Gene loci information

Transcript annotation

  • This transcript has been annotated as Glycogen [starch] synthase.

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 g11259 g11259.t5 TSS g11259.t5 15145247 15145247
chr_1 g11259 g11259.t5 isoform g11259.t5 15145478 15147543
chr_1 g11259 g11259.t5 exon g11259.t5.exon1 15145478 15145485
chr_1 g11259 g11259.t5 exon g11259.t5.exon2 15146298 15147146
chr_1 g11259 g11259.t5 cds g11259.t5.CDS1 15146392 15147146
chr_1 g11259 g11259.t5 exon g11259.t5.exon3 15147210 15147543
chr_1 g11259 g11259.t5 cds g11259.t5.CDS2 15147210 15147543
chr_1 g11259 g11259.t5 TTS g11259.t5 NA NA

Sequences

>g11259.t5 Gene=g11259 Length=1191
TATAATTTGACGTCATTAGGAAAATAAAAATTGAACGTCATTACAACTTGAGAGCAAACA
AAATTTAAATCAAACAATTTTATTAACAACAACGTTTTCAAGATGAGTCGGAGAATTTCT
CGTGTTGAATCAGGCGCCGATCTTTTGGATTTCCTTGATAGAGGTCAAAGTGCATCAAGT
GAGAATCGCTTCACTTTTGAAGTAGCATGGGAAGCAGCAAATAAAGTTGGTGGAATCTAT
ACTGTCATCCGATCAAAAGCATTTGTGTCAACTGAAGAGCTTGGTGATCAATATTGTCTT
ATGGGACCTTATAAGGAAGAATGTGCACGACAAGAAGTTGAAGAATTTGAATTTCCAAAT
AATTCTCCTTATCAATGGGCTGTAAATGCAATTCGATCACTCGGTTACAAGGTTCATTGT
GGCAGATGGCTTGTTGATGGTAATCCTCAGATTATTCTATTTGATATTGGCTCAGCTGCA
TGGAAATTGGATGAATTTAGACAAGAATTGTGGGAAAAATGCAGTGTTGGTATTCCTCAT
TTAGACATTGAATGTAATGATGCTGTTATTCTCGGTTACATGATTGCTCAATTTATTAGC
GAGTTTAAGAGTGCTGCAGAACGTTTTTCTCAAGAACGTGGCCTATCTGAACCTAAAATT
GTGACACATTTTCATGAATGGCAAGCAGGTGTTGGTCTTATTGCAATTCGAACAAGACAT
ATTGATGTAGCGACAGTTTTTACGACTCATGCAACTTTATTAGGACGTTACTTGTGTGCT
GGCAATACTGATTTCTACAATAACTTGGCCAAATTTTCTGTCGACGAGGAGGCGGGAAAA
CGTCAAATCTATCATCGTTACTGCATTGAACGTGCAGCAACTCATCTCGCACATGTGTTC
ACAACAGTGTCCGAAATCACTGGCTATGAAGCAGAGCACTTGTTGAAAAGAAAAGCAGAT
GTTATTACACCCAATGGATTAAATGTTAAGAAATTTTCTGCCATTCATGAGTTTCAAAAT
TTGCATGCAATGGCCAAAGAGAAAATTCACGAATTCACTCGTGGACACTTTTTTGGGCAT
TTTGATTTCAATTTAGACAAAACACTGTACTTTTTCATCGCTGGTCGTTATGAGTTTAGC
AATAAAGGTGCAGATATTTTTATCGAAGCTCTTGCTCGATTAAATCATTAT

>g11259.t5 Gene=g11259 Length=363
MSRRISRVESGADLLDFLDRGQSASSENRFTFEVAWEAANKVGGIYTVIRSKAFVSTEEL
GDQYCLMGPYKEECARQEVEEFEFPNNSPYQWAVNAIRSLGYKVHCGRWLVDGNPQIILF
DIGSAAWKLDEFRQELWEKCSVGIPHLDIECNDAVILGYMIAQFISEFKSAAERFSQERG
LSEPKIVTHFHEWQAGVGLIAIRTRHIDVATVFTTHATLLGRYLCAGNTDFYNNLAKFSV
DEEAGKRQIYHRYCIERAATHLAHVFTTVSEITGYEAEHLLKRKADVITPNGLNVKKFSA
IHEFQNLHAMAKEKIHEFTRGHFFGHFDFNLDKTLYFFIAGRYEFSNKGADIFIEALARL
NHY

Protein features from InterProScan

Transcript Database ID Name Start End E.value
5 g11259.t5 Gene3D G3DSA:3.40.50.2000 Glycogen Phosphorylase B; 31 293 0
4 g11259.t5 Gene3D G3DSA:3.40.50.2000 Glycogen Phosphorylase B; 294 362 0
2 g11259.t5 PANTHER PTHR10176 GLYCOGEN SYNTHASE 21 363 0
1 g11259.t5 Pfam PF05693 Glycogen synthase 33 363 0
3 g11259.t5 SUPERFAMILY SSF53756 UDP-Glycosyltransferase/glycogen phosphorylase 38 361 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: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. There were no conditions that were differentially expressed