General information for g4514.t9
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.t9 | isoform | g4514.t9 | 2962253 | 2963964 |
| chr_2 | g4514 | g4514.t9 | exon | g4514.t9.exon1 | 2962253 | 2963374 |
| chr_2 | g4514 | g4514.t9 | cds | g4514.t9.CDS1 | 2962254 | 2963374 |
| chr_2 | g4514 | g4514.t9 | exon | g4514.t9.exon2 | 2963444 | 2963964 |
| chr_2 | g4514 | g4514.t9 | cds | g4514.t9.CDS2 | 2963444 | 2963942 |
| chr_2 | g4514 | g4514.t9 | TSS | g4514.t9 | NA | NA |
| chr_2 | g4514 | g4514.t9 | TTS | g4514.t9 | NA | NA |
Sequences
>g4514.t9 Gene=g4514 Length=1643
TTATTTGTCGTTGGAATTTTATATGGGTCGATCATTGCAAAATACAATGATTAATATTGG
TCTACAAGGAACTGTTGATGAAGCTCTCTATCAAATGGGTTTAGACATTGAAGAATTGGA
AGATATGGAGCAAGATGCCGGTCTCGGAAATGGTGGTCTCGGTCGTTTAGCTGCGTGCTT
CTTAGACTCAATGGCAACTCTTGCGATGCCTGCCGTTGGTTATGGTATTCGTTATGATTA
TGGTATCTTTGCACAACGTATTCGCAACTTTGAACAAACTGAAGAGCCTGATGATTGGTT
GCGTTTCGGTTGTCCATGGGAAAAAGCTCGTCCTGAATACATGATTCCAGTCAACTTTTT
TGGACGTGTCATGGACACTCCTGATGGAAAACGCTGGACTGATACTCAGATCGTTTACGC
TATGCCCTATGATAACCCGATTCCTGGTTATAATAATAATGTTGTTAACACTTTGCGATT
GTGGAGTGCAAAATCACCTATTGAGTTTAATTTGAAATTCTTTAATGATGGTGATTACAT
TCAAGCCGTCTTGGACCGTAATTTGGCTGAAAACATTTCAAGAGTCCTTTATCCAAATGA
CAACATGTTTGAGGGCAAGGAATTGCGTTTGAAGCAACAATATTTCTTATCAGCTGCTTC
ACTTGCCGATATCGTTCGTCGCTATAAATCATCTAAATTTGCTCAGTCAAAGAATCCTCG
TGATGCAATGAAATTCATGCACGAAAAGGTTGCCATTCAACTCAATGATACTCATCCATC
AATTTCAATTCCAGAGTTGATGCGTATTTTGGTTGATGAAGAGAAGCTCTCTTGGGATGA
TGCATGGACTGTAACAACAAAAGTCTTTGCATATACCAATCACACTGTATTGCCAGAAGC
TTTAGAAAGATGGCCAACTTCACTCTTGCAATCAATGTTGCCTCGTCATTTGGAGATCAT
TTATCATATTAACTTCTTGTGGATGCAACAGGTTGAGAAACTTTATCCTGGTGATTGGGA
TCGTATGCGCCGCATGTCATGTGTTGAAGAAGAGGGTGAAAAACGCATTAATATGGCACG
CTTATCTATTATTGGATCACATGCTGTCAACGGTGTCGCTGCAATTCATACTGAAATTTT
GAAGCGTGATATTTTCCGTGATTTCTATGAAGTTTTTCCTGACAAATTCCAGAACAAAAC
AAATGGTATAACACCAAGACGTTGGTTATTATTGTGTAATCCCGGTTTGGCTGATTTGAT
CTGCGAAAAAATTGGGGATGAATGGCCAGTTCATTTGGATCAATTAGTTCAATTGAAGAA
ATGGGCTAAAGATCCAACTTTCCAGCGTGCTGTCGCTAAAGTTAAGCAAGAAAACAAATT
TAAGCTTGCCGATATTCTCGAGAAAGATTATGGTGTCAAAGTCAATCCATCATCGATGTT
TGATATTCAAGTCAAGCGTATACATGAATATAAACGTCAATTGTTAAACTTGCTTTACAT
TGTCACTATGTACAATCGTATTAAGCGCGATCCAACTGCCAATTTCGTGCCACGCACAGT
CATGATTGGAGGTAAAGCTGCTCCTGGTTACTATATGGCAAAGAAGATAATTCAATTGAT
CTGTAAAGTCGGCCATGCTGTCA
>g4514.t9 Gene=g4514 Length=540
MGRSLQNTMINIGLQGTVDEALYQMGLDIEELEDMEQDAGLGNGGLGRLAACFLDSMATL
AMPAVGYGIRYDYGIFAQRIRNFEQTEEPDDWLRFGCPWEKARPEYMIPVNFFGRVMDTP
DGKRWTDTQIVYAMPYDNPIPGYNNNVVNTLRLWSAKSPIEFNLKFFNDGDYIQAVLDRN
LAENISRVLYPNDNMFEGKELRLKQQYFLSAASLADIVRRYKSSKFAQSKNPRDAMKFMH
EKVAIQLNDTHPSISIPELMRILVDEEKLSWDDAWTVTTKVFAYTNHTVLPEALERWPTS
LLQSMLPRHLEIIYHINFLWMQQVEKLYPGDWDRMRRMSCVEEEGEKRINMARLSIIGSH
AVNGVAAIHTEILKRDIFRDFYEVFPDKFQNKTNGITPRRWLLLCNPGLADLICEKIGDE
WPVHLDQLVQLKKWAKDPTFQRAVAKVKQENKFKLADILEKDYGVKVNPSSMFDIQVKRI
HEYKRQLLNLLYIVTMYNRIKRDPTANFVPRTVMIGGKAAPGYYMAKKIIQLICKVGHAV
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g4514.t9 | Gene3D | G3DSA:3.40.50.2000 | Glycogen Phosphorylase B; | 1 | 399 | 0 |
| 5 | g4514.t9 | Gene3D | G3DSA:3.40.50.2000 | Glycogen Phosphorylase B; | 400 | 540 | 0 |
| 2 | g4514.t9 | PANTHER | PTHR11468 | GLYCOGEN PHOSPHORYLASE | 1 | 540 | 0 |
| 3 | g4514.t9 | PANTHER | PTHR11468:SF13 | GLYCOGEN PHOSPHORYLASE, MUSCLE FORM | 1 | 540 | 0 |
| 1 | g4514.t9 | Pfam | PF00343 | Carbohydrate phosphorylase | 23 | 540 | 0 |
| 4 | g4514.t9 | SUPERFAMILY | SSF53756 | UDP-Glycosyltransferase/glycogen phosphorylase | 1 | 538 | 0 |
| 7 | g4514.t9 | TIGRFAM | TIGR02093 | P_ylase: glycogen/starch/alpha-glucan phosphorylases | 1 | 540 | 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 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.
