General information for g13300.t54
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Trehalose-6-phosphate phosphatase.
Parent gene
- The parent gene g13300 is located on chr_1: 29008579..29009204 (+ 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_1 | g13300 | g13300.t54 | TSS | g13300.t54 | 29008120 | 29008120 |
| chr_1 | g13300 | g13300.t54 | isoform | g13300.t54 | 29008145 | 29009204 |
| chr_1 | g13300 | g13300.t54 | exon | g13300.t54.exon1 | 29008145 | 29008530 |
| chr_1 | g13300 | g13300.t54 | cds | g13300.t54.CDS1 | 29008521 | 29008530 |
| chr_1 | g13300 | g13300.t54 | exon | g13300.t54.exon2 | 29008653 | 29008906 |
| chr_1 | g13300 | g13300.t54 | cds | g13300.t54.CDS2 | 29008653 | 29008906 |
| chr_1 | g13300 | g13300.t54 | exon | g13300.t54.exon3 | 29008971 | 29009004 |
| chr_1 | g13300 | g13300.t54 | cds | g13300.t54.CDS3 | 29008971 | 29009004 |
| chr_1 | g13300 | g13300.t54 | exon | g13300.t54.exon4 | 29009056 | 29009204 |
| chr_1 | g13300 | g13300.t54 | cds | g13300.t54.CDS4 | 29009056 | 29009204 |
| chr_1 | g13300 | g13300.t54 | TTS | g13300.t54 | 29009276 | 29009276 |
Sequences
>g13300.t54 Gene=g13300 Length=823
ATGACAATACTACACAAGCTAACTTTAAATCTCATTTTCACAGTCTTCGTTGTGAGTGCA
TTGAGAATTGTCGAACAATTAGATTTGAAACTTGAGCCACAAATGGAAGATTTAGAAAAA
TACTTGGAGGATTATGTGTCGAATAAACCATTCGCGTTATTACTCGATTATGACGGCACG
TTGGCTGCCATTCAACCACATCCAAATATGACATACATGACTGAATATACCAAAGAAGCG
CTATTGAACATCTCATCTTACCCCAACGTGTATTTAGCAGTTATATCCGGAAGGGGAGTT
GATGATGTGAAGACAAAAGTTGGTATCGATGGAATTGTTTATGCTGGAAATCATGGTCTC
GAAATTTTATATCCTAATGGAACTCGAAAATCTTAAAAGAGACGGAAGTTGGGTCGAAAA
TAAGAAATTCTCAGTAACTTTTCACTTTAGAGCTGTGCCTGAAAAAGATCATGAGAAAAT
CAACAATGAAGCTAAGGAAATTATCGAGAAATTTGGATATCGAGCAAATCCAGCTCATTG
CGCTATTGAAGCAAAACCACCGGTAGTATGGCATAAGGGCAAGGCAGCCGAATATATTTT
AAATCACTCATTTGGTAAAGATTGGAGAGAAAAAATTCAAGTTGTGTTTGCTGGCGATGA
TACAACCGATGAAGATGTTTTCGAGTTACTTCAAGGAATTGGTGTTACTTTTAGAGTCAC
AAAGGATCCAAACATTGTGACTAAAGCAACTTACAAAGTGCCATCAACTGAAGCTGTTAC
AAAGGTTCTACAATGGGTCGATAAAAAATTTGGAAATAAATAA
>g13300.t54 Gene=g13300 Length=148
MELENLKRDGSWVENKKFSVTFHFRAVPEKDHEKINNEAKEIIEKFGYRANPAHCAIEAK
PPVVWHKGKAAEYILNHSFGKDWREKIQVVFAGDDTTDEDVFELLQGIGVTFRVTKDPNI
VTKATYKVPSTEAVTKVLQWVDKKFGNK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g13300.t54 | Gene3D | G3DSA:3.40.50.1000 | - | 22 | 147 | 0 |
| 2 | g13300.t54 | PANTHER | PTHR43768 | TREHALOSE 6-PHOSPHATE PHOSPHATASE | 9 | 139 | 0 |
| 3 | g13300.t54 | PANTHER | PTHR43768:SF3 | TREHALOSE 6-PHOSPHATE PHOSPHATASE | 9 | 139 | 0 |
| 1 | g13300.t54 | Pfam | PF02358 | Trehalose-phosphatase | 9 | 128 | 0 |
| 4 | g13300.t54 | SUPERFAMILY | SSF56784 | HAD-like | 8 | 141 | 0 |
| 6 | g13300.t54 | TIGRFAM | TIGR00685 | T6PP: trehalose-phosphatase | 7 | 141 | 0 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0005992 | trehalose biosynthetic 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