General information for g8516.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Ribose-phosphate pyrophosphokinase 1.
Parent gene
- The parent gene g8516 is located on chr_2: 31109203..31111553 (- 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 | g8516 | g8516.t2 | TTS | g8516.t2 | 31106094 | 31106094 |
| chr_2 | g8516 | g8516.t2 | isoform | g8516.t2 | 31106395 | 31111041 |
| chr_2 | g8516 | g8516.t2 | exon | g8516.t2.exon1 | 31106395 | 31106946 |
| chr_2 | g8516 | g8516.t2 | cds | g8516.t2.CDS1 | 31106395 | 31106946 |
| chr_2 | g8516 | g8516.t2 | exon | g8516.t2.exon2 | 31107005 | 31107103 |
| chr_2 | g8516 | g8516.t2 | cds | g8516.t2.CDS2 | 31107005 | 31107103 |
| chr_2 | g8516 | g8516.t2 | exon | g8516.t2.exon3 | 31109643 | 31109782 |
| chr_2 | g8516 | g8516.t2 | cds | g8516.t2.CDS3 | 31109643 | 31109782 |
| chr_2 | g8516 | g8516.t2 | exon | g8516.t2.exon4 | 31109855 | 31109898 |
| chr_2 | g8516 | g8516.t2 | cds | g8516.t2.CDS4 | 31109855 | 31109898 |
| chr_2 | g8516 | g8516.t2 | exon | g8516.t2.exon5 | 31110920 | 31111041 |
| chr_2 | g8516 | g8516.t2 | cds | g8516.t2.CDS5 | 31110920 | 31111041 |
| chr_2 | g8516 | g8516.t2 | TSS | g8516.t2 | 31111077 | 31111077 |
Sequences
>g8516.t2 Gene=g8516 Length=957
ATGCCTAACATTAAAGTGTTTTCTGGAACTTCACATCCTGATTTAGCTCAAAGAATCGTA
GATCGGTTAGGTATTGACTTGGGAAAAGTTGTAACAAAAAAATTTTCAAACCTGGAAACA
TGTGTGGAGATCGGAGAATCAGTACGTGGAGAGGATGTGTATATCGTTCAATCTGGTTCG
GGAGAAATTAATGACAACTTGATGGAACTTTTAATTATGATAAACGCATGCAAAATTGCA
TCAGCTTCAAGAGTGACAGCTGTGATACCATGTTTTCCATATGCAAGACAAGACAAAAAA
GACAAGAGTAGAGCACCCATTTCGGCAAAACTTGTTGCAAACATGTTGTCAGTTGCTGGT
GCTGACCATATCATTACAATGGATCTTCATGCTTCTCAAATACAGGGTTTCTTTGATATA
CCAGTGGATAATCTCTACGCAGAACCAGCAGTTCTGAAATGGATAAAAGAAAATATTCAG
GAGTGGCGTAACTCGATTATCGTTTCTCCTGATGCTGGCGGTGCTAAACGTGTGACATCT
ATTGCTGATCGTCTTAATGTAGAATTTGCATTGATTCACAAAGAACGCAAAAAAGCAAAT
GAAGTTGCATCAATGGTGTTAGTTGGAGATGTAAAAGACAGAGTAGCAATTTTAGTTGAT
GACATGGCTGATACATGTGGAACAATTTGTCATGCAGCCGAGAAGCTTTTAGAAGCAGGA
GCAACAAAAGTTTATGCCATTTTAACACATGGGATTTTTAGCGGTCCAGCTATTTCGCGA
ATAAATAATGCATGTTTCGAGGCGGTCGTTGTCACGAATACAATTCCACAAGATGGTCAT
ATGAAGGACTGTCCAAAAATACAGTGCATTGATGTGTCTATGATGTTTGCAGAAGCAGTT
CGTAGAACACATAATGGAGAAAGTGTCAGCTATCTTTTTAGTAATGTTCCATATTAG
>g8516.t2 Gene=g8516 Length=318
MPNIKVFSGTSHPDLAQRIVDRLGIDLGKVVTKKFSNLETCVEIGESVRGEDVYIVQSGS
GEINDNLMELLIMINACKIASASRVTAVIPCFPYARQDKKDKSRAPISAKLVANMLSVAG
ADHIITMDLHASQIQGFFDIPVDNLYAEPAVLKWIKENIQEWRNSIIVSPDAGGAKRVTS
IADRLNVEFALIHKERKKANEVASMVLVGDVKDRVAILVDDMADTCGTICHAAEKLLEAG
ATKVYAILTHGIFSGPAISRINNACFEAVVVTNTIPQDGHMKDCPKIQCIDVSMMFAEAV
RRTHNGESVSYLFSNVPY
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g8516.t2 | CDD | cd06223 | PRTases_typeI | 147 | 274 | 3.10857E-26 |
| 8 | g8516.t2 | Gene3D | G3DSA:3.40.50.2020 | - | 7 | 304 | 1.2E-131 |
| 7 | g8516.t2 | Gene3D | G3DSA:3.40.50.2020 | - | 147 | 290 | 1.2E-131 |
| 5 | g8516.t2 | Hamap | MF_00583_B | Putative ribose-phosphate pyrophosphokinase [prs]. | 4 | 314 | 43.173237 |
| 3 | g8516.t2 | PANTHER | PTHR10210 | RIBOSE-PHOSPHATE DIPHOSPHOKINASE FAMILY MEMBER | 1 | 317 | 2.9E-201 |
| 4 | g8516.t2 | PANTHER | PTHR10210:SF105 | PHOSPHORIBOSYL PYROPHOSPHATE SYNTHETASE 1-LIKE 3-RELATED | 1 | 317 | 2.9E-201 |
| 2 | g8516.t2 | Pfam | PF13793 | N-terminal domain of ribose phosphate pyrophosphokinase | 4 | 120 | 4.3E-46 |
| 1 | g8516.t2 | Pfam | PF14572 | Phosphoribosyl synthetase-associated domain | 203 | 313 | 4.6E-38 |
| 10 | g8516.t2 | ProSitePatterns | PS00114 | Phosphoribosyl pyrophosphate synthase signature. | 128 | 143 | - |
| 11 | g8516.t2 | SMART | SM01400 | Pribosyltran_N_2 | 4 | 120 | 8.5E-75 |
| 6 | g8516.t2 | SUPERFAMILY | SSF53271 | PRTase-like | 69 | 306 | 2.09E-64 |
| 12 | g8516.t2 | TIGRFAM | TIGR01251 | ribP_PPkin: ribose-phosphate diphosphokinase | 4 | 314 | 1.5E-122 |
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:0000287 | magnesium ion binding | MF |
| GO:0004749 | ribose phosphate diphosphokinase activity | MF |
| GO:0009116 | nucleoside metabolic process | BP |
| GO:0009165 | nucleotide biosynthetic process | BP |
| GO:0009156 | ribonucleoside monophosphate biosynthetic process | BP |
| GO:0044249 | cellular biosynthetic process | BP |
KEGG
Orthology
- This transcript has been annotated with K00948 (ribose-phosphate pyrophosphokinase)
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.
