Gene loci information

Transcript annotation

  • This transcript has been annotated as Trehalose-6-phosphate synthase beta].

Parent gene

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.t17 TTS g13302.t17 29010178 29010178
chr_1 g13302 g13302.t17 isoform g13302.t17 29010236 29015173
chr_1 g13302 g13302.t17 exon g13302.t17.exon1 29010236 29010977
chr_1 g13302 g13302.t17 cds g13302.t17.CDS1 29010804 29010977
chr_1 g13302 g13302.t17 exon g13302.t17.exon2 29011047 29011209
chr_1 g13302 g13302.t17 cds g13302.t17.CDS2 29011047 29011209
chr_1 g13302 g13302.t17 exon g13302.t17.exon3 29011284 29011414
chr_1 g13302 g13302.t17 cds g13302.t17.CDS3 29011284 29011414
chr_1 g13302 g13302.t17 exon g13302.t17.exon4 29011483 29011810
chr_1 g13302 g13302.t17 cds g13302.t17.CDS4 29011483 29011810
chr_1 g13302 g13302.t17 exon g13302.t17.exon5 29011883 29012166
chr_1 g13302 g13302.t17 cds g13302.t17.CDS5 29011883 29012166
chr_1 g13302 g13302.t17 exon g13302.t17.exon6 29012226 29012422
chr_1 g13302 g13302.t17 cds g13302.t17.CDS6 29012226 29012422
chr_1 g13302 g13302.t17 exon g13302.t17.exon7 29012487 29013176
chr_1 g13302 g13302.t17 cds g13302.t17.CDS7 29012487 29013176
chr_1 g13302 g13302.t17 exon g13302.t17.exon8 29013279 29013372
chr_1 g13302 g13302.t17 cds g13302.t17.CDS8 29013279 29013372
chr_1 g13302 g13302.t17 exon g13302.t17.exon9 29013456 29013560
chr_1 g13302 g13302.t17 cds g13302.t17.CDS9 29013456 29013560
chr_1 g13302 g13302.t17 exon g13302.t17.exon10 29013625 29013682
chr_1 g13302 g13302.t17 cds g13302.t17.CDS10 29013625 29013682
chr_1 g13302 g13302.t17 exon g13302.t17.exon11 29015022 29015173
chr_1 g13302 g13302.t17 cds g13302.t17.CDS11 29015022 29015173
chr_1 g13302 g13302.t17 TSS g13302.t17 29015404 29015404

Sequences

>g13302.t17 Gene=g13302 Length=2944
ATGACAAAGGAAAATGATCCAAAACATGAACCGGAAATAACTGTTACTGCAGCTGAGCAG
TCAGCACCTAAGAGCAAACTTATTGTTGTTTCCAATCGTTTACCATTTGTTCTTAAGAAG
GACATTAGTGGAAAATTATATCGTCAAGCAAGTGCCGGTGGATTAGTCACAGCAGTTGCT
CCTGTTGTTATTAAGGGAAAAGGACAATGGGTCGGCTGGCCAGGTATGCATCTTCCCAAA
GATTTTGATGACTTACAAATTCCCGAATCTGATCCAAACGATCAAACACCAACCGCTGGT
TTAAAATCAGAGCAAGTAGTAACAGTCAATATGAGCCCTGATCTTTTCGAAGACTACTAT
AATGGTTGCTGTAATGGAACACATTGGCCTCTTTTCCATTCAATGCCGGGTCGTGCTATT
TTCTCAACTGATCACTGGAGAGCGTATGTGGCCGCTAACATTATGTTTGCTGATAAGACC
ATTGAAGCAATTGAGCGTTGCACAAAGAACGGCGGACCACCACCCATTGTTTGGATTCAT
GATTATCATTTGATGCTTTGTGCAAATTATGTTCGTGAGAAGGCTGAAGAAAAGAATCTC
AACATTCAACTTGCATTCTTTTTGCATATTCCATTTCCACCATGGGATATTTTCCGTTTG
TTCCCATGGGCTGACGAAATTCTTCAAGGAATGCTTGCTTGCGATATGGTTGGCTTCCAC
ATTCGCGATTATTGTATCAATTTTGTTGACTGCTGTCAAAGAAGTCTCGGTTGTCGTGTT
GATCGCAAAAATCTTTTAGTTGAACATGGTGGACGTTCTGTTCGTGTTCGTCCATTGCCA
ATTGGAATTCCTTTCGATAGATTTGTCGAATTGGCAAAAAGTGCAAAGAGAATCATCAAG
ACAAAGCAAAAGATTATTTTGGGAGTTGATCGTCTTGATTATACAAAAGGATTAGTCAAT
CGCTTGAAAGCTTTTGAAATTTTACTCGAAAAGCATCCAGAGCATCGTGGAACTGTCAGT
TTCTTGCAAATCTCAGTTCCATCACGTACTGATGTAGCTGAATATCAGCAATTAAAAGAA
GAAATGGATCAACTTGTTGGTCGCATAAACGGACGTTTCTCAACAGCTGTTTGGGCACCA
ATCCGTTATATTTATGGTTGTGTTAGTCAAAGTGAATTGGCAGCTTATTACCGTGATGCA
GCAGTTGCTCTTGTGACACCACTTCGTGATGGTATGAATCTCGTTGCAAAAGAATTTGTG
GCATGTCAAATTAATGAACCTCCTGGTGTCTTGATTGTCAGTCCATTTGCTGGTGCAGGA
GAAACAATGCATGAAGCTTTAGTATGCAATCCATATGAAATTTCAGAAGCAGCTGAAGTT
ATTCATCGTGCTTTGACAATGCCAGAAGATGAAAGATCATTGCGAATGAGCAGATTACGT
CGTAGAGAAATGGAAAATGATGTTAATTATTGGATGCGGTCATTTATGAAAGCAATGGGA
TCAGACATAGAGCAAGATGAGATCGGAACAACTAGTTTGCAACCAGTCACAATTGATGAC
TTTGATGATTATTTGTTGAATTACATCGGCTATTCACACAAGCTTGCTCTTTTGCTTGAT
TATGATGGTACATTGGCACCCATTGCTCCACATCCTGATCTTGCTACGCTTCCACAAGAA
ACAAAGAATGTTTTGCATCGTTTGAGCAATTTAAATGAAGTCTATATTGCAGTCATTTCT
GGTCGTAGTGTTGAAAATGTTAAAAACATGGTTGGAATCGAAGGCATCACATATGCCGGT
AATCACGGTTTAGAAATTTTGCATCCCGATGGAAGTAAGTTCGTTCACCCTATGCCAGTC
GAATATGAGGAAAAAGTCAGTAAATTATTGAGAGCATTGCAAGATTCGGTTTGTCATGAT
GGAGCTTGGGTAGAGAACAAAGGTGCCCTTTTGACTTTCCATTATCGTGATACACCAAAT
GAAATGCGTCCACAAATGATTGACAAGGCAAAATTTTTGATTGAGCATTTTGGATTCACT
GCAAGTGAATCACTATGTGCTATTGAAGCTAAGCCACCAGTCCCTTGGAATAAAGGACGT
GCTTCAATTTATATTCTTCGTACTGCATTTGGTGTTGATTGGAGTGAGAGAATCAAAATT
ATTTACGTTGGAGATGACGTCACTGATGAGGACGCAATGATGTTTAAAGAACATCATTTT
TTGAATATTTCCAAAAATGCTTTCTATACTCTTTATTCTCTCGTATCTAGGCTCTACGAG
GCATGGCAGCGACGTTCAGAATCGCAAGTTCCAATATTATTAAAACCGCAGCTGAACGCC
GTTTGCCCTCCACCGATTCCGTTCTCACCATGTTAAAATGGATTGAGCGTCATTTTATGA
ATAAACGTCCACGTAAGATCTCAAATAATCAGCGACCAAAGAAAGTTTCTTCATTTAACA
ATAACAATAGTATCGGTTTTCCTATCCATATGTCATTCGACTTAACCACCTCCCCTTCAA
GAAGTCCACGTTCATCTCCATTACCAAGCCCATCCTATAGTCAAGAAAGTAGCAGCAGTA
ACAGTAGCAGCAGCAGTGAAGAATCATAGAATTTCTTTTTATTTAGTAAATTTTTAATTA
TCAATAATCTTGATAGGTTCAATAGAGTTTTTTTAATCGTTCCTAATAATTTTTACAAAT
TTTCAATGAAATAATTTGATGAAATTCTAATATATATAGAATTTTAATGTTATGCCAAAA
ATTTTTAAAATTAAATAATTATTATTGTCTCTTCTTTTCTATTGGACATTCTAGACAATG
CATAAAAATATTTTTCAAAACGAATTTTATAAATAAGGCAAAAAAACTTAAATTTAAGGA
GAAAAAATTTATTTCTGTGAATTATAAAATATTTCTTTATTCAAATTTGAAAATAAGTCG
CTAT

>g13302.t17 Gene=g13302 Length=791
MTKENDPKHEPEITVTAAEQSAPKSKLIVVSNRLPFVLKKDISGKLYRQASAGGLVTAVA
PVVIKGKGQWVGWPGMHLPKDFDDLQIPESDPNDQTPTAGLKSEQVVTVNMSPDLFEDYY
NGCCNGTHWPLFHSMPGRAIFSTDHWRAYVAANIMFADKTIEAIERCTKNGGPPPIVWIH
DYHLMLCANYVREKAEEKNLNIQLAFFLHIPFPPWDIFRLFPWADEILQGMLACDMVGFH
IRDYCINFVDCCQRSLGCRVDRKNLLVEHGGRSVRVRPLPIGIPFDRFVELAKSAKRIIK
TKQKIILGVDRLDYTKGLVNRLKAFEILLEKHPEHRGTVSFLQISVPSRTDVAEYQQLKE
EMDQLVGRINGRFSTAVWAPIRYIYGCVSQSELAAYYRDAAVALVTPLRDGMNLVAKEFV
ACQINEPPGVLIVSPFAGAGETMHEALVCNPYEISEAAEVIHRALTMPEDERSLRMSRLR
RREMENDVNYWMRSFMKAMGSDIEQDEIGTTSLQPVTIDDFDDYLLNYIGYSHKLALLLD
YDGTLAPIAPHPDLATLPQETKNVLHRLSNLNEVYIAVISGRSVENVKNMVGIEGITYAG
NHGLEILHPDGSKFVHPMPVEYEEKVSKLLRALQDSVCHDGAWVENKGALLTFHYRDTPN
EMRPQMIDKAKFLIEHFGFTASESLCAIEAKPPVPWNKGRASIYILRTAFGVDWSERIKI
IYVGDDVTDEDAMMFKEHHFLNISKNAFYTLYSLVSRLYEAWQRRSESQVPILLKPQLNA
VCPPPIPFSPC

Protein features from InterProScan

Transcript Database ID Name Start End E.value
13 g13302.t17 CDD cd03788 GT20_TPS 26 499 0
14 g13302.t17 CDD cd01627 HAD_TPP 536 744 0
9 g13302.t17 Gene3D G3DSA:3.40.50.2000 Glycogen Phosphorylase B; 51 496 0
10 g13302.t17 Gene3D G3DSA:3.40.50.2000 Glycogen Phosphorylase B; 285 485 0
7 g13302.t17 Gene3D G3DSA:3.40.50.1000 - 537 737 0
8 g13302.t17 Gene3D G3DSA:3.30.70.1020 - 619 693 0
3 g13302.t17 PANTHER PTHR10788:SF97 BCDNA.GH08860 16 741 0
4 g13302.t17 PANTHER PTHR10788 TREHALOSE-6-PHOSPHATE SYNTHASE 16 741 0
1 g13302.t17 Pfam PF00982 Glycosyltransferase family 20 26 499 0
2 g13302.t17 Pfam PF02358 Trehalose-phosphatase 538 735 0
5 g13302.t17 SUPERFAMILY SSF53756 UDP-Glycosyltransferase/glycogen phosphorylase 25 499 0
6 g13302.t17 SUPERFAMILY SSF56784 HAD-like 536 736 0
12 g13302.t17 TIGRFAM TIGR00685 T6PP: trehalose-phosphatase 533 733 0
11 g13302.t17 TIGRFAM TIGR01484 HAD-SF-IIB: HAD hydrolase, family IIB 537 737 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

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.

Raw TPM values