General information for g4514.t12
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Glycogen phosphorylase.
Parent gene
- The parent gene g4514 is located on chr_2: 2964455..2965103 (- 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_2 | g4514 | g4514.t12 | isoform | g4514.t12 | 2963357 | 2964955 |
| chr_2 | g4514 | g4514.t12 | exon | g4514.t12.exon1 | 2963357 | 2963374 |
| chr_2 | g4514 | g4514.t12 | cds | g4514.t12.CDS1 | 2963358 | 2963374 |
| chr_2 | g4514 | g4514.t12 | exon | g4514.t12.exon2 | 2963480 | 2963972 |
| chr_2 | g4514 | g4514.t12 | cds | g4514.t12.CDS2 | 2963480 | 2963972 |
| chr_2 | g4514 | g4514.t12 | exon | g4514.t12.exon3 | 2964713 | 2964955 |
| chr_2 | g4514 | g4514.t12 | cds | g4514.t12.CDS3 | 2964713 | 2964955 |
| chr_2 | g4514 | g4514.t12 | TSS | g4514.t12 | 2965128 | 2965128 |
| chr_2 | g4514 | g4514.t12 | TTS | g4514.t12 | NA | NA |
Sequences
>g4514.t12 Gene=g4514 Length=754
ATGAGTCGTCCTATTTCTGATAGCGATAAGCGCAAGCAAATTTCGGTTCGCGGAATAGCC
CAAGTTGAAGACGTTGGCGAAGTAAAAAAGGGCTTTAATCGTCATTTGCATTTTACATTA
ATTAAAGATCGTAATGTTGCCACACCGCGAGATTATTATTTTGCACTTGCTCATTGCGTT
AAAGATCATTTGGTATCAAGATGGATTCGTACTCAACAACACTATTTTGAGAAAGATCCA
AAGCGTGTTTATTATTTGTCGTTGGAATTTTATATGGGTCGATCATTGCAAAATACAATG
ATTAATATTGGTCTACAAGGAACTGTTGATGAAGCTCTCTATCAAATGGGTTTAGACATT
GAAGAATTGGAAGATATGGAGCAAGATGCCGGTCTCGGAAATGGTGGTCTCGGTCGTTTA
GCTGCGTGCTTCTTAGACTCAATGGCAACTCTTGCGATGCCTGCCGTTGGTTATGGTATT
CGTTATGATTATGGTATCTTTGCACAACGTATTCGCAACTTTGAACAAACTGAAGAGCCT
GATGATTGGTTGCGTTTCGGTTGTCCATGGGAAAAAGCTCGTCCTGAATACATGATTCCA
GTCAACTTTTTTGGACGTGTCATGGACACTCCTGATGGAAAACGCTGGACTGATACTCAG
ATCGTTTACGCTATGCCCTATGATAACCCGATTCCTGGTTATAATAATAATGTTGTTAAC
ACTTTGCGATTGTGGATTAATGATGGTGATTACA
>g4514.t12 Gene=g4514 Length=251
MSRPISDSDKRKQISVRGIAQVEDVGEVKKGFNRHLHFTLIKDRNVATPRDYYFALAHCV
KDHLVSRWIRTQQHYFEKDPKRVYYLSLEFYMGRSLQNTMINIGLQGTVDEALYQMGLDI
EELEDMEQDAGLGNGGLGRLAACFLDSMATLAMPAVGYGIRYDYGIFAQRIRNFEQTEEP
DDWLRFGCPWEKARPEYMIPVNFFGRVMDTPDGKRWTDTQIVYAMPYDNPIPGYNNNVVN
TLRLWINDGDY
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g4514.t12 | Gene3D | G3DSA:3.40.50.2000 | Glycogen Phosphorylase B; | 13 | 249 | 0 |
| 2 | g4514.t12 | PANTHER | PTHR11468 | GLYCOGEN PHOSPHORYLASE | 1 | 246 | 0 |
| 3 | g4514.t12 | PANTHER | PTHR11468:SF13 | GLYCOGEN PHOSPHORYLASE, MUSCLE FORM | 1 | 246 | 0 |
| 1 | g4514.t12 | Pfam | PF00343 | Carbohydrate phosphorylase | 114 | 245 | 0 |
| 4 | g4514.t12 | SUPERFAMILY | SSF53756 | UDP-Glycosyltransferase/glycogen phosphorylase | 24 | 245 | 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