General information for g13302.t16
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Trehalose-6-phosphate synthase beta].
Parent gene
- The parent gene g13302 is located on chr_1: 29013994..29015173 (- 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 | g13302 | g13302.t16 | TTS | g13302.t16 | 29010178 | 29010178 |
| chr_1 | g13302 | g13302.t16 | isoform | g13302.t16 | 29010236 | 29013176 |
| chr_1 | g13302 | g13302.t16 | exon | g13302.t16.exon1 | 29010236 | 29011209 |
| chr_1 | g13302 | g13302.t16 | cds | g13302.t16.CDS1 | 29011026 | 29011209 |
| chr_1 | g13302 | g13302.t16 | exon | g13302.t16.exon2 | 29011284 | 29011414 |
| chr_1 | g13302 | g13302.t16 | cds | g13302.t16.CDS2 | 29011284 | 29011414 |
| chr_1 | g13302 | g13302.t16 | exon | g13302.t16.exon3 | 29011483 | 29011810 |
| chr_1 | g13302 | g13302.t16 | cds | g13302.t16.CDS3 | 29011483 | 29011810 |
| chr_1 | g13302 | g13302.t16 | exon | g13302.t16.exon4 | 29011883 | 29012166 |
| chr_1 | g13302 | g13302.t16 | cds | g13302.t16.CDS4 | 29011883 | 29012166 |
| chr_1 | g13302 | g13302.t16 | exon | g13302.t16.exon5 | 29012226 | 29012422 |
| chr_1 | g13302 | g13302.t16 | cds | g13302.t16.CDS5 | 29012226 | 29012422 |
| chr_1 | g13302 | g13302.t16 | exon | g13302.t16.exon6 | 29012487 | 29013176 |
| chr_1 | g13302 | g13302.t16 | cds | g13302.t16.CDS6 | 29012487 | 29013123 |
| chr_1 | g13302 | g13302.t16 | TSS | g13302.t16 | NA | NA |
Sequences
>g13302.t16 Gene=g13302 Length=2604
GTCGTGCTATTTTCTCAACTGATCACTGGAGAGCGTATGTGGCCGCTAACATTATGTTTG
CTGATAAGACCATTGAAGCAATTGAGCGTTGCACAAAGAACGGCGGACCACCACCCATTG
TTTGGATTCATGATTATCATTTGATGCTTTGTGCAAATTATGTTCGTGAGAAGGCTGAAG
AAAAGAATCTCAACATTCAACTTGCATTCTTTTTGCATATTCCATTTCCACCATGGGATA
TTTTCCGTTTGTTCCCATGGGCTGACGAAATTCTTCAAGGAATGCTTGCTTGCGATATGG
TTGGCTTCCACATTCGCGATTATTGTATCAATTTTGTTGACTGCTGTCAAAGAAGTCTCG
GTTGTCGTGTTGATCGCAAAAATCTTTTAGTTGAACATGGTGGACGTTCTGTTCGTGTTC
GTCCATTGCCAATTGGAATTCCTTTCGATAGATTTGTCGAATTGGCAAAAAGTGCAAAGA
GAATCATCAAGACAAAGCAAAAGATTATTTTGGGAGTTGATCGTCTTGATTATACAAAAG
GATTAGTCAATCGCTTGAAAGCTTTTGAAATTTTACTCGAAAAGCATCCAGAGCATCGTG
GAACTGTCAGTTTCTTGCAAATCTCAGTTCCATCACGTACTGATGTAGCTGAATATCAGC
AATTAAAAGAAGAAATGGATCAACTTGTTGGTCGCATAAACGGACGTTTCTCAACAGCTG
TTTGGGCACCAATCCGTTATATTTATGGTTGTGTTAGTCAAAGTGAATTGGCAGCTTATT
ACCGTGATGCAGCAGTTGCTCTTGTGACACCACTTCGTGATGGTATGAATCTCGTTGCAA
AAGAATTTGTGGCATGTCAAATTAATGAACCTCCTGGTGTCTTGATTGTCAGTCCATTTG
CTGGTGCAGGAGAAACAATGCATGAAGCTTTAGTATGCAATCCATATGAAATTTCAGAAG
CAGCTGAAGTTATTCATCGTGCTTTGACAATGCCAGAAGATGAAAGATCATTGCGAATGA
GCAGATTACGTCGTAGAGAAATGGAAAATGATGTTAATTATTGGATGCGGTCATTTATGA
AAGCAATGGGATCAGACATAGAGCAAGATGAGATCGGAACAACTAGTTTGCAACCAGTCA
CAATTGATGACTTTGATGATTATTTGTTGAATTACATCGGCTATTCACACAAGCTTGCTC
TTTTGCTTGATTATGATGGTACATTGGCACCCATTGCTCCACATCCTGATCTTGCTACGC
TTCCACAAGAAACAAAGAATGTTTTGCATCGTTTGAGCAATTTAAATGAAGTCTATATTG
CAGTCATTTCTGGTCGTAGTGTTGAAAATGTTAAAAACATGGTTGGAATCGAAGGCATCA
CATATGCCGGTAATCACGGTTTAGAAATTTTGCATCCCGATGGAAGTAAGTTCGTTCACC
CTATGCCAGTCGAATATGAGGAAAAAGTCAGTAAATTATTGAGAGCATTGCAAGATTCGG
TTTGTCATGATGGAGCTTGGGTAGAGAACAAAGGTGCCCTTTTGACTTTCCATTATCGTG
ATACACCAAATGAAATGCGTCCACAAATGATTGACAAGGCAAAATTTTTGATTGAGCATT
TTGGATTCACTGCAAGTGAATCACTATGTGCTATTGAAGCTAAGCCACCAGTCCCTTGGA
ATAAAGGACGTGCTTCAATTTATATTCTTCGTACTGCATTTGGTGTTGATTGGAGTGAGA
GAATCAAAATTATTTACGTTGGAGATGACGTCACTGATGAGGACGCAATGATGGTAAATT
CGAACAAATTTTAAAAAAAAATTCATCTAATTGGATTGACTCATTTTTCAAAATTTTTTC
AGTTTAAAGAACATCATTTTTTGAATATTTCCAAAAATGCTTTCTATACTCTTTATTCTC
TCGTATCTAGGCTCTACGAGGCATGGCAGCGACGTTCAGAATCGCAAGTTCCAATATTAT
TAAAACCGCAGCTGAACGCCGTTTGCCCTCCACCGATTCCGTTCTCACCATGTTAAAATG
GATTGAGCGTCATTTTATGAATAAACGTCCACGTAAGATCTCAAATAATCAGCGACCAAA
GAAAGTTTCTTCATTTAACAATAACAATAGTATCGGTTTTCCTATCCATATGTCATTCGA
CTTAACCACCTCCCCTTCAAGAAGTCCACGTTCATCTCCATTACCAAGCCCATCCTATAG
TCAAGAAAGTAGCAGCAGTAACAGTAGCAGCAGCAGTGAAGAATCATAGAATTTCTTTTT
ATTTAGTAAATTTTTAATTATCAATAATCTTGATAGGTTCAATAGAGTTTTTTTAATCGT
TCCTAATAATTTTTACAAATTTTCAATGAAATAATTTGATGAAATTCTAATATATATAGA
ATTTTAATGTTATGCCAAAAATTTTTAAAATTAAATAATTATTATTGTCTCTTCTTTTCT
ATTGGACATTCTAGACAATGCATAAAAATATTTTTCAAAACGAATTTTATAAATAAGGCA
AAAAAACTTAAATTTAAGGAGAAAAAATTTATTTCTGTGAATTATAAAATATTTCTTTAT
TCAAATTTGAAAATAAGTCGCTAT
>g13302.t16 Gene=g13302 Length=586
MFADKTIEAIERCTKNGGPPPIVWIHDYHLMLCANYVREKAEEKNLNIQLAFFLHIPFPP
WDIFRLFPWADEILQGMLACDMVGFHIRDYCINFVDCCQRSLGCRVDRKNLLVEHGGRSV
RVRPLPIGIPFDRFVELAKSAKRIIKTKQKIILGVDRLDYTKGLVNRLKAFEILLEKHPE
HRGTVSFLQISVPSRTDVAEYQQLKEEMDQLVGRINGRFSTAVWAPIRYIYGCVSQSELA
AYYRDAAVALVTPLRDGMNLVAKEFVACQINEPPGVLIVSPFAGAGETMHEALVCNPYEI
SEAAEVIHRALTMPEDERSLRMSRLRRREMENDVNYWMRSFMKAMGSDIEQDEIGTTSLQ
PVTIDDFDDYLLNYIGYSHKLALLLDYDGTLAPIAPHPDLATLPQETKNVLHRLSNLNEV
YIAVISGRSVENVKNMVGIEGITYAGNHGLEILHPDGSKFVHPMPVEYEEKVSKLLRALQ
DSVCHDGAWVENKGALLTFHYRDTPNEMRPQMIDKAKFLIEHFGFTASESLCAIEAKPPV
PWNKGRASIYILRTAFGVDWSERIKIIYVGDDVTDEDAMMVNSNKF
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 13 | g13302.t16 | CDD | cd03788 | GT20_TPS | 1 | 345 | 0 |
| 14 | g13302.t16 | CDD | cd01627 | HAD_TPP | 382 | 579 | 0 |
| 10 | g13302.t16 | Gene3D | G3DSA:3.40.50.2000 | Glycogen Phosphorylase B; | 1 | 144 | 0 |
| 9 | g13302.t16 | Gene3D | G3DSA:3.40.50.2000 | Glycogen Phosphorylase B; | 145 | 329 | 0 |
| 7 | g13302.t16 | Gene3D | G3DSA:3.40.50.1000 | - | 383 | 584 | 0 |
| 8 | g13302.t16 | Gene3D | G3DSA:3.30.70.1020 | - | 465 | 539 | 0 |
| 3 | g13302.t16 | PANTHER | PTHR10788:SF97 | BCDNA.GH08860 | 2 | 574 | 0 |
| 4 | g13302.t16 | PANTHER | PTHR10788 | TREHALOSE-6-PHOSPHATE SYNTHASE | 2 | 574 | 0 |
| 1 | g13302.t16 | Pfam | PF00982 | Glycosyltransferase family 20 | 2 | 345 | 0 |
| 2 | g13302.t16 | Pfam | PF02358 | Trehalose-phosphatase | 384 | 579 | 0 |
| 5 | g13302.t16 | SUPERFAMILY | SSF53756 | UDP-Glycosyltransferase/glycogen phosphorylase | 19 | 345 | 0 |
| 6 | g13302.t16 | SUPERFAMILY | SSF56784 | HAD-like | 382 | 581 | 0 |
| 12 | g13302.t16 | TIGRFAM | TIGR00685 | T6PP: trehalose-phosphatase | 379 | 580 | 0 |
| 11 | g13302.t16 | TIGRFAM | TIGR01484 | HAD-SF-IIB: HAD hydrolase, family IIB | 383 | 581 | 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.
