General information for g8516.t1
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.t1 | TTS | g8516.t1 | 31106094 | 31106094 |
| chr_2 | g8516 | g8516.t1 | isoform | g8516.t1 | 31106395 | 31111041 |
| chr_2 | g8516 | g8516.t1 | exon | g8516.t1.exon1 | 31106395 | 31106946 |
| chr_2 | g8516 | g8516.t1 | cds | g8516.t1.CDS1 | 31106395 | 31106946 |
| chr_2 | g8516 | g8516.t1 | exon | g8516.t1.exon2 | 31107005 | 31107103 |
| chr_2 | g8516 | g8516.t1 | cds | g8516.t1.CDS2 | 31107005 | 31107103 |
| chr_2 | g8516 | g8516.t1 | exon | g8516.t1.exon3 | 31108824 | 31108880 |
| chr_2 | g8516 | g8516.t1 | cds | g8516.t1.CDS3 | 31108824 | 31108880 |
| chr_2 | g8516 | g8516.t1 | exon | g8516.t1.exon4 | 31109643 | 31109782 |
| chr_2 | g8516 | g8516.t1 | cds | g8516.t1.CDS4 | 31109643 | 31109782 |
| chr_2 | g8516 | g8516.t1 | exon | g8516.t1.exon5 | 31109855 | 31109898 |
| chr_2 | g8516 | g8516.t1 | cds | g8516.t1.CDS5 | 31109855 | 31109898 |
| chr_2 | g8516 | g8516.t1 | exon | g8516.t1.exon6 | 31110920 | 31111041 |
| chr_2 | g8516 | g8516.t1 | cds | g8516.t1.CDS6 | 31110920 | 31111041 |
| chr_2 | g8516 | g8516.t1 | TSS | g8516.t1 | 31111077 | 31111077 |
Sequences
>g8516.t1 Gene=g8516 Length=1014
ATGCCTAACATTAAAGTGTTTTCTGGAACTTCACATCCTGATTTAGCTCAAAGAATCGTA
GATCGGTTAGGTATTGACTTGGGAAAAGTTGTAACAAAAAAATTTTCAAACCTGGAAACA
TGTGTGGAGATCGGAGAATCAGTACGTGGAGAGGATGTGTATATCGTTCAATCTGGTTCG
GGAGAAATTAATGACAACTTGATGGAACTTTTAATTATGATAAACGCATGCAAAATTGCA
TCAGCTTCAAGAGTGACAGCTGTGATACCATGTTTTCCATATGCAAGACAAGACAAAAAA
GACAAGTCTGGCGATGAAAAGTTAGCTCAACTGATGAAGAAGTCAAATGAATGGAAATTT
CGGAGTAGAGCACCCATTTCGGCAAAACTTGTTGCAAACATGTTGTCAGTTGCTGGTGCT
GACCATATCATTACAATGGATCTTCATGCTTCTCAAATACAGGGTTTCTTTGATATACCA
GTGGATAATCTCTACGCAGAACCAGCAGTTCTGAAATGGATAAAAGAAAATATTCAGGAG
TGGCGTAACTCGATTATCGTTTCTCCTGATGCTGGCGGTGCTAAACGTGTGACATCTATT
GCTGATCGTCTTAATGTAGAATTTGCATTGATTCACAAAGAACGCAAAAAAGCAAATGAA
GTTGCATCAATGGTGTTAGTTGGAGATGTAAAAGACAGAGTAGCAATTTTAGTTGATGAC
ATGGCTGATACATGTGGAACAATTTGTCATGCAGCCGAGAAGCTTTTAGAAGCAGGAGCA
ACAAAAGTTTATGCCATTTTAACACATGGGATTTTTAGCGGTCCAGCTATTTCGCGAATA
AATAATGCATGTTTCGAGGCGGTCGTTGTCACGAATACAATTCCACAAGATGGTCATATG
AAGGACTGTCCAAAAATACAGTGCATTGATGTGTCTATGATGTTTGCAGAAGCAGTTCGT
AGAACACATAATGGAGAAAGTGTCAGCTATCTTTTTAGTAATGTTCCATATTAG
>g8516.t1 Gene=g8516 Length=337
MPNIKVFSGTSHPDLAQRIVDRLGIDLGKVVTKKFSNLETCVEIGESVRGEDVYIVQSGS
GEINDNLMELLIMINACKIASASRVTAVIPCFPYARQDKKDKSGDEKLAQLMKKSNEWKF
RSRAPISAKLVANMLSVAGADHIITMDLHASQIQGFFDIPVDNLYAEPAVLKWIKENIQE
WRNSIIVSPDAGGAKRVTSIADRLNVEFALIHKERKKANEVASMVLVGDVKDRVAILVDD
MADTCGTICHAAEKLLEAGATKVYAILTHGIFSGPAISRINNACFEAVVVTNTIPQDGHM
KDCPKIQCIDVSMMFAEAVRRTHNGESVSYLFSNVPY
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 10 | g8516.t1 | CDD | cd06223 | PRTases_typeI | 166 | 293 | 1.00596E-26 |
| 9 | g8516.t1 | Gene3D | G3DSA:3.40.50.2020 | - | 7 | 323 | 4.2E-127 |
| 8 | g8516.t1 | Gene3D | G3DSA:3.40.50.2020 | - | 166 | 309 | 4.2E-127 |
| 3 | g8516.t1 | PANTHER | PTHR10210 | RIBOSE-PHOSPHATE DIPHOSPHOKINASE FAMILY MEMBER | 1 | 111 | 4.3E-196 |
| 5 | g8516.t1 | PANTHER | PTHR10210:SF105 | PHOSPHORIBOSYL PYROPHOSPHATE SYNTHETASE 1-LIKE 3-RELATED | 1 | 111 | 4.3E-196 |
| 4 | g8516.t1 | PANTHER | PTHR10210 | RIBOSE-PHOSPHATE DIPHOSPHOKINASE FAMILY MEMBER | 118 | 336 | 4.3E-196 |
| 6 | g8516.t1 | PANTHER | PTHR10210:SF105 | PHOSPHORIBOSYL PYROPHOSPHATE SYNTHETASE 1-LIKE 3-RELATED | 118 | 336 | 4.3E-196 |
| 2 | g8516.t1 | Pfam | PF13793 | N-terminal domain of ribose phosphate pyrophosphokinase | 4 | 139 | 3.2E-41 |
| 1 | g8516.t1 | Pfam | PF14572 | Phosphoribosyl synthetase-associated domain | 222 | 332 | 5.2E-38 |
| 11 | g8516.t1 | ProSitePatterns | PS00114 | Phosphoribosyl pyrophosphate synthase signature. | 147 | 162 | - |
| 12 | g8516.t1 | SMART | SM01400 | Pribosyltran_N_2 | 4 | 139 | 7.6E-67 |
| 7 | g8516.t1 | SUPERFAMILY | SSF53271 | PRTase-like | 69 | 325 | 6.45E-60 |
| 13 | g8516.t1 | TIGRFAM | TIGR01251 | ribP_PPkin: ribose-phosphate diphosphokinase | 4 | 106 | 3.1E-35 |
| 14 | g8516.t1 | TIGRFAM | TIGR01251 | ribP_PPkin: ribose-phosphate diphosphokinase | 119 | 333 | 6.2E-82 |
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.
