Gene loci information

Transcript annotation

  • This transcript has been annotated as Farnesyl pyrophosphate synthase.

Parent gene

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.t6 TSS g5787.t6 11938237 11938237
chr_2 g5787 g5787.t6 isoform g5787.t6 11939045 11940195
chr_2 g5787 g5787.t6 exon g5787.t6.exon1 11939045 11939224
chr_2 g5787 g5787.t6 cds g5787.t6.CDS1 11939171 11939224
chr_2 g5787 g5787.t6 exon g5787.t6.exon2 11939311 11939902
chr_2 g5787 g5787.t6 cds g5787.t6.CDS2 11939311 11939902
chr_2 g5787 g5787.t6 exon g5787.t6.exon3 11940014 11940195
chr_2 g5787 g5787.t6 cds g5787.t6.CDS3 11940014 11940195
chr_2 g5787 g5787.t6 TTS g5787.t6 11940341 11940341

Sequences

>g5787.t6 Gene=g5787 Length=954
AAGTATGACAAAATCTATGGACCGAAGTGGCTATCAAAACTTTTACAATATAACGTACCC
AATGGAAAAAAATACAGAGGACTCATCCTTGTAGAAGCATTTAAAATTCTCGCAAAGGAT
GGTCAAATGACTGATGAGAATTTAAAACTTGCTCAAACTCTCGGTTGGTGCATTGAAATG
TTGCAAGCTGTATTCATTATCGATGACGACATCATTGATGGAAGCACAACTCGGCGTGGC
CATAAATGTTGGTATCAATTAGAAGATGTTGGTTTAGCTGCAATCAATGATGCGATGATG
ATCGAAAATGGCATTTATTATTTACTCAAGAAATATTTTAGACAAGCAGAATATTACCAA
GAAGTTGTCGATTTGTTTCATGAAGTAAGCTTTATAACATCTTTGGGACAACTTCAGGAC
ATTAAAACAGCACATACTCTCGATTTGAATTTCTTCACAATGGAGATGTATAAATCAATT
GTGGCAAATAAAACTGCATATTATTCGTTTTATTTGCCTGTTGCACTCGCCATGCATATG
ACAGGTTACAAAGATCCTGAAGTGTTCAGACAAACCAAAACTATCTTACTTGAGATAGGA
AATTTCTTTCAAGTTCAAGACGACTTTATTGATTGCTTTGGTGATCCGTCTATCACTGGA
AAAGTTGGCACTGATATTCAAGATGGAAAATGCACGTGGCTGTCTGTAGTAGCATTACAA
CGAGCAAATGAGGATCAGCGATTATTAATGAAAGATTGCTACGGTCAAAAAGATCCTGAA
AAAGTTGAGCGCGTTAAAGAGTTATATGAAGATTTGTTATTACCACATACATATGAGATC
TATGAAGAAGAGTCATATAAAATTATCAATACTCATATTCAACAGATTTCTCGAGGATTA
CCACACAAATTATTTTTCAAGATTTTAGAGAAAATCTATAGACGCAATTCTTAA

>g5787.t6 Gene=g5787 Length=275
MTDENLKLAQTLGWCIEMLQAVFIIDDDIIDGSTTRRGHKCWYQLEDVGLAAINDAMMIE
NGIYYLLKKYFRQAEYYQEVVDLFHEVSFITSLGQLQDIKTAHTLDLNFFTMEMYKSIVA
NKTAYYSFYLPVALAMHMTGYKDPEVFRQTKTILLEIGNFFQVQDDFIDCFGDPSITGKV
GTDIQDGKCTWLSVVALQRANEDQRLLMKDCYGQKDPEKVERVKELYEDLLLPHTYEIYE
EESYKIINTHIQQISRGLPHKLFFKILEKIYRRNS

Protein features from InterProScan

Transcript Database ID Name Start End E.value
8 g5787.t6 CDD cd00685 Trans_IPPS_HT 3 273 9.81378E-54
7 g5787.t6 Gene3D G3DSA:1.10.600.10 Farnesyl Diphosphate Synthase 1 275 1.3E-89
2 g5787.t6 PANTHER PTHR11525:SF0 FARNESYL PYROPHOSPHATE SYNTHASE 2 274 8.0E-114
3 g5787.t6 PANTHER PTHR11525 FARNESYL-PYROPHOSPHATE SYNTHETASE 2 274 8.0E-114
1 g5787.t6 Pfam PF00348 Polyprenyl synthetase 4 229 2.4E-75
6 g5787.t6 ProSitePatterns PS00723 Polyprenyl synthases signature 1. 24 38 -
5 g5787.t6 ProSitePatterns PS00444 Polyprenyl synthases signature 2. 157 169 -
9 g5787.t6 SFLD SFLDS00005 Isoprenoid Synthase Type I 10 269 0.0
4 g5787.t6 SUPERFAMILY SSF48576 Terpenoid synthases 2 274 3.84E-73

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g5787/g5787.t6; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5787.t6.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

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.

Raw TPM values