Gene loci information

Transcript annotation

  • This transcript has been annotated as Glycogen phosphorylase.

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_2 g4514 g4514.t11 isoform g4514.t11 2962850 2964955
chr_2 g4514 g4514.t11 exon g4514.t11.exon1 2962850 2963374
chr_2 g4514 g4514.t11 cds g4514.t11.CDS1 2962851 2963374
chr_2 g4514 g4514.t11 exon g4514.t11.exon2 2963444 2963972
chr_2 g4514 g4514.t11 cds g4514.t11.CDS2 2963444 2963870
chr_2 g4514 g4514.t11 exon g4514.t11.exon3 2964709 2964955
chr_2 g4514 g4514.t11 TSS g4514.t11 2965128 2965128
chr_2 g4514 g4514.t11 TTS g4514.t11 NA NA

Sequences

>g4514.t11 Gene=g4514 Length=1301
ATGAGTCGTCCTATTTCTGATAGCGATAAGCGCAAGCAAATTTCGGTTCGCGGAATAGCC
CAAGTTGAAGACGTTGGCGAAGTAAAAAAGGGCTTTAATCGTCATTTGCATTTTACATTA
ATTAAAGATCGTAATGTTGCCACACCGCGAGATTATTATTTTGCACTTGCTCATTGCGTT
AAAGATCATTTGGTATCAAGATGGATTCGTACTCAACAACACTATTTTGAGAAAGATCCA
AAGGTGACGTGTTTATTATTTGTCGTTGGAATTTTATATGGGTCGATCATTGCAAAATAC
AATGATTAATATTGGTCTACAAGGAACTGTTGATGAAGCTCTCTATCAAATGGGTTTAGA
CATTGAAGAATTGGAAGATATGGAGCAAGATGCCGGTCTCGGAAATGGTGGTCTCGGTCG
TTTAGCTGCGTGCTTCTTAGACTCAATGGCAACTCTTGCGATGCCTGCCGTTGGTTATGG
TATTCGTTATGATTATGGTATCTTTGCACAACGTATTCGCAACTTTGAACAAACTGAAGA
GCCTGATGATTGGTTGCGTTTCGGTTGTCCATGGGAAAAAGCTCGTCCTGAATACATGAT
TCCAGTCAACTTTTTTGGACGTGTCATGGACACTCCTGATGGAAAACGCTGGACTGATAC
TCAGATCGTTTACGCTATGCCCTATGATAACCCGATTCCTGGTTATAATAATAATGTTGT
TAACACTTTGCGATTGTGGAGTGCAAAATCACCTATTGAGTTTAATTTGAAATTCTTTAA
TGATGGTGATTACATTCAAGCCGTCTTGGACCGTAATTTGGCTGAAAACATTTCAAGAGT
CCTTTATCCAAATGACAACATGTTTGAGGGCAAGGAATTGCGTTTGAAGCAACAATATTT
CTTATCAGCTGCTTCACTTGCCGATATCGTTCGTCGCTATAAATCATCTAAATTTGCTCA
GTCAAAGAATCCTCGTGATGCAATGAAATTCATGCACGAAAAGGTTGCCATTCAACTCAA
TGATACTCATCCATCAATTTCAATTCCAGAGTTGATGCGTATTTTGGTTGATGAAGAGAA
GCTCTCTTGGGATGATGCATGGACTGTAACAACAAAAGTCTTTGCATATACCAATCACAC
TGTATTGCCAGAAGCTTTAGAAAGATGGCCAACTTCACTCTTGCAATCAATGTTGCCTCG
TCATTTGGAGATCATTTATCATATTAACTTCTTGTGGATGCAACAGGTTGAGAAACTTTA
TCCTGGTGATTGGGATCGTATGCGCCGCATGTCATGTGTTG

>g4514.t11 Gene=g4514 Length=317
MGLDIEELEDMEQDAGLGNGGLGRLAACFLDSMATLAMPAVGYGIRYDYGIFAQRIRNFE
QTEEPDDWLRFGCPWEKARPEYMIPVNFFGRVMDTPDGKRWTDTQIVYAMPYDNPIPGYN
NNVVNTLRLWSAKSPIEFNLKFFNDGDYIQAVLDRNLAENISRVLYPNDNMFEGKELRLK
QQYFLSAASLADIVRRYKSSKFAQSKNPRDAMKFMHEKVAIQLNDTHPSISIPELMRILV
DEEKLSWDDAWTVTTKVFAYTNHTVLPEALERWPTSLLQSMLPRHLEIIYHINFLWMQQV
EKLYPGDWDRMRRMSCV

Protein features from InterProScan

Transcript Database ID Name Start End E.value
5 g4514.t11 Gene3D G3DSA:3.40.50.2000 Glycogen Phosphorylase B; 1 317 0
2 g4514.t11 PANTHER PTHR11468 GLYCOGEN PHOSPHORYLASE 1 317 0
3 g4514.t11 PANTHER PTHR11468:SF13 GLYCOGEN PHOSPHORYLASE, MUSCLE FORM 1 317 0
1 g4514.t11 Pfam PF00343 Carbohydrate phosphorylase 1 316 0
4 g4514.t11 SUPERFAMILY SSF53756 UDP-Glycosyltransferase/glycogen phosphorylase 1 316 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:0005975 carbohydrate metabolic process BP
GO:0008184 glycogen phosphorylase 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