General information for g4514.t1
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.t1 | TTS | g4514.t1 | 2961162 | 2961162 |
| chr_2 | g4514 | g4514.t1 | isoform | g4514.t1 | 2961503 | 2964955 |
| chr_2 | g4514 | g4514.t1 | exon | g4514.t1.exon1 | 2961503 | 2961655 |
| chr_2 | g4514 | g4514.t1 | cds | g4514.t1.CDS1 | 2961503 | 2961655 |
| chr_2 | g4514 | g4514.t1 | exon | g4514.t1.exon2 | 2961716 | 2962017 |
| chr_2 | g4514 | g4514.t1 | cds | g4514.t1.CDS2 | 2961716 | 2962017 |
| chr_2 | g4514 | g4514.t1 | exon | g4514.t1.exon3 | 2962076 | 2963374 |
| chr_2 | g4514 | g4514.t1 | cds | g4514.t1.CDS3 | 2962076 | 2963374 |
| chr_2 | g4514 | g4514.t1 | exon | g4514.t1.exon4 | 2963444 | 2963972 |
| chr_2 | g4514 | g4514.t1 | cds | g4514.t1.CDS4 | 2963444 | 2963972 |
| chr_2 | g4514 | g4514.t1 | exon | g4514.t1.exon5 | 2964713 | 2964955 |
| chr_2 | g4514 | g4514.t1 | cds | g4514.t1.CDS5 | 2964713 | 2964955 |
| chr_2 | g4514 | g4514.t1 | TSS | g4514.t1 | 2965128 | 2965128 |
Sequences
>g4514.t1 Gene=g4514 Length=2526
ATGAGTCGTCCTATTTCTGATAGCGATAAGCGCAAGCAAATTTCGGTTCGCGGAATAGCC
CAAGTTGAAGACGTTGGCGAAGTAAAAAAGGGCTTTAATCGTCATTTGCATTTTACATTA
ATTAAAGATCGTAATGTTGCCACACCGCGAGATTATTATTTTGCACTTGCTCATTGCGTT
AAAGATCATTTGGTATCAAGATGGATTCGTACTCAACAACACTATTTTGAGAAAGATCCA
AAGCGTGTTTATTATTTGTCGTTGGAATTTTATATGGGTCGATCATTGCAAAATACAATG
ATTAATATTGGTCTACAAGGAACTGTTGATGAAGCTCTCTATCAAATGGGTTTAGACATT
GAAGAATTGGAAGATATGGAGCAAGATGCCGGTCTCGGAAATGGTGGTCTCGGTCGTTTA
GCTGCGTGCTTCTTAGACTCAATGGCAACTCTTGCGATGCCTGCCGTTGGTTATGGTATT
CGTTATGATTATGGTATCTTTGCACAACGTATTCGCAACTTTGAACAAACTGAAGAGCCT
GATGATTGGTTGCGTTTCGGTTGTCCATGGGAAAAAGCTCGTCCTGAATACATGATTCCA
GTCAACTTTTTTGGACGTGTCATGGACACTCCTGATGGAAAACGCTGGACTGATACTCAG
ATCGTTTACGCTATGCCCTATGATAACCCGATTCCTGGTTATAATAATAATGTTGTTAAC
ACTTTGCGATTGTGGAGTGCAAAATCACCTATTGAGTTTAATTTGAAATTCTTTAATGAT
GGTGATTACATTCAAGCCGTCTTGGACCGTAATTTGGCTGAAAACATTTCAAGAGTCCTT
TATCCAAATGACAACATGTTTGAGGGCAAGGAATTGCGTTTGAAGCAACAATATTTCTTA
TCAGCTGCTTCACTTGCCGATATCGTTCGTCGCTATAAATCATCTAAATTTGCTCAGTCA
AAGAATCCTCGTGATGCAATGAAATTCATGCACGAAAAGGTTGCCATTCAACTCAATGAT
ACTCATCCATCAATTTCAATTCCAGAGTTGATGCGTATTTTGGTTGATGAAGAGAAGCTC
TCTTGGGATGATGCATGGACTGTAACAACAAAAGTCTTTGCATATACCAATCACACTGTA
TTGCCAGAAGCTTTAGAAAGATGGCCAACTTCACTCTTGCAATCAATGTTGCCTCGTCAT
TTGGAGATCATTTATCATATTAACTTCTTGTGGATGCAACAGGTTGAGAAACTTTATCCT
GGTGATTGGGATCGTATGCGCCGCATGTCATGTGTTGAAGAAGAGGGTGAAAAACGCATT
AATATGGCACGCTTATCTATTATTGGATCACATGCTGTCAACGGTGTCGCTGCAATTCAT
ACTGAAATTTTGAAGCGTGATATTTTCCGTGATTTCTATGAAGTTTTTCCTGACAAATTC
CAGAACAAAACAAATGGTATAACACCAAGACGTTGGTTATTATTGTGTAATCCCGGTTTG
GCTGATTTGATCTGCGAAAAAATTGGGGATGAATGGCCAGTTCATTTGGATCAATTAGTT
CAATTGAAGAAATGGGCTAAAGATCCAACTTTCCAGCGTGCTGTCGCTAAAGTTAAGCAA
GAAAACAAATTTAAGCTTGCCGATATTCTCGAGAAAGATTATGGTGTCAAAGTCAATCCA
TCATCGATGTTTGATATTCAAGTCAAGCGTATACATGAATATAAACGTCAATTGTTAAAC
TTGCTTTACATTGTCACTATGTACAATCGTATTAAGCGCGATCCAACTGCCAATTTCGTG
CCACGCACAGTCATGATTGGAGGTAAAGCTGCTCCTGGTTACTATATGGCAAAGAAGATA
ATTCAATTGATCTGTAAAGTCGGCCATGCTGTCAACAACGATCCAATCGTTGGAGATAAA
TTGAAAGTTATCTATTTGGAAAATTATCGCGTAACATTGGCGGAAAAGATTATGCCAGCA
GCTGATTTATCACAACAAATCTCAACAGCTGGTACAGAGGCATCAGGAACTGGTAACATG
AAATTCATGTTGAACGGTGCTCTCACTATTGGTACACTTGATGGAGCTAATATTGAGATG
GCTGAAGAAATGGGAATGGAAAACATTTTCATTTTTGGTATGACTGTTGAACAAGTCGAA
GCATTACGCAATTATAATGCATGGGATTATTATAATCGAAATGCTGAATTGAAGCAAGTC
ATTGATCAGATTTCAGGCGGCTATTATAGCCCTGGAAATCCTGATGAATTCAAGGACGTT
ACCAATATGTTGATGCAATATGATCGTTTCTTCACATTTGCTGATTACGATGACTATGTT
AAAAAGCAAGACGAAGTCTCTGCTACTTATCAAAATCAATCAAAATGGGTTGAAATGGCA
ATTCATAATATTGCTAGCAGTGGCAAATTCTCAAGCGATCGTACAATCAGCGAATATGCT
CGCGAAATTTGGGGTGTTCAGCCTTCATATGAGAAATTGCCAAACCCACATGAAGTTATT
GCCTAA
>g4514.t1 Gene=g4514 Length=841
MSRPISDSDKRKQISVRGIAQVEDVGEVKKGFNRHLHFTLIKDRNVATPRDYYFALAHCV
KDHLVSRWIRTQQHYFEKDPKRVYYLSLEFYMGRSLQNTMINIGLQGTVDEALYQMGLDI
EELEDMEQDAGLGNGGLGRLAACFLDSMATLAMPAVGYGIRYDYGIFAQRIRNFEQTEEP
DDWLRFGCPWEKARPEYMIPVNFFGRVMDTPDGKRWTDTQIVYAMPYDNPIPGYNNNVVN
TLRLWSAKSPIEFNLKFFNDGDYIQAVLDRNLAENISRVLYPNDNMFEGKELRLKQQYFL
SAASLADIVRRYKSSKFAQSKNPRDAMKFMHEKVAIQLNDTHPSISIPELMRILVDEEKL
SWDDAWTVTTKVFAYTNHTVLPEALERWPTSLLQSMLPRHLEIIYHINFLWMQQVEKLYP
GDWDRMRRMSCVEEEGEKRINMARLSIIGSHAVNGVAAIHTEILKRDIFRDFYEVFPDKF
QNKTNGITPRRWLLLCNPGLADLICEKIGDEWPVHLDQLVQLKKWAKDPTFQRAVAKVKQ
ENKFKLADILEKDYGVKVNPSSMFDIQVKRIHEYKRQLLNLLYIVTMYNRIKRDPTANFV
PRTVMIGGKAAPGYYMAKKIIQLICKVGHAVNNDPIVGDKLKVIYLENYRVTLAEKIMPA
ADLSQQISTAGTEASGTGNMKFMLNGALTIGTLDGANIEMAEEMGMENIFIFGMTVEQVE
ALRNYNAWDYYNRNAELKQVIDQISGGYYSPGNPDEFKDVTNMLMQYDRFFTFADYDDYV
KKQDEVSATYQNQSKWVEMAIHNIASSGKFSSDRTISEYAREIWGVQPSYEKLPNPHEVI
A
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g4514.t1 | CDD | cd04300 | GT35_Glycogen_Phosphorylase | 29 | 826 | 0.0 |
| 5 | g4514.t1 | Gene3D | G3DSA:3.40.50.2000 | Glycogen Phosphorylase B; | 13 | 490 | 8.3E-235 |
| 6 | g4514.t1 | Gene3D | G3DSA:3.40.50.2000 | Glycogen Phosphorylase B; | 491 | 811 | 1.0E-154 |
| 2 | g4514.t1 | PANTHER | PTHR11468 | GLYCOGEN PHOSPHORYLASE | 1 | 838 | 0.0 |
| 3 | g4514.t1 | PANTHER | PTHR11468:SF13 | GLYCOGEN PHOSPHORYLASE, MUSCLE FORM | 1 | 838 | 0.0 |
| 7 | g4514.t1 | PIRSF | PIRSF000460 | Glucan_phosphorylase_GlgP | 13 | 838 | 3.0E-239 |
| 1 | g4514.t1 | Pfam | PF00343 | Carbohydrate phosphorylase | 114 | 826 | 0.0 |
| 9 | g4514.t1 | ProSitePatterns | PS00102 | Phosphorylase pyridoxal-phosphate attachment site. | 673 | 685 | - |
| 4 | g4514.t1 | SUPERFAMILY | SSF53756 | UDP-Glycosyltransferase/glycogen phosphorylase | 25 | 828 | 0.0 |
| 10 | g4514.t1 | TIGRFAM | TIGR02093 | P_ylase: glycogen/starch/alpha-glucan phosphorylases | 26 | 826 | 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.
