General information for g4514.t5
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.t5 | isoform | g4514.t5 | 2961061 | 2963972 |
| chr_2 | g4514 | g4514.t5 | exon | g4514.t5.exon1 | 2961061 | 2961655 |
| chr_2 | g4514 | g4514.t5 | cds | g4514.t5.CDS1 | 2961503 | 2961655 |
| chr_2 | g4514 | g4514.t5 | exon | g4514.t5.exon2 | 2961716 | 2962017 |
| chr_2 | g4514 | g4514.t5 | cds | g4514.t5.CDS2 | 2961716 | 2962017 |
| chr_2 | g4514 | g4514.t5 | exon | g4514.t5.exon3 | 2962076 | 2963374 |
| chr_2 | g4514 | g4514.t5 | cds | g4514.t5.CDS3 | 2962076 | 2963374 |
| chr_2 | g4514 | g4514.t5 | exon | g4514.t5.exon4 | 2963444 | 2963972 |
| chr_2 | g4514 | g4514.t5 | cds | g4514.t5.CDS4 | 2963444 | 2963942 |
| chr_2 | g4514 | g4514.t5 | TSS | g4514.t5 | NA | NA |
| chr_2 | g4514 | g4514.t5 | TTS | g4514.t5 | NA | NA |
Sequences
>g4514.t5 Gene=g4514 Length=2725
CGTGTTTATTATTTGTCGTTGGAATTTTATATGGGTCGATCATTGCAAAATACAATGATT
AATATTGGTCTACAAGGAACTGTTGATGAAGCTCTCTATCAAATGGGTTTAGACATTGAA
GAATTGGAAGATATGGAGCAAGATGCCGGTCTCGGAAATGGTGGTCTCGGTCGTTTAGCT
GCGTGCTTCTTAGACTCAATGGCAACTCTTGCGATGCCTGCCGTTGGTTATGGTATTCGT
TATGATTATGGTATCTTTGCACAACGTATTCGCAACTTTGAACAAACTGAAGAGCCTGAT
GATTGGTTGCGTTTCGGTTGTCCATGGGAAAAAGCTCGTCCTGAATACATGATTCCAGTC
AACTTTTTTGGACGTGTCATGGACACTCCTGATGGAAAACGCTGGACTGATACTCAGATC
GTTTACGCTATGCCCTATGATAACCCGATTCCTGGTTATAATAATAATGTTGTTAACACT
TTGCGATTGTGGAGTGCAAAATCACCTATTGAGTTTAATTTGAAATTCTTTAATGATGGT
GATTACATTCAAGCCGTCTTGGACCGTAATTTGGCTGAAAACATTTCAAGAGTCCTTTAT
CCAAATGACAACATGTTTGAGGGCAAGGAATTGCGTTTGAAGCAACAATATTTCTTATCA
GCTGCTTCACTTGCCGATATCGTTCGTCGCTATAAATCATCTAAATTTGCTCAGTCAAAG
AATCCTCGTGATGCAATGAAATTCATGCACGAAAAGGTTGCCATTCAACTCAATGATACT
CATCCATCAATTTCAATTCCAGAGTTGATGCGTATTTTGGTTGATGAAGAGAAGCTCTCT
TGGGATGATGCATGGACTGTAACAACAAAAGTCTTTGCATATACCAATCACACTGTATTG
CCAGAAGCTTTAGAAAGATGGCCAACTTCACTCTTGCAATCAATGTTGCCTCGTCATTTG
GAGATCATTTATCATATTAACTTCTTGTGGATGCAACAGGTTGAGAAACTTTATCCTGGT
GATTGGGATCGTATGCGCCGCATGTCATGTGTTGAAGAAGAGGGTGAAAAACGCATTAAT
ATGGCACGCTTATCTATTATTGGATCACATGCTGTCAACGGTGTCGCTGCAATTCATACT
GAAATTTTGAAGCGTGATATTTTCCGTGATTTCTATGAAGTTTTTCCTGACAAATTCCAG
AACAAAACAAATGGTATAACACCAAGACGTTGGTTATTATTGTGTAATCCCGGTTTGGCT
GATTTGATCTGCGAAAAAATTGGGGATGAATGGCCAGTTCATTTGGATCAATTAGTTCAA
TTGAAGAAATGGGCTAAAGATCCAACTTTCCAGCGTGCTGTCGCTAAAGTTAAGCAAGAA
AACAAATTTAAGCTTGCCGATATTCTCGAGAAAGATTATGGTGTCAAAGTCAATCCATCA
TCGATGTTTGATATTCAAGTCAAGCGTATACATGAATATAAACGTCAATTGTTAAACTTG
CTTTACATTGTCACTATGTACAATCGTATTAAGCGCGATCCAACTGCCAATTTCGTGCCA
CGCACAGTCATGATTGGAGGTAAAGCTGCTCCTGGTTACTATATGGCAAAGAAGATAATT
CAATTGATCTGTAAAGTCGGCCATGCTGTCAACAACGATCCAATCGTTGGAGATAAATTG
AAAGTTATCTATTTGGAAAATTATCGCGTAACATTGGCGGAAAAGATTATGCCAGCAGCT
GATTTATCACAACAAATCTCAACAGCTGGTACAGAGGCATCAGGAACTGGTAACATGAAA
TTCATGTTGAACGGTGCTCTCACTATTGGTACACTTGATGGAGCTAATATTGAGATGGCT
GAAGAAATGGGAATGGAAAACATTTTCATTTTTGGTATGACTGTTGAACAAGTCGAAGCA
TTACGCAATTATAATGCATGGGATTATTATAATCGAAATGCTGAATTGAAGCAAGTCATT
GATCAGATTTCAGGCGGCTATTATAGCCCTGGAAATCCTGATGAATTCAAGGACGTTACC
AATATGTTGATGCAATATGATCGTTTCTTCACATTTGCTGATTACGATGACTATGTTAAA
AAGCAAGACGAAGTCTCTGCTACTTATCAAAATCAATCAAAATGGGTTGAAATGGCAATT
CATAATATTGCTAGCAGTGGCAAATTCTCAAGCGATCGTACAATCAGCGAATATGCTCGC
GAAATTTGGGGTGTTCAGCCTTCATATGAGAAATTGCCAAACCCACATGAAGTTATTGCC
TAAATCAGCCCTAAATGTTCTGATGTTTTTGTCGCGTCATGAAAGTTTTCATGCTTATAT
TGTTTCACTTATGATGCGAATATAAACTGCCCTAAAACATCATATTAATCTCGCCATAGA
ACAATTTAAAAATTTAATGTTTTTTGTTTTAAAGTTTTAGTTGATGATTTCTATATATTA
TACATACATACAATTATTGTGTTTCTTTTTGTAATTTTATTTAGTTTTTATGAATGTTAT
TATATAATCAAAAGGGAAAAAATCTGAAAATTAATTTCTTGTTAATAAAATAAAAATTTT
AAAAATAAAAAGATACAATATTCTAAAGTTTAAAAAAATCAATCAAAAACCATGTTTTTT
GAACTGTTTAAGTAGCTTTTATATATTTTATTCAAATCGAGTTAATAAAACTATTCAAAT
AATGTAATAAATAACAATGTGGGTT
>g4514.t5 Gene=g4514 Length=750
MGRSLQNTMINIGLQGTVDEALYQMGLDIEELEDMEQDAGLGNGGLGRLAACFLDSMATL
AMPAVGYGIRYDYGIFAQRIRNFEQTEEPDDWLRFGCPWEKARPEYMIPVNFFGRVMDTP
DGKRWTDTQIVYAMPYDNPIPGYNNNVVNTLRLWSAKSPIEFNLKFFNDGDYIQAVLDRN
LAENISRVLYPNDNMFEGKELRLKQQYFLSAASLADIVRRYKSSKFAQSKNPRDAMKFMH
EKVAIQLNDTHPSISIPELMRILVDEEKLSWDDAWTVTTKVFAYTNHTVLPEALERWPTS
LLQSMLPRHLEIIYHINFLWMQQVEKLYPGDWDRMRRMSCVEEEGEKRINMARLSIIGSH
AVNGVAAIHTEILKRDIFRDFYEVFPDKFQNKTNGITPRRWLLLCNPGLADLICEKIGDE
WPVHLDQLVQLKKWAKDPTFQRAVAKVKQENKFKLADILEKDYGVKVNPSSMFDIQVKRI
HEYKRQLLNLLYIVTMYNRIKRDPTANFVPRTVMIGGKAAPGYYMAKKIIQLICKVGHAV
NNDPIVGDKLKVIYLENYRVTLAEKIMPAADLSQQISTAGTEASGTGNMKFMLNGALTIG
TLDGANIEMAEEMGMENIFIFGMTVEQVEALRNYNAWDYYNRNAELKQVIDQISGGYYSP
GNPDEFKDVTNMLMQYDRFFTFADYDDYVKKQDEVSATYQNQSKWVEMAIHNIASSGKFS
SDRTISEYAREIWGVQPSYEKLPNPHEVIA
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g4514.t5 | CDD | cd04300 | GT35_Glycogen_Phosphorylase | 1 | 735 | 0.0 |
| 6 | g4514.t5 | Gene3D | G3DSA:3.40.50.2000 | Glycogen Phosphorylase B; | 1 | 399 | 8.5E-202 |
| 5 | g4514.t5 | Gene3D | G3DSA:3.40.50.2000 | Glycogen Phosphorylase B; | 400 | 720 | 8.1E-155 |
| 2 | g4514.t5 | PANTHER | PTHR11468 | GLYCOGEN PHOSPHORYLASE | 1 | 747 | 0.0 |
| 3 | g4514.t5 | PANTHER | PTHR11468:SF13 | GLYCOGEN PHOSPHORYLASE, MUSCLE FORM | 1 | 747 | 0.0 |
| 7 | g4514.t5 | PIRSF | PIRSF000460 | Glucan_phosphorylase_GlgP | 1 | 747 | 1.5E-222 |
| 1 | g4514.t5 | Pfam | PF00343 | Carbohydrate phosphorylase | 23 | 735 | 0.0 |
| 9 | g4514.t5 | ProSitePatterns | PS00102 | Phosphorylase pyridoxal-phosphate attachment site. | 582 | 594 | - |
| 4 | g4514.t5 | SUPERFAMILY | SSF53756 | UDP-Glycosyltransferase/glycogen phosphorylase | 1 | 737 | 0.0 |
| 10 | g4514.t5 | TIGRFAM | TIGR02093 | P_ylase: glycogen/starch/alpha-glucan phosphorylases | 1 | 735 | 0.0 |
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:0030170 | pyridoxal phosphate binding | MF |
| GO:0008184 | glycogen phosphorylase activity | MF |
| GO:0004645 | 1,4-alpha-oligoglucan phosphorylase activity | MF |
KEGG
Orthology
- This transcript has been annotated with K00688 (glycogen phosphorylase)
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.
