General information for g7656.t1
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.t1 | TSS | g7656.t1 | 25095961 | 25095961 |
| chr_2 | g7656 | g7656.t1 | isoform | g7656.t1 | 25095992 | 25097681 |
| chr_2 | g7656 | g7656.t1 | exon | g7656.t1.exon1 | 25095992 | 25096072 |
| chr_2 | g7656 | g7656.t1 | cds | g7656.t1.CDS1 | 25095992 | 25096072 |
| chr_2 | g7656 | g7656.t1 | exon | g7656.t1.exon2 | 25096166 | 25096320 |
| chr_2 | g7656 | g7656.t1 | cds | g7656.t1.CDS2 | 25096166 | 25096320 |
| chr_2 | g7656 | g7656.t1 | exon | g7656.t1.exon3 | 25096842 | 25097197 |
| chr_2 | g7656 | g7656.t1 | cds | g7656.t1.CDS3 | 25096842 | 25097197 |
| chr_2 | g7656 | g7656.t1 | exon | g7656.t1.exon4 | 25097258 | 25097410 |
| chr_2 | g7656 | g7656.t1 | cds | g7656.t1.CDS4 | 25097258 | 25097410 |
| chr_2 | g7656 | g7656.t1 | exon | g7656.t1.exon5 | 25097476 | 25097681 |
| chr_2 | g7656 | g7656.t1 | cds | g7656.t1.CDS5 | 25097476 | 25097681 |
| chr_2 | g7656 | g7656.t1 | TTS | g7656.t1 | 25098315 | 25098315 |
Sequences
>g7656.t1 Gene=g7656 Length=951
ATGGCATCATTTAACACAGAAGAGTTTAATGAGATATTAGAAAAATGTAAAGATCGATCG
CAACAAGAGAAACAAGATCAAACGCTTTTGCAACCCTTTCACTACATCAAACAAATTCCT
GGAAAACAGATCAGATCAAAGCTTGGACTGGCATTTAATTATTGGCTTAAAATACACACT
GAAAAACTAGCAAAGATTTCTGAAATAGTCCAAATGCTTCATAACAGCTCATTATTAATT
GATGATATAGAGGATAATTCAATTTTACGTAGAGGTATTCCTGTAGCACATTCTATATAT
GGAGTAGCAAGTACAATTAATTCTGCCAATTATGTGCTCTTTCTTGCACTTGAAAAAGTT
CAACAACTCGGGCATCCTGATGCCACAAAAGTTTACACTGAACAATTGCTAGAATTGCAT
CGCGGCCAAGGAATGGAAATTTATTGGCGAGATAATTTCTTATGTCCAGAAGAATCTGAC
TATAAGCTAATGACCATTCGTAAAACAGGAGGACTCTTTATGCTTGCAATTCGATTGATG
TTATTATTTAGCGATAATGAACGAGATTTTACTAAATTGACGGCCTTACTTGGTTTATAT
TTTCAAATACGTGATGATTATTGCAATTTGAGCCTTAAAGAATATTCAGAAAACAAGAGT
TTCTGTGAAGATTTGACTGAGGGAAAATTCAGTTTTCCAATTATTCATGCGATTCAATCG
CAAAGTGAGGATAAACAGGTGTTACATATTTTACGCCAACGAACTCGAGACATTGAAGTT
AAAAAATATTGCGTTTCATTGTTAGAAAAAATGGGAAGTTTTCGATACACACGTGAAACA
TTAGATGCACTTGATAAAGAAGCACGGAAAGAAGTTGCACAATTAGGACCAAATCCAATT
ATGGAAGAACTACTGGATGAGCTCTTAAGTTGGAAAACAACTGCGGATTAA
>g7656.t1 Gene=g7656 Length=316
MASFNTEEFNEILEKCKDRSQQEKQDQTLLQPFHYIKQIPGKQIRSKLGLAFNYWLKIHT
EKLAKISEIVQMLHNSSLLIDDIEDNSILRRGIPVAHSIYGVASTINSANYVLFLALEKV
QQLGHPDATKVYTEQLLELHRGQGMEIYWRDNFLCPEESDYKLMTIRKTGGLFMLAIRLM
LLFSDNERDFTKLTALLGLYFQIRDDYCNLSLKEYSENKSFCEDLTEGKFSFPIIHAIQS
QSEDKQVLHILRQRTRDIEVKKYCVSLLEKMGSFRYTRETLDALDKEARKEVAQLGPNPI
MEELLDELLSWKTTAD
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g7656.t1 | CDD | cd00685 | Trans_IPPS_HT | 26 | 239 | 8.66988E-67 |
| 7 | g7656.t1 | Gene3D | G3DSA:1.10.600.10 | Farnesyl Diphosphate Synthase | 18 | 315 | 8.8E-113 |
| 2 | g7656.t1 | PANTHER | PTHR12001:SF44 | GERANYLGERANYL PYROPHOSPHATE SYNTHASE | 10 | 311 | 6.8E-148 |
| 3 | g7656.t1 | PANTHER | PTHR12001 | GERANYLGERANYL PYROPHOSPHATE SYNTHASE | 10 | 311 | 6.8E-148 |
| 1 | g7656.t1 | Pfam | PF00348 | Polyprenyl synthetase | 27 | 267 | 5.7E-67 |
| 6 | g7656.t1 | ProSitePatterns | PS00723 | Polyprenyl synthases signature 1. | 78 | 92 | - |
| 5 | g7656.t1 | ProSitePatterns | PS00444 | Polyprenyl synthases signature 2. | 197 | 209 | - |
| 9 | g7656.t1 | SFLD | SFLDG01017 | Polyprenyl Transferase Like | 8 | 304 | 0.0 |
| 10 | g7656.t1 | SFLD | SFLDS00005 | Isoprenoid Synthase Type I | 8 | 304 | 0.0 |
| 4 | g7656.t1 | SUPERFAMILY | SSF48576 | Terpenoid synthases | 26 | 306 | 2.02E-77 |
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 transcript has been annotated with K00804 (geranylgeranyl diphosphate synthase, type III)
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.
