General information for g13300.t4
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.t4 | isoform | g13300.t4 | 29007543 | 29009204 |
| chr_1 | g13300 | g13300.t4 | exon | g13300.t4.exon1 | 29007543 | 29007941 |
| chr_1 | g13300 | g13300.t4 | exon | g13300.t4.exon2 | 29008121 | 29008530 |
| chr_1 | g13300 | g13300.t4 | cds | g13300.t4.CDS1 | 29008145 | 29008530 |
| chr_1 | g13300 | g13300.t4 | exon | g13300.t4.exon3 | 29008591 | 29008906 |
| chr_1 | g13300 | g13300.t4 | cds | g13300.t4.CDS2 | 29008591 | 29008906 |
| chr_1 | g13300 | g13300.t4 | exon | g13300.t4.exon4 | 29008971 | 29009004 |
| chr_1 | g13300 | g13300.t4 | cds | g13300.t4.CDS3 | 29008971 | 29009004 |
| chr_1 | g13300 | g13300.t4 | exon | g13300.t4.exon5 | 29009056 | 29009204 |
| chr_1 | g13300 | g13300.t4 | cds | g13300.t4.CDS4 | 29009056 | 29009204 |
| chr_1 | g13300 | g13300.t4 | TTS | g13300.t4 | 29009276 | 29009276 |
| chr_1 | g13300 | g13300.t4 | TSS | g13300.t4 | NA | NA |
Sequences
>g13300.t4 Gene=g13300 Length=1308
TTATCTTTTGATAAACATTGAATATTATAAATAATGCGCAATTTCTAAAGCAACACATGC
ATTATATGGAGGAAAAATTTCATTTAATTTCTTATCTGTCTCCACAAATTTTATAAACAA
ACGGTTAGTCGCTCACACACGAATAATTATCAATATTTACGAAATAAAAAAAAGTTCCTT
CGTTCATTCACATTTGTTTATGAAGAAAAGAGAGAAATCTTCTCAGTTACTCTCTCTCAA
TAAACACGCATATTTCAAAGAAAAAATTGTTTGTGAATGTTGTAGATAAGAAGATTCTTA
ATTCGCTCTCAATATTGAGATTTGTTTTTAAAAGTTACTCTCAGTTTTCACGTGAATCTC
AACAGAATCAGACTATTATATTTCTTTCTGTTTTTTGTGATCACTCTCTGATAATAATAA
TTCATGACAATACTACACAAGCTAACTTTAAATCTCATTTTCACAGTCTTCGTTGTGAGT
GCATTGAGAATTGTCGAACAATTAGATTTGAAACTTGAGCCACAAATGGAAGATTTAGAA
AAATACTTGGAGGATTATGTGTCGAATAAACCATTCGCGTTATTACTCGATTATGACGGC
ACGTTGGCTGCCATTCAACCACATCCAAATATGACATACATGACTGAATATACCAAAGAA
GCGCTATTGAACATCTCATCTTACCCCAACGTGTATTTAGCAGTTATATCCGGAAGGGGA
GTTGATGATGTGAAGACAAAAGTTGGTATCGATGGAATTGTTTATGCTGGAAATCATGGT
CTCGAAATTTTATATCCTAATGGAACTCGTTACATACACGAAGTTCCAAGTGATGTTAAA
GCAAATTTTACAAAAATGGTGGAAGCTTTAGAAAATCTTAAAAGAGACGGAAGTTGGGTC
GAAAATAAGAAATTCTCAGTAACTTTTCACTTTAGAGCTGTGCCTGAAAAAGATCATGAG
AAAATCAACAATGAAGCTAAGGAAATTATCGAGAAATTTGGATATCGAGCAAATCCAGCT
CATTGCGCTATTGAAGCAAAACCACCGGTAGTATGGCATAAGGGCAAGGCAGCCGAATAT
ATTTTAAATCACTCATTTGGTAAAGATTGGAGAGAAAAAATTCAAGTTGTGTTTGCTGGC
GATGATACAACCGATGAAGATGTTTTCGAGTTACTTCAAGGAATTGGTGTTACTTTTAGA
GTCACAAAGGATCCAAACATTGTGACTAAAGCAACTTACAAAGTGCCATCAACTGAAGCT
GTTACAAAGGTTCTACAATGGGTCGATAAAAAATTTGGAAATAAATAA
>g13300.t4 Gene=g13300 Length=294
MTILHKLTLNLIFTVFVVSALRIVEQLDLKLEPQMEDLEKYLEDYVSNKPFALLLDYDGT
LAAIQPHPNMTYMTEYTKEALLNISSYPNVYLAVISGRGVDDVKTKVGIDGIVYAGNHGL
EILYPNGTRYIHEVPSDVKANFTKMVEALENLKRDGSWVENKKFSVTFHFRAVPEKDHEK
INNEAKEIIEKFGYRANPAHCAIEAKPPVVWHKGKAAEYILNHSFGKDWREKIQVVFAGD
DTTDEDVFELLQGIGVTFRVTKDPNIVTKATYKVPSTEAVTKVLQWVDKKFGNK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 13 | g13300.t4 | CDD | cd01627 | HAD_TPP | 52 | 280 | 1.26513E-58 |
| 6 | g13300.t4 | Gene3D | G3DSA:3.40.50.1000 | - | 53 | 274 | 3.8E-40 |
| 7 | g13300.t4 | Gene3D | G3DSA:3.30.70.1020 | - | 135 | 208 | 3.8E-40 |
| 2 | g13300.t4 | PANTHER | PTHR43768 | TREHALOSE 6-PHOSPHATE PHOSPHATASE | 40 | 285 | 1.4E-49 |
| 3 | g13300.t4 | PANTHER | PTHR43768:SF3 | TREHALOSE 6-PHOSPHATE PHOSPHATASE | 40 | 285 | 1.4E-49 |
| 1 | g13300.t4 | Pfam | PF02358 | Trehalose-phosphatase | 54 | 274 | 1.9E-39 |
| 9 | g13300.t4 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 22 | - |
| 10 | g13300.t4 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 6 | - |
| 11 | g13300.t4 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 7 | 18 | - |
| 12 | g13300.t4 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 19 | 22 | - |
| 8 | g13300.t4 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 23 | 294 | - |
| 4 | g13300.t4 | SUPERFAMILY | SSF56784 | HAD-like | 52 | 287 | 7.56E-36 |
| 5 | g13300.t4 | SignalP_EUK | SignalP-noTM | SignalP-noTM | 1 | 20 | - |
| 16 | g13300.t4 | TIGRFAM | TIGR00685 | T6PP: trehalose-phosphatase | 52 | 287 | 4.4E-42 |
| 15 | g13300.t4 | TIGRFAM | TIGR01484 | HAD-SF-IIB: HAD hydrolase, family IIB | 53 | 255 | 2.8E-20 |
| 14 | g13300.t4 | 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 transcript has been annotated with K01087 (trehalose 6-phosphate phosphatase)
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.
