General information for g11259.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Glycogen [starch] synthase.
Parent gene
- The parent gene g11259 is located on chr_1: 15147214..15149727 (+ 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 | g11259 | g11259.t1 | isoform | g11259.t1 | 15146392 | 15149035 |
| chr_1 | g11259 | g11259.t1 | exon | g11259.t1.exon1 | 15146392 | 15147146 |
| chr_1 | g11259 | g11259.t1 | cds | g11259.t1.CDS1 | 15146392 | 15147146 |
| chr_1 | g11259 | g11259.t1 | exon | g11259.t1.exon2 | 15147210 | 15147549 |
| chr_1 | g11259 | g11259.t1 | cds | g11259.t1.CDS2 | 15147210 | 15147549 |
| chr_1 | g11259 | g11259.t1 | exon | g11259.t1.exon3 | 15147626 | 15147792 |
| chr_1 | g11259 | g11259.t1 | cds | g11259.t1.CDS3 | 15147626 | 15147792 |
| chr_1 | g11259 | g11259.t1 | exon | g11259.t1.exon4 | 15147868 | 15148014 |
| chr_1 | g11259 | g11259.t1 | cds | g11259.t1.CDS4 | 15147868 | 15148014 |
| chr_1 | g11259 | g11259.t1 | exon | g11259.t1.exon5 | 15148235 | 15148365 |
| chr_1 | g11259 | g11259.t1 | cds | g11259.t1.CDS5 | 15148235 | 15148365 |
| chr_1 | g11259 | g11259.t1 | exon | g11259.t1.exon6 | 15148432 | 15148733 |
| chr_1 | g11259 | g11259.t1 | cds | g11259.t1.CDS6 | 15148432 | 15148733 |
| chr_1 | g11259 | g11259.t1 | exon | g11259.t1.exon7 | 15148793 | 15149035 |
| chr_1 | g11259 | g11259.t1 | cds | g11259.t1.CDS7 | 15148793 | 15149035 |
| chr_1 | g11259 | g11259.t1 | TTS | g11259.t1 | 15149714 | 15149714 |
| chr_1 | g11259 | g11259.t1 | TSS | g11259.t1 | NA | NA |
Sequences
>g11259.t1 Gene=g11259 Length=2085
ATGAGTCGGAGAATTTCTCGTGTTGAATCAGGCGCCGATCTTTTGGATTTCCTTGATAGA
GGTCAAAGTGCATCAAGTGAGAATCGCTTCACTTTTGAAGTAGCATGGGAAGCAGCAAAT
AAAGTTGGTGGAATCTATACTGTCATCCGATCAAAAGCATTTGTGTCAACTGAAGAGCTT
GGTGATCAATATTGTCTTATGGGACCTTATAAGGAAGAATGTGCACGACAAGAAGTTGAA
GAATTTGAATTTCCAAATAATTCTCCTTATCAATGGGCTGTAAATGCAATTCGATCACTC
GGTTACAAGGTTCATTGTGGCAGATGGCTTGTTGATGGTAATCCTCAGATTATTCTATTT
GATATTGGCTCAGCTGCATGGAAATTGGATGAATTTAGACAAGAATTGTGGGAAAAATGC
AGTGTTGGTATTCCTCATTTAGACATTGAATGTAATGATGCTGTTATTCTCGGTTACATG
ATTGCTCAATTTATTAGCGAGTTTAAGAGTGCTGCAGAACGTTTTTCTCAAGAACGTGGC
CTATCTGAACCTAAAATTGTGACACATTTTCATGAATGGCAAGCAGGTGTTGGTCTTATT
GCAATTCGAACAAGACATATTGATGTAGCGACAGTTTTTACGACTCATGCAACTTTATTA
GGACGTTACTTGTGTGCTGGCAATACTGATTTCTACAATAACTTGGCCAAATTTTCTGTC
GACGAGGAGGCGGGAAAACGTCAAATCTATCATCGTTACTGCATTGAACGTGCAGCAACT
CATCTCGCACATGTGTTCACAACAGTGTCCGAAATCACTGGCTATGAAGCAGAGCACTTG
TTGAAAAGAAAAGCAGATGTTATTACACCCAATGGATTAAATGTTAAGAAATTTTCTGCC
ATTCATGAGTTTCAAAATTTGCATGCAATGGCCAAAGAGAAAATTCACGAATTCACTCGT
GGACACTTTTTTGGGCATTTTGATTTCAATTTAGACAAAACACTGTACTTTTTCATCGCT
GGTCGTTATGAGTTTAGCAATAAAGGTGCAGATATTTTTATCGAAGCTCTTGCTCGATTA
AATCATTATCTTAAGTCATCACTGCCAGATACGACTGTCGTCGCATTTCTTATTTTTCCT
GCAAAAACAAATAATTTCAATGTTGAATCGCTTCGCGGTCATGCTGTCACTAAACAATTG
CGTGACACAATTCAACATGTACAGCAAGATATTGGCAGACGCATGTACGACACGTGCCTA
TCTGGCCGTTTACCTGATGGCAATCAACTTCTCACTAAAGAAGATATTGTCAAAATTAAA
CGTTGTCTCTATTCATTACAACGTCATAGCATGCCGCCAGTTACAACACACAACATTGTT
GACGATTGGAATGATCCTGTTCTTAACTCTATTCGACGATGCAATCTATTCAATACAGTT
CATGATCGTGTCAAAATTGTGTTCCATCCTGAGTTTTTAAACTCAACTAACCCACTTTTT
GGTTTGGAATATGAAGAATTTGTACGTGGTTGTCATTTAGGAGTTTTTCCATCATACTAC
GAACCATGGGGTTATACTCCAGCAGAATGTACAGTTATGGGAATTCTTAGTGTTACAACA
AATCTTTCTGGCTTTGGTTGCTTTATGCAGGAACATATCGCGGATCCTAAGTCTTATGGT
ATTTATATTGTTGATAGAAGATTTATCGGCTTGGAAAATACCATTCAACAGTTGGCGCAA
TTTATGTACGATTTCAGTAAAATGAATCGTCGTCAAAGAATTATTATGCGCAACAGAACT
GAACGTTTGAGTGATTTACTTGATTGGAGAAATTTGGGAATTTATTATCGTCAAGCTCGT
ATCAAAGCATTGCAGACTGTTTATCCCGATTATGTTGATGAAATTGGTGAAAGTGTTTAT
AGCCGAGCTGGTAATTTCAATTTCCCTCGTCCCGTTAGTGCTCCACCATCACCATCTTCA
TCACGTCATACAACACCAGCTCCATCATTGCATGGTTCTGATGATGAAGAAGATAGTGTT
GATGAAGATCAAGAACTGCATGAATTGGGAATGAATAATAAATGA
>g11259.t1 Gene=g11259 Length=694
MSRRISRVESGADLLDFLDRGQSASSENRFTFEVAWEAANKVGGIYTVIRSKAFVSTEEL
GDQYCLMGPYKEECARQEVEEFEFPNNSPYQWAVNAIRSLGYKVHCGRWLVDGNPQIILF
DIGSAAWKLDEFRQELWEKCSVGIPHLDIECNDAVILGYMIAQFISEFKSAAERFSQERG
LSEPKIVTHFHEWQAGVGLIAIRTRHIDVATVFTTHATLLGRYLCAGNTDFYNNLAKFSV
DEEAGKRQIYHRYCIERAATHLAHVFTTVSEITGYEAEHLLKRKADVITPNGLNVKKFSA
IHEFQNLHAMAKEKIHEFTRGHFFGHFDFNLDKTLYFFIAGRYEFSNKGADIFIEALARL
NHYLKSSLPDTTVVAFLIFPAKTNNFNVESLRGHAVTKQLRDTIQHVQQDIGRRMYDTCL
SGRLPDGNQLLTKEDIVKIKRCLYSLQRHSMPPVTTHNIVDDWNDPVLNSIRRCNLFNTV
HDRVKIVFHPEFLNSTNPLFGLEYEEFVRGCHLGVFPSYYEPWGYTPAECTVMGILSVTT
NLSGFGCFMQEHIADPKSYGIYIVDRRFIGLENTIQQLAQFMYDFSKMNRRQRIIMRNRT
ERLSDLLDWRNLGIYYRQARIKALQTVYPDYVDEIGESVYSRAGNFNFPRPVSAPPSPSS
SRHTTPAPSLHGSDDEEDSVDEDQELHELGMNNK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g11259.t1 | CDD | cd03793 | GT3_GSY2-like | 28 | 625 | 0.0 |
| 8 | g11259.t1 | Gene3D | G3DSA:3.40.50.2000 | Glycogen Phosphorylase B; | 31 | 625 | 1.2E-266 |
| 7 | g11259.t1 | Gene3D | G3DSA:3.40.50.2000 | Glycogen Phosphorylase B; | 294 | 610 | 1.2E-266 |
| 6 | g11259.t1 | Gene3D | G3DSA:1.20.20.30 | - | 386 | 466 | 1.2E-266 |
| 5 | g11259.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 651 | 694 | - |
| 2 | g11259.t1 | PANTHER | PTHR10176 | GLYCOGEN SYNTHASE | 21 | 681 | 0.0 |
| 1 | g11259.t1 | Pfam | PF05693 | Glycogen synthase | 33 | 678 | 0.0 |
| 3 | g11259.t1 | SUPERFAMILY | SSF53756 | UDP-Glycosyltransferase/glycogen phosphorylase | 41 | 362 | 1.17E-14 |
| 4 | g11259.t1 | SUPERFAMILY | SSF53756 | UDP-Glycosyltransferase/glycogen phosphorylase | 504 | 612 | 3.04E-8 |
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:0005978 | glycogen biosynthetic process | BP |
| GO:0004373 | glycogen (starch) synthase activity | MF |
KEGG
Orthology
- This transcript has been annotated with K00693 (glycogen synthase)
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.
