General information for g7656.t17
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Geranylgeranyl pyrophosphate synthase.
Parent gene
- The parent gene g7656 is located on chr_2: 25097681..25098300 (+ 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 | g7656 | g7656.t17 | TSS | g7656.t17 | 25095961 | 25095961 |
| chr_2 | g7656 | g7656.t17 | isoform | g7656.t17 | 25095992 | 25098300 |
| chr_2 | g7656 | g7656.t17 | exon | g7656.t17.exon1 | 25095992 | 25096320 |
| chr_2 | g7656 | g7656.t17 | cds | g7656.t17.CDS1 | 25096298 | 25096320 |
| chr_2 | g7656 | g7656.t17 | exon | g7656.t17.exon2 | 25096842 | 25097197 |
| chr_2 | g7656 | g7656.t17 | cds | g7656.t17.CDS2 | 25096842 | 25097197 |
| chr_2 | g7656 | g7656.t17 | exon | g7656.t17.exon3 | 25097258 | 25097410 |
| chr_2 | g7656 | g7656.t17 | cds | g7656.t17.CDS3 | 25097258 | 25097410 |
| chr_2 | g7656 | g7656.t17 | exon | g7656.t17.exon4 | 25097476 | 25098300 |
| chr_2 | g7656 | g7656.t17 | cds | g7656.t17.CDS4 | 25097476 | 25097681 |
| chr_2 | g7656 | g7656.t17 | TTS | g7656.t17 | 25098315 | 25098315 |
Sequences
>g7656.t17 Gene=g7656 Length=1663
ATGGCATCATTTAACACAGAAGAGTTTAATGAGATATTAGAAAAATGTAAAGATCGATCG
CAACAAGAGAAACAAGATCAAGTGAGTAAAAATTTTAAGAAAAAAGTGTAAAGTCAGCTG
AGTGTTATCGAATTTATATTTTATAAGGCTCTTTGTCATTAAATTTATTTTTAGACGCTT
TTGCAACCCTTTCACTACATCAAACAAATTCCTGGAAAACAGATCAGATCAAAGCTTGGA
CTGGCATTTAATTATTGGCTTAAAATACACACTGAAAAACTAGCAAAGATTTCTGAAATA
GTCCAAATGCTTCATAACAGCTCATTATTAATTGATGATATAGAGGATAATTCAATTTTA
CGTAGAGGTATTCCTGTAGCACATTCTATATATGGAGTAGCAAGTACAATTAATTCTGCC
AATTATGTGCTCTTTCTTGCACTTGAAAAAGTTCAACAACTCGGGCATCCTGATGCCACA
AAAGTTTACACTGAACAATTGCTAGAATTGCATCGCGGCCAAGGAATGGAAATTTATTGG
CGAGATAATTTCTTATGTCCAGAAGAATCTGACTATAAGCTAATGACCATTCGTAAAACA
GGAGGACTCTTTATGCTTGCAATTCGATTGATGTTATTATTTAGCGATAATGAACGAGAT
TTTACTAAATTGACGGCCTTACTTGGTTTATATTTTCAAATACGTGATGATTATTGCAAT
TTGAGCCTTAAAGAATATTCAGAAAACAAGAGTTTCTGTGAAGATTTGACTGAGGGAAAA
TTCAGTTTTCCAATTATTCATGCGATTCAATCGCAAAGTGAGGATAAACAGGTGTTACAT
ATTTTACGCCAACGAACTCGAGACATTGAAGTTAAAAAATATTGCGTTTCATTGTTAGAA
AAAATGGGAAGTTTTCGATACACACGTGAAACATTAGATGCACTTGATAAAGAAGCACGG
AAAGAAGTTGCACAATTAGGACCAAATCCAATTATGGAAGAACTACTGGATGAGCTCTTA
AGTTGGAAAACAACTGCGGATTAAAAAGTATTTTTCATAAAGTACATTTTTAACACAATC
TTTTTTTTTTCGTAACTACATAACTTTATATTTTTATGGGTTTTCGAAACATTCTTCAAA
TATGTTACTTATACATTTAATCTTCATTTAAAATTCGAATTTTTATATCTTAATTAATTT
TAACTATCTATACATATATATGTTATGTGTGTGTCATAATCTCAGGTTGAACTAATGATT
ATTTTATTTTAAATCAAATCACTCGCCTGATGCTCAAACATTTTTTAAAATATTTATTAA
AATTTACCTAATATTTTTTAATTAAAATCAAAAATGTCTATATAAAGTGCTAATTTCAAC
CATATTCACGATTTAGAATTTTTTAAAAAAAATTTCTAGTGTTGAGTAATTCTATACATC
TATTTAAAAAGAATCAAGTGATTGACTAAAAGTAGAAACTTTAAAAGCAAAAATTTTTAA
ATGGACTTAAAATTATACCTATTAATAATGATTATATTGTATTTAGAGAGCACTATAAGC
TTTTTGCACTTTTAATGTGTAATTAAAAATTATGAAGGAATTTTATACGAAAAAACCAAA
ATTTTTATTGGGAAACAAGTAAAAATTAAAGCAAATTGTTGAT
>g7656.t17 Gene=g7656 Length=245
MLHNSSLLIDDIEDNSILRRGIPVAHSIYGVASTINSANYVLFLALEKVQQLGHPDATKV
YTEQLLELHRGQGMEIYWRDNFLCPEESDYKLMTIRKTGGLFMLAIRLMLLFSDNERDFT
KLTALLGLYFQIRDDYCNLSLKEYSENKSFCEDLTEGKFSFPIIHAIQSQSEDKQVLHIL
RQRTRDIEVKKYCVSLLEKMGSFRYTRETLDALDKEARKEVAQLGPNPIMEELLDELLSW
KTTAD
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g7656.t17 | CDD | cd00685 | Trans_IPPS_HT | 1 | 168 | 7.21954E-56 |
| 7 | g7656.t17 | Gene3D | G3DSA:1.10.600.10 | Farnesyl Diphosphate Synthase | 1 | 244 | 1.1E-95 |
| 2 | g7656.t17 | PANTHER | PTHR12001:SF44 | GERANYLGERANYL PYROPHOSPHATE SYNTHASE | 1 | 240 | 3.6E-123 |
| 3 | g7656.t17 | PANTHER | PTHR12001 | GERANYLGERANYL PYROPHOSPHATE SYNTHASE | 1 | 240 | 3.6E-123 |
| 1 | g7656.t17 | Pfam | PF00348 | Polyprenyl synthetase | 1 | 196 | 1.6E-56 |
| 6 | g7656.t17 | ProSitePatterns | PS00723 | Polyprenyl synthases signature 1. | 7 | 21 | - |
| 5 | g7656.t17 | ProSitePatterns | PS00444 | Polyprenyl synthases signature 2. | 126 | 138 | - |
| 9 | g7656.t17 | SFLD | SFLDS00005 | Isoprenoid Synthase Type I | 1 | 230 | 5.3E-33 |
| 4 | g7656.t17 | SUPERFAMILY | SSF48576 | Terpenoid synthases | 1 | 235 | 2.02E-66 |
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 |
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.
