General information for g5787.t4
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Farnesyl pyrophosphate synthase.
Parent gene
- The parent gene g5787 is located on chr_2: 11939318..11940195 (+ 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 | g5787 | g5787.t4 | isoform | g5787.t4 | 11937813 | 11940195 |
| chr_2 | g5787 | g5787.t4 | exon | g5787.t4.exon1 | 11937813 | 11938273 |
| chr_2 | g5787 | g5787.t4 | TSS | g5787.t4 | 11937868 | 11937868 |
| chr_2 | g5787 | g5787.t4 | exon | g5787.t4.exon2 | 11938909 | 11939224 |
| chr_2 | g5787 | g5787.t4 | cds | g5787.t4.CDS1 | 11938997 | 11939224 |
| chr_2 | g5787 | g5787.t4 | exon | g5787.t4.exon3 | 11939311 | 11939902 |
| chr_2 | g5787 | g5787.t4 | cds | g5787.t4.CDS2 | 11939311 | 11939902 |
| chr_2 | g5787 | g5787.t4 | exon | g5787.t4.exon4 | 11940014 | 11940195 |
| chr_2 | g5787 | g5787.t4 | cds | g5787.t4.CDS3 | 11940014 | 11940195 |
| chr_2 | g5787 | g5787.t4 | TTS | g5787.t4 | 11940341 | 11940341 |
Sequences
>g5787.t4 Gene=g5787 Length=1551
TGTGAATGTATTGGTTAATTGTTGTTGTGATAACAATCGGTCTCTCTCATTTTTTTCCTG
ATAACTGTTATTATTTGCAACGATAAAATTTTTAATTAGTCAGAACAGACATTGTACCGA
ATTCAATAAAAATAAATTCATGTCGTATTATACAAAGTTTTTATTGCAAATCTATTACGG
ATCATTTATTTAATAGCGAAAAAACATAAAGAGAACGAAGAAGAATAACAAAAACTTCCT
CAAAAAAATCTTTCGACGTTCAATTTAAACAGGTTTATAGAGAGAAGTGAATAAAAAGAG
AGAGATTATACCACATACAGATTGATTGTGTTATTCTGAAAAAAGATTTAACCGCATACC
TCTTAGATTATTTACTCAAGAGTATTTTTAGACTATATTCAGAATAAAACTGTGAGAGAG
AAGCAACAGCAGTTAAGCGAGTCAGTCCGTATAATATAAAAAACTCTGTCAACACATAAC
CATACGCACGCACTTTCGGAAGCTGCAATTAATAAAGCAGCTGTTAGTAAGAATGATATT
CGTAATTTTATGAGTGTGTGGCCAGATATAGTACGAGATTTAAATGATTATGCAAAAAAG
TATGACAAAATCTATGGACCGAAGTGGCTATCAAAACTTTTACAATATAACGTACCCAAT
GGAAAAAAATACAGAGGACTCATCCTTGTAGAAGCATTTAAAATTCTCGCAAAGGATGGT
CAAATGACTGATGAGAATTTAAAACTTGCTCAAACTCTCGGTTGGTGCATTGAAATGTTG
CAAGCTGTATTCATTATCGATGACGACATCATTGATGGAAGCACAACTCGGCGTGGCCAT
AAATGTTGGTATCAATTAGAAGATGTTGGTTTAGCTGCAATCAATGATGCGATGATGATC
GAAAATGGCATTTATTATTTACTCAAGAAATATTTTAGACAAGCAGAATATTACCAAGAA
GTTGTCGATTTGTTTCATGAAGTAAGCTTTATAACATCTTTGGGACAACTTCAGGACATT
AAAACAGCACATACTCTCGATTTGAATTTCTTCACAATGGAGATGTATAAATCAATTGTG
GCAAATAAAACTGCATATTATTCGTTTTATTTGCCTGTTGCACTCGCCATGCATATGACA
GGTTACAAAGATCCTGAAGTGTTCAGACAAACCAAAACTATCTTACTTGAGATAGGAAAT
TTCTTTCAAGTTCAAGACGACTTTATTGATTGCTTTGGTGATCCGTCTATCACTGGAAAA
GTTGGCACTGATATTCAAGATGGAAAATGCACGTGGCTGTCTGTAGTAGCATTACAACGA
GCAAATGAGGATCAGCGATTATTAATGAAAGATTGCTACGGTCAAAAAGATCCTGAAAAA
GTTGAGCGCGTTAAAGAGTTATATGAAGATTTGTTATTACCACATACATATGAGATCTAT
GAAGAAGAGTCATATAAAATTATCAATACTCATATTCAACAGATTTCTCGAGGATTACCA
CACAAATTATTTTTCAAGATTTTAGAGAAAATCTATAGACGCAATTCTTAA
>g5787.t4 Gene=g5787 Length=333
MSVWPDIVRDLNDYAKKYDKIYGPKWLSKLLQYNVPNGKKYRGLILVEAFKILAKDGQMT
DENLKLAQTLGWCIEMLQAVFIIDDDIIDGSTTRRGHKCWYQLEDVGLAAINDAMMIENG
IYYLLKKYFRQAEYYQEVVDLFHEVSFITSLGQLQDIKTAHTLDLNFFTMEMYKSIVANK
TAYYSFYLPVALAMHMTGYKDPEVFRQTKTILLEIGNFFQVQDDFIDCFGDPSITGKVGT
DIQDGKCTWLSVVALQRANEDQRLLMKDCYGQKDPEKVERVKELYEDLLLPHTYEIYEEE
SYKIINTHIQQISRGLPHKLFFKILEKIYRRNS
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g5787.t4 | CDD | cd00685 | Trans_IPPS_HT | 24 | 331 | 7.99015E-60 |
| 7 | g5787.t4 | Gene3D | G3DSA:1.10.600.10 | Farnesyl Diphosphate Synthase | 1 | 333 | 5.0E-101 |
| 2 | g5787.t4 | PANTHER | PTHR11525:SF0 | FARNESYL PYROPHOSPHATE SYNTHASE | 2 | 332 | 1.7E-128 |
| 3 | g5787.t4 | PANTHER | PTHR11525 | FARNESYL-PYROPHOSPHATE SYNTHETASE | 2 | 332 | 1.7E-128 |
| 1 | g5787.t4 | Pfam | PF00348 | Polyprenyl synthetase | 25 | 287 | 8.0E-85 |
| 6 | g5787.t4 | ProSitePatterns | PS00723 | Polyprenyl synthases signature 1. | 82 | 96 | - |
| 5 | g5787.t4 | ProSitePatterns | PS00444 | Polyprenyl synthases signature 2. | 215 | 227 | - |
| 9 | g5787.t4 | SFLD | SFLDG01017 | Polyprenyl Transferase Like | 12 | 331 | 0.0 |
| 10 | g5787.t4 | SFLD | SFLDS00005 | Isoprenoid Synthase Type I | 12 | 331 | 0.0 |
| 4 | g5787.t4 | SUPERFAMILY | SSF48576 | Terpenoid synthases | 2 | 332 | 2.52E-82 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5787/g5787.t4; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5787.t4.fa.iupred3.txt does not exist
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0016765 | transferase activity, transferring alkyl or aryl (other than methyl) groups | MF |
| GO:0008299 | isoprenoid biosynthetic process | BP |
KEGG
Orthology
- This transcript has been annotated with K00787 (farnesyl diphosphate synthase)
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.
