General information for g13300.t56
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.t56 | TSS | g13300.t56 | 29008120 | 29008120 |
| chr_1 | g13300 | g13300.t56 | isoform | g13300.t56 | 29008145 | 29009204 |
| chr_1 | g13300 | g13300.t56 | exon | g13300.t56.exon1 | 29008145 | 29008530 |
| chr_1 | g13300 | g13300.t56 | cds | g13300.t56.CDS1 | 29008145 | 29008530 |
| chr_1 | g13300 | g13300.t56 | exon | g13300.t56.exon2 | 29008591 | 29008889 |
| chr_1 | g13300 | g13300.t56 | cds | g13300.t56.CDS2 | 29008591 | 29008889 |
| chr_1 | g13300 | g13300.t56 | exon | g13300.t56.exon3 | 29009056 | 29009204 |
| chr_1 | g13300 | g13300.t56 | cds | g13300.t56.CDS3 | 29009056 | 29009204 |
| chr_1 | g13300 | g13300.t56 | TTS | g13300.t56 | 29009276 | 29009276 |
Sequences
>g13300.t56 Gene=g13300 Length=834
ATGACAATACTACACAAGCTAACTTTAAATCTCATTTTCACAGTCTTCGTTGTGAGTGCA
TTGAGAATTGTCGAACAATTAGATTTGAAACTTGAGCCACAAATGGAAGATTTAGAAAAA
TACTTGGAGGATTATGTGTCGAATAAACCATTCGCGTTATTACTCGATTATGACGGCACG
TTGGCTGCCATTCAACCACATCCAAATATGACATACATGACTGAATATACCAAAGAAGCG
CTATTGAACATCTCATCTTACCCCAACGTGTATTTAGCAGTTATATCCGGAAGGGGAGTT
GATGATGTGAAGACAAAAGTTGGTATCGATGGAATTGTTTATGCTGGAAATCATGGTCTC
GAAATTTTATATCCTAATGGAACTCGTTACATACACGAAGTTCCAAGTGATGTTAAAGCA
AATTTTACAAAAATGGTGGAAGCTTTAGAAAATCTTAAAAGAGACGGAAGTTGGGTCGAA
AATAAGAAATTCTCAGTAACTTTTCACTTTAGAGCTGTGCCTGAAAAAGATCATGAGAAA
ATCAACAATGAAGCTAAGGAAATTATCGAGAAATTTGGATATCGAGCAAATCCAGCTCAT
TGCGCTATTGAAGCAAAACCACCGGTAGTATGGCATAAGGGCAAGGCAGCCGAATATATT
TTAAATCACTCATTTGGTAAAGATTATGTTTTCGAGTTACTTCAAGGAATTGGTGTTACT
TTTAGAGTCACAAAGGATCCAAACATTGTGACTAAAGCAACTTACAAAGTGCCATCAACT
GAAGCTGTTACAAAGGTTCTACAATGGGTCGATAAAAAATTTGGAAATAAATAA
>g13300.t56 Gene=g13300 Length=277
MTILHKLTLNLIFTVFVVSALRIVEQLDLKLEPQMEDLEKYLEDYVSNKPFALLLDYDGT
LAAIQPHPNMTYMTEYTKEALLNISSYPNVYLAVISGRGVDDVKTKVGIDGIVYAGNHGL
EILYPNGTRYIHEVPSDVKANFTKMVEALENLKRDGSWVENKKFSVTFHFRAVPEKDHEK
INNEAKEIIEKFGYRANPAHCAIEAKPPVVWHKGKAAEYILNHSFGKDYVFELLQGIGVT
FRVTKDPNIVTKATYKVPSTEAVTKVLQWVDKKFGNK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g13300.t56 | Gene3D | G3DSA:3.40.50.1000 | - | 53 | 224 | 2.0E-28 |
| 7 | g13300.t56 | Gene3D | G3DSA:3.30.70.1020 | - | 135 | 208 | 2.0E-28 |
| 2 | g13300.t56 | PANTHER | PTHR43768 | TREHALOSE 6-PHOSPHATE PHOSPHATASE | 40 | 268 | 5.3E-39 |
| 3 | g13300.t56 | PANTHER | PTHR43768:SF3 | TREHALOSE 6-PHOSPHATE PHOSPHATASE | 40 | 268 | 5.3E-39 |
| 1 | g13300.t56 | Pfam | PF02358 | Trehalose-phosphatase | 54 | 227 | 7.9E-32 |
| 9 | g13300.t56 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 22 | - |
| 10 | g13300.t56 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 6 | - |
| 11 | g13300.t56 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 7 | 18 | - |
| 12 | g13300.t56 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 19 | 22 | - |
| 8 | g13300.t56 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 23 | 277 | - |
| 4 | g13300.t56 | SUPERFAMILY | SSF56784 | HAD-like | 52 | 270 | 4.13E-27 |
| 5 | g13300.t56 | SignalP_EUK | SignalP-noTM | SignalP-noTM | 1 | 20 | - |
| 15 | g13300.t56 | TIGRFAM | TIGR00685 | T6PP: trehalose-phosphatase | 52 | 227 | 1.0E-31 |
| 14 | g13300.t56 | TIGRFAM | TIGR01484 | HAD-SF-IIB: HAD hydrolase, family IIB | 53 | 225 | 6.7E-14 |
| 13 | g13300.t56 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 7 | 24 | - |
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