General information for g4793.t4
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Isopentenyl-diphosphate Delta-isomerase 1.
Parent gene
- The parent gene g4793 is located on chr_2: 4994668..4996006 (- 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 | g4793 | g4793.t4 | TTS | g4793.t4 | 4994118 | 4994118 |
| chr_2 | g4793 | g4793.t4 | isoform | g4793.t4 | 4994120 | 4996006 |
| chr_2 | g4793 | g4793.t4 | exon | g4793.t4.exon1 | 4994120 | 4994982 |
| chr_2 | g4793 | g4793.t4 | cds | g4793.t4.CDS1 | 4994933 | 4994982 |
| chr_2 | g4793 | g4793.t4 | exon | g4793.t4.exon2 | 4995291 | 4995441 |
| chr_2 | g4793 | g4793.t4 | cds | g4793.t4.CDS2 | 4995291 | 4995441 |
| chr_2 | g4793 | g4793.t4 | exon | g4793.t4.exon3 | 4995719 | 4996006 |
| chr_2 | g4793 | g4793.t4 | cds | g4793.t4.CDS3 | 4995719 | 4996006 |
| chr_2 | g4793 | g4793.t4 | TSS | g4793.t4 | 4996019 | 4996019 |
Sequences
>g4793.t4 Gene=g4793 Length=1302
ATGTTGAAGAGAATAGTTCCTCCCTCAATTAATTTGATGAGCAAGTCACGTTATAGTTTC
GCTCATAAGTTAGTAGAAGCGGGAATAGAGAGCGAGAAGCAAGAACTATTTCTTGATTCA
GAAAACTGCATTCTTGTAGATTCTAATGACAAACCAATCGGCTTTTCATCAAAGCGTGAT
TGTCATAAAGTAGATGAAAGTCAGCATATCAAACTGCATCGAGCATTCAGTGTATTCTTA
TTCAATCAGAATGGAGAAATGTTAATGCAAAAAAGGTCAAGTCATAAGATTACATTTCCT
AATTGCTATACAAACGCATGCTGCTCACATCCACTGTACGATTTAGAAAATGAAAGAGAA
GAATTGAATGCAATTGGTATCAAGAAAGCAGCACAGAGGCGGCTTAATTTTGAATTGGGC
ATTCCAACTAGTCAGGTGAGTTCGACCAGAAAACTTTCATTATCTAACACGCATACATTA
TTTGGATAAAGGTGATGGAAAATATGGCGAGCACGAAATAGATTACATACTTTTTCTTCA
AAAAAATGTTGATGTCAAGCCAAATCCAGGTGAAGTTAGTGAGATCTGTTGGATCAAGCG
TGAAAATATGGATGAACAGATTGAAGCATTAGATGGTAATCTCACACCTTGGTTTCGATT
AATATATAATTCAGGTCAACTTGGATTATGGTGGAAAAATCTTCATCAACTCAAGAAATT
TGAAGATTATAACACAATACATAAACTCAATTAAACATGTGAAATCTTGACTCGAAATTT
TAACGTATGACAATAATGATGATCACTAGTTTTTTTTTTCTCGATTTTTAATAGTAGACT
TAAAGTCATTGTAGATTATCAATTATCGTAGGATAATCGAAAACGAAGATGCAATAATTT
ATCTAGTTAATATTTAGTTACTCAAGGAAGCGGAAAGTACTGTAAAAATAATTAAATATT
AGTCTTAGAATTTCATTCGTCAATCATTATTTATAAAATATAGGAATATGAGTGTTTGAA
ATTGAGCAGTGTAAAAACAATTGCATATCATCTGTTCAAATTATCTCAATAGCACACCTA
TTTAAAGATTAAAAAAATATATATTTAGGGAAAAACAACTTCTTATCTCAACAATAAAAA
TAAATAATTGACAACACTCAGCAAGACAGGAAAAAATTAACTTGAGATTTAACTTTATTT
TTCTTCAAAATTGTTATACAAAAACTGATGTGTACACACAATACCTAATAATCGGCAGAT
ATACTTAACAAAAAAAGTCAATAAAACATTTCATTGAAGACT
>g4793.t4 Gene=g4793 Length=162
MLKRIVPPSINLMSKSRYSFAHKLVEAGIESEKQELFLDSENCILVDSNDKPIGFSSKRD
CHKVDESQHIKLHRAFSVFLFNQNGEMLMQKRSSHKITFPNCYTNACCSHPLYDLENERE
ELNAIGIKKAAQRRLNFELGIPTSQVSSTRKLSLSNTHTLFG
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g4793.t4 | Gene3D | G3DSA:3.90.79.10 | Nucleoside Triphosphate Pyrophosphohydrolase | 11 | 159 | 0.000 |
| 2 | g4793.t4 | PANTHER | PTHR10885 | ISOPENTENYL-DIPHOSPHATE DELTA-ISOMERASE | 31 | 150 | 0.000 |
| 3 | g4793.t4 | PANTHER | PTHR10885:SF0 | ISOPENTENYL-DIPHOSPHATE DELTA ISOMERASE 1 | 31 | 150 | 0.000 |
| 1 | g4793.t4 | Pfam | PF00293 | NUDIX domain | 71 | 149 | 0.000 |
| 7 | g4793.t4 | ProSiteProfiles | PS51462 | Nudix hydrolase domain profile. | 71 | 162 | 10.189 |
| 4 | g4793.t4 | SUPERFAMILY | SSF55811 | Nudix | 41 | 145 | 0.000 |
| 6 | g4793.t4 | TIGRFAM | TIGR02150 | IPP_isom_1: isopentenyl-diphosphate delta-isomerase | 43 | 147 | 0.000 |
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:0008299 | isoprenoid biosynthetic process | BP |
| GO:0016787 | hydrolase activity | MF |
| GO:0004452 | isopentenyl-diphosphate delta-isomerase 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.
