General information for g11259.t7
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.t7 | isoform | g11259.t7 | 15147214 | 15149727 |
| chr_1 | g11259 | g11259.t7 | exon | g11259.t7.exon1 | 15147214 | 15147549 |
| chr_1 | g11259 | g11259.t7 | cds | g11259.t7.CDS1 | 15147382 | 15147549 |
| chr_1 | g11259 | g11259.t7 | exon | g11259.t7.exon2 | 15147626 | 15147792 |
| chr_1 | g11259 | g11259.t7 | cds | g11259.t7.CDS2 | 15147626 | 15147792 |
| chr_1 | g11259 | g11259.t7 | exon | g11259.t7.exon3 | 15147868 | 15148014 |
| chr_1 | g11259 | g11259.t7 | cds | g11259.t7.CDS3 | 15147868 | 15148014 |
| chr_1 | g11259 | g11259.t7 | exon | g11259.t7.exon4 | 15148235 | 15148365 |
| chr_1 | g11259 | g11259.t7 | cds | g11259.t7.CDS4 | 15148235 | 15148365 |
| chr_1 | g11259 | g11259.t7 | exon | g11259.t7.exon5 | 15148432 | 15148733 |
| chr_1 | g11259 | g11259.t7 | cds | g11259.t7.CDS5 | 15148432 | 15148733 |
| chr_1 | g11259 | g11259.t7 | exon | g11259.t7.exon6 | 15148793 | 15149727 |
| chr_1 | g11259 | g11259.t7 | cds | g11259.t7.CDS6 | 15148793 | 15149035 |
| chr_1 | g11259 | g11259.t7 | TTS | g11259.t7 | 15149714 | 15149714 |
| chr_1 | g11259 | g11259.t7 | TSS | g11259.t7 | NA | NA |
Sequences
>g11259.t7 Gene=g11259 Length=2018
TGCATTGAACGTGCAGCAACTCATCTCGCACATGTGTTCACAACAGTGTCCGAAATCACT
GGCTATGAAGCAGAGCACTTGTTGAAAAGAAAAGCAGATGTTATTACACCCAATGGATTA
AATGTTAAGAAATTTTCTGCCATTCATGAGTTTCAAAATTTGCATGCAATGGCCAAAGAG
AAAATTCACGAATTCACTCGTGGACACTTTTTTGGGCATTTTGATTTCAATTTAGACAAA
ACACTGTACTTTTTCATCGCTGGTCGTTATGAGTTTAGCAATAAAGGTGCAGATATTTTT
ATCGAAGCTCTTGCTCGATTAAATCATTATCTTAAGTCATCACTGCCAGATACGACTGTC
GTCGCATTTCTTATTTTTCCTGCAAAAACAAATAATTTCAATGTTGAATCGCTTCGCGGT
CATGCTGTCACTAAACAATTGCGTGACACAATTCAACATGTACAGCAAGATATTGGCAGA
CGCATGTACGACACGTGCCTATCTGGCCGTTTACCTGATGGCAATCAACTTCTCACTAAA
GAAGATATTGTCAAAATTAAACGTTGTCTCTATTCATTACAACGTCATAGCATGCCGCCA
GTTACAACACACAACATTGTTGACGATTGGAATGATCCTGTTCTTAACTCTATTCGACGA
TGCAATCTATTCAATACAGTTCATGATCGTGTCAAAATTGTGTTCCATCCTGAGTTTTTA
AACTCAACTAACCCACTTTTTGGTTTGGAATATGAAGAATTTGTACGTGGTTGTCATTTA
GGAGTTTTTCCATCATACTACGAACCATGGGGTTATACTCCAGCAGAATGTACAGTTATG
GGAATTCTTAGTGTTACAACAAATCTTTCTGGCTTTGGTTGCTTTATGCAGGAACATATC
GCGGATCCTAAGTCTTATGGTATTTATATTGTTGATAGAAGATTTATCGGCTTGGAAAAT
ACCATTCAACAGTTGGCGCAATTTATGTACGATTTCAGTAAAATGAATCGTCGTCAAAGA
ATTATTATGCGCAACAGAACTGAACGTTTGAGTGATTTACTTGATTGGAGAAATTTGGGA
ATTTATTATCGTCAAGCTCGTATCAAAGCATTGCAGACTGTTTATCCCGATTATGTTGAT
GAAATTGGTGAAAGTGTTTATAGCCGAGCTGGTAATTTCAATTTCCCTCGTCCCGTTAGT
GCTCCACCATCACCATCTTCATCACGTCATACAACACCAGCTCCATCATTGCATGGTTCT
GATGATGAAGAAGATAGTGTTGATGAAGATCAAGAACTGCATGAATTGGGAATGAATAAT
AAATGAGAACGAAAGAAAAGGCGAAAGGGAAAGGAGAAAACAGTCTTATGATTGTAAATA
AACAACAGCAATTAGAAGCTCTCAAATTGTCAAAGTCATAATAATTACAGGATAATTATT
ATTATCAACTTTTATCCCTTTGTGTTCATGTATCCGTACATATCTTTATTTTTTCTTACT
TACTTATTTTTTGCCATATTAAGAATCAAATGTTATAAATATTATAGTCTATAGAATTTT
TTAATTCGTTGTTTTTTGATAATTAATTTCCATCATTAATTTTTTGTTAAATCGTGACAA
ATATTATCTAATCGTCAATACATATATAATTCGATGATGCCATTACATTTATAATAAAAT
CTTTAAAGCAACTTATGTAGCTGTTCTAATATTAAAACATAACATATATCGTTTGTGCAA
TAAGGAGCTAAAGTGATCGAAACCCAAGAAAGATTAAATGAGAGAAATATGGATTTAATT
AGTCGTAGAAAAAACAAATTCGAGATAGTCACAAGAGTGATGGTTTCATTTTCTAATTTA
ATTTTTAAAATATTTTATTGAAATATTATGTAGAACTGCAATTTGTTTGAGAAAACTATC
AGACTTATTTTAGTAGCATATTAATAAATATTAGTTCAAAGTGAGAATGAAAGATATTAA
TAATAAAAATATATTTTTGAAAAACATAAATTTTATTT
>g11259.t7 Gene=g11259 Length=385
MAKEKIHEFTRGHFFGHFDFNLDKTLYFFIAGRYEFSNKGADIFIEALARLNHYLKSSLP
DTTVVAFLIFPAKTNNFNVESLRGHAVTKQLRDTIQHVQQDIGRRMYDTCLSGRLPDGNQ
LLTKEDIVKIKRCLYSLQRHSMPPVTTHNIVDDWNDPVLNSIRRCNLFNTVHDRVKIVFH
PEFLNSTNPLFGLEYEEFVRGCHLGVFPSYYEPWGYTPAECTVMGILSVTTNLSGFGCFM
QEHIADPKSYGIYIVDRRFIGLENTIQQLAQFMYDFSKMNRRQRIIMRNRTERLSDLLDW
RNLGIYYRQARIKALQTVYPDYVDEIGESVYSRAGNFNFPRPVSAPPSPSSSRHTTPAPS
LHGSDDEEDSVDEDQELHELGMNNK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g11259.t7 | Gene3D | G3DSA:1.20.20.30 | - | 77 | 153 | 1.2E-30 |
| 4 | g11259.t7 | MobiDBLite | mobidb-lite | consensus disorder prediction | 342 | 385 | - |
| 2 | g11259.t7 | PANTHER | PTHR10176 | GLYCOGEN SYNTHASE | 2 | 373 | 7.4E-185 |
| 1 | g11259.t7 | Pfam | PF05693 | Glycogen synthase | 1 | 369 | 3.0E-195 |
| 3 | g11259.t7 | SUPERFAMILY | SSF53756 | UDP-Glycosyltransferase/glycogen phosphorylase | 194 | 303 | 1.05E-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 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.
