General information for g5787.t1
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.t1 | TSS | g5787.t1 | 11938237 | 11938237 |
| chr_2 | g5787 | g5787.t1 | isoform | g5787.t1 | 11938356 | 11940195 |
| chr_2 | g5787 | g5787.t1 | exon | g5787.t1.exon1 | 11938356 | 11938462 |
| chr_2 | g5787 | g5787.t1 | cds | g5787.t1.CDS1 | 11938356 | 11938462 |
| chr_2 | g5787 | g5787.t1 | exon | g5787.t1.exon2 | 11938909 | 11939224 |
| chr_2 | g5787 | g5787.t1 | cds | g5787.t1.CDS2 | 11938909 | 11939224 |
| chr_2 | g5787 | g5787.t1 | exon | g5787.t1.exon3 | 11939311 | 11939902 |
| chr_2 | g5787 | g5787.t1 | cds | g5787.t1.CDS3 | 11939311 | 11939902 |
| chr_2 | g5787 | g5787.t1 | exon | g5787.t1.exon4 | 11940014 | 11940195 |
| chr_2 | g5787 | g5787.t1 | cds | g5787.t1.CDS4 | 11940014 | 11940195 |
| chr_2 | g5787 | g5787.t1 | TTS | g5787.t1 | 11940341 | 11940341 |
Sequences
>g5787.t1 Gene=g5787 Length=1197
ATGTTGCGATCAGTCTTTAAAATTCTTACGCCAAATATAAGAGCATTAGCGATAAATGAA
TCGCGTAAATTAATGCATACTTCCGCAAAAGTCTTATCAAATAATAGAACTCTGTCAACA
CATAACCATACGCACGCACTTTCGGAAGCTGCAATTAATAAAGCAGCTGTTAGTAAGAAT
GATATTCGTAATTTTATGAGTGTGTGGCCAGATATAGTACGAGATTTAAATGATTATGCA
AAAAAGTATGACAAAATCTATGGACCGAAGTGGCTATCAAAACTTTTACAATATAACGTA
CCCAATGGAAAAAAATACAGAGGACTCATCCTTGTAGAAGCATTTAAAATTCTCGCAAAG
GATGGTCAAATGACTGATGAGAATTTAAAACTTGCTCAAACTCTCGGTTGGTGCATTGAA
ATGTTGCAAGCTGTATTCATTATCGATGACGACATCATTGATGGAAGCACAACTCGGCGT
GGCCATAAATGTTGGTATCAATTAGAAGATGTTGGTTTAGCTGCAATCAATGATGCGATG
ATGATCGAAAATGGCATTTATTATTTACTCAAGAAATATTTTAGACAAGCAGAATATTAC
CAAGAAGTTGTCGATTTGTTTCATGAAGTAAGCTTTATAACATCTTTGGGACAACTTCAG
GACATTAAAACAGCACATACTCTCGATTTGAATTTCTTCACAATGGAGATGTATAAATCA
ATTGTGGCAAATAAAACTGCATATTATTCGTTTTATTTGCCTGTTGCACTCGCCATGCAT
ATGACAGGTTACAAAGATCCTGAAGTGTTCAGACAAACCAAAACTATCTTACTTGAGATA
GGAAATTTCTTTCAAGTTCAAGACGACTTTATTGATTGCTTTGGTGATCCGTCTATCACT
GGAAAAGTTGGCACTGATATTCAAGATGGAAAATGCACGTGGCTGTCTGTAGTAGCATTA
CAACGAGCAAATGAGGATCAGCGATTATTAATGAAAGATTGCTACGGTCAAAAAGATCCT
GAAAAAGTTGAGCGCGTTAAAGAGTTATATGAAGATTTGTTATTACCACATACATATGAG
ATCTATGAAGAAGAGTCATATAAAATTATCAATACTCATATTCAACAGATTTCTCGAGGA
TTACCACACAAATTATTTTTCAAGATTTTAGAGAAAATCTATAGACGCAATTCTTAA
>g5787.t1 Gene=g5787 Length=398
MLRSVFKILTPNIRALAINESRKLMHTSAKVLSNNRTLSTHNHTHALSEAAINKAAVSKN
DIRNFMSVWPDIVRDLNDYAKKYDKIYGPKWLSKLLQYNVPNGKKYRGLILVEAFKILAK
DGQMTDENLKLAQTLGWCIEMLQAVFIIDDDIIDGSTTRRGHKCWYQLEDVGLAAINDAM
MIENGIYYLLKKYFRQAEYYQEVVDLFHEVSFITSLGQLQDIKTAHTLDLNFFTMEMYKS
IVANKTAYYSFYLPVALAMHMTGYKDPEVFRQTKTILLEIGNFFQVQDDFIDCFGDPSIT
GKVGTDIQDGKCTWLSVVALQRANEDQRLLMKDCYGQKDPEKVERVKELYEDLLLPHTYE
IYEEESYKIINTHIQQISRGLPHKLFFKILEKIYRRNS
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g5787.t1 | CDD | cd00685 | Trans_IPPS_HT | 89 | 396 | 1.03818E-58 |
| 7 | g5787.t1 | Gene3D | G3DSA:1.10.600.10 | Farnesyl Diphosphate Synthase | 55 | 398 | 1.1E-102 |
| 2 | g5787.t1 | PANTHER | PTHR11525:SF0 | FARNESYL PYROPHOSPHATE SYNTHASE | 63 | 397 | 8.3E-130 |
| 3 | g5787.t1 | PANTHER | PTHR11525 | FARNESYL-PYROPHOSPHATE SYNTHETASE | 63 | 397 | 8.3E-130 |
| 1 | g5787.t1 | Pfam | PF00348 | Polyprenyl synthetase | 90 | 352 | 1.4E-84 |
| 6 | g5787.t1 | ProSitePatterns | PS00723 | Polyprenyl synthases signature 1. | 147 | 161 | - |
| 5 | g5787.t1 | ProSitePatterns | PS00444 | Polyprenyl synthases signature 2. | 280 | 292 | - |
| 9 | g5787.t1 | SFLD | SFLDG01017 | Polyprenyl Transferase Like | 75 | 396 | 0.0 |
| 10 | g5787.t1 | SFLD | SFLDS00005 | Isoprenoid Synthase Type I | 75 | 396 | 0.0 |
| 4 | g5787.t1 | SUPERFAMILY | SSF48576 | Terpenoid synthases | 57 | 397 | 1.12E-83 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5787/g5787.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5787.t1.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.
