTTAAAAGAGAAATTGATGAATGGTTCACAAATT
TGCCAAATGCTCATGCGACATCAAACTGGGTTCTTGGAAATCATGACAAACCAAGATTTG
CTTCACGTTATGGAACTGAAAGAGTTGATGGAATGTTGATGCTTTTGCTACTTCTTCCCG
GAGTTGCAGTAACCTATATG
>g5994.t6 Gene=g5994 Length=124
MVREWRKLIDDFNAAHPGNTRVIFTEAYANVSFTMKYYGSEAEPIAHFPFNFLLIEKLNE
GSNANDFKREIDEWFTNLPNAHATSNWVLGNHDKPRFASRYGTERVDGMLMLLLLLPGVA
VTYM
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g5994.t6 | Gene3D | G3DSA:3.20.20.80 | Glycosidases | 1 | 124 | 2.4E-21 |
| 2 | g5994.t6 | PANTHER | PTHR10357 | ALPHA-AMYLASE FAMILY MEMBER | 1 | 123 | 9.1E-48 |
| 3 | g5994.t6 | PANTHER | PTHR10357:SF177 | FI17312P1-RELATED | 1 | 123 | 9.1E-48 |
| 1 | g5994.t6 | Pfam | PF00128 | Alpha amylase, catalytic domain | 3 | 123 | 3.9E-14 |
| 6 | g5994.t6 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 105 | - |
| 8 | g5994.t6 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 106 | 123 | - |
| 7 | g5994.t6 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 124 | 124 | - |
| 4 | g5994.t6 | SUPERFAMILY | SSF51445 | (Trans)glycosidases | 5 | 124 | 1.13E-12 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5994/g5994.t6; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5994.t6.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