General information for g5787.t7
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.t7 | TSS | g5787.t7 | 11938298 | 11938298 |
| chr_2 | g5787 | g5787.t7 | isoform | g5787.t7 | 11939318 | 11940195 |
| chr_2 | g5787 | g5787.t7 | exon | g5787.t7.exon1 | 11939318 | 11939902 |
| chr_2 | g5787 | g5787.t7 | cds | g5787.t7.CDS1 | 11939425 | 11939902 |
| chr_2 | g5787 | g5787.t7 | exon | g5787.t7.exon2 | 11940014 | 11940195 |
| chr_2 | g5787 | g5787.t7 | cds | g5787.t7.CDS2 | 11940014 | 11940195 |
| chr_2 | g5787 | g5787.t7 | TTS | g5787.t7 | 11940341 | 11940341 |
Sequences
>g5787.t7 Gene=g5787 Length=767
CTGTATTCATTATCGATGACGACATCATTGATGGAAGCACAACTCGGCGTGGCCATAAAT
GTTGGTATCAATTAGAAGATGTTGGTTTAGCTGCAATCAATGATGCGATGATGATCGAAA
ATGGCATTTATTATTTACTCAAGAAATATTTTAGACAAGCAGAATATTACCAAGAAGTTG
TCGATTTGTTTCATGAAGTAAGCTTTATAACATCTTTGGGACAACTTCAGGACATTAAAA
CAGCACATACTCTCGATTTGAATTTCTTCACAATGGAGATGTATAAATCAATTGTGGCAA
ATAAAACTGCATATTATTCGTTTTATTTGCCTGTTGCACTCGCCATGCATATGACAGGTT
ACAAAGATCCTGAAGTGTTCAGACAAACCAAAACTATCTTACTTGAGATAGGAAATTTCT
TTCAAGTTCAAGACGACTTTATTGATTGCTTTGGTGATCCGTCTATCACTGGAAAAGTTG
GCACTGATATTCAAGATGGAAAATGCACGTGGCTGTCTGTAGTAGCATTACAACGAGCAA
ATGAGGATCAGCGATTATTAATGAAAGATTGCTACGGTCAAAAAGATCCTGAAAAAGTTG
AGCGCGTTAAAGAGTTATATGAAGATTTGTTATTACCACATACATATGAGATCTATGAAG
AAGAGTCATATAAAATTATCAATACTCATATTCAACAGATTTCTCGAGGATTACCACACA
AATTATTTTTCAAGATTTTAGAGAAAATCTATAGACGCAATTCTTAA
>g5787.t7 Gene=g5787 Length=219
MMIENGIYYLLKKYFRQAEYYQEVVDLFHEVSFITSLGQLQDIKTAHTLDLNFFTMEMYK
SIVANKTAYYSFYLPVALAMHMTGYKDPEVFRQTKTILLEIGNFFQVQDDFIDCFGDPSI
TGKVGTDIQDGKCTWLSVVALQRANEDQRLLMKDCYGQKDPEKVERVKELYEDLLLPHTY
EIYEEESYKIINTHIQQISRGLPHKLFFKILEKIYRRNS
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g5787.t7 | Gene3D | G3DSA:1.10.600.10 | Farnesyl Diphosphate Synthase | 1 | 219 | 1.4E-65 |
| 2 | g5787.t7 | PANTHER | PTHR11525:SF0 | FARNESYL PYROPHOSPHATE SYNTHASE | 1 | 218 | 1.1E-83 |
| 3 | g5787.t7 | PANTHER | PTHR11525 | FARNESYL-PYROPHOSPHATE SYNTHETASE | 1 | 218 | 1.1E-83 |
| 1 | g5787.t7 | Pfam | PF00348 | Polyprenyl synthetase | 2 | 173 | 2.3E-51 |
| 5 | g5787.t7 | ProSitePatterns | PS00444 | Polyprenyl synthases signature 2. | 101 | 113 | - |
| 4 | g5787.t7 | SUPERFAMILY | SSF48576 | Terpenoid synthases | 7 | 218 | 3.08E-53 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5787/g5787.t7; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5787.t7.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 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.
