General information for g7656.t15
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.t15 | TSS | g7656.t15 | 25095961 | 25095961 |
| chr_2 | g7656 | g7656.t15 | isoform | g7656.t15 | 25095992 | 25098300 |
| chr_2 | g7656 | g7656.t15 | exon | g7656.t15.exon1 | 25095992 | 25096072 |
| chr_2 | g7656 | g7656.t15 | exon | g7656.t15.exon2 | 25096166 | 25096324 |
| chr_2 | g7656 | g7656.t15 | exon | g7656.t15.exon3 | 25096842 | 25097197 |
| chr_2 | g7656 | g7656.t15 | cds | g7656.t15.CDS1 | 25097038 | 25097197 |
| chr_2 | g7656 | g7656.t15 | exon | g7656.t15.exon4 | 25097258 | 25097410 |
| chr_2 | g7656 | g7656.t15 | cds | g7656.t15.CDS2 | 25097258 | 25097410 |
| chr_2 | g7656 | g7656.t15 | exon | g7656.t15.exon5 | 25097476 | 25098300 |
| chr_2 | g7656 | g7656.t15 | cds | g7656.t15.CDS3 | 25097476 | 25097681 |
| chr_2 | g7656 | g7656.t15 | TTS | g7656.t15 | 25098315 | 25098315 |
Sequences
>g7656.t15 Gene=g7656 Length=1574
ATGGCATCATTTAACACAGAAGAGTTTAATGAGATATTAGAAAAATGTAAAGATCGATCG
CAACAAGAGAAACAAGATCAAACGCTTTTGCAACCCTTTCACTACATCAAACAAATTCCT
GGAAAACAGATCAGATCAAAGCTTGGACTGGCATTTAATTATTGGCTTAAAATACACACT
GAAAAACTAGCAAAGATTTCTGAAATAGTCCAAATGCTTCATAACAGCTCATTATTGTAA
AATTGATGATATAGAGGATAATTCAATTTTACGTAGAGGTATTCCTGTAGCACATTCTAT
ATATGGAGTAGCAAGTACAATTAATTCTGCCAATTATGTGCTCTTTCTTGCACTTGAAAA
AGTTCAACAACTCGGGCATCCTGATGCCACAAAAGTTTACACTGAACAATTGCTAGAATT
GCATCGCGGCCAAGGAATGGAAATTTATTGGCGAGATAATTTCTTATGTCCAGAAGAATC
TGACTATAAGCTAATGACCATTCGTAAAACAGGAGGACTCTTTATGCTTGCAATTCGATT
GATGTTATTATTTAGCGATAATGAACGAGATTTTACTAAATTGACGGCCTTACTTGGTTT
ATATTTTCAAATACGTGATGATTATTGCAATTTGAGCCTTAAAGAATATTCAGAAAACAA
GAGTTTCTGTGAAGATTTGACTGAGGGAAAATTCAGTTTTCCAATTATTCATGCGATTCA
ATCGCAAAGTGAGGATAAACAGGTGTTACATATTTTACGCCAACGAACTCGAGACATTGA
AGTTAAAAAATATTGCGTTTCATTGTTAGAAAAAATGGGAAGTTTTCGATACACACGTGA
AACATTAGATGCACTTGATAAAGAAGCACGGAAAGAAGTTGCACAATTAGGACCAAATCC
AATTATGGAAGAACTACTGGATGAGCTCTTAAGTTGGAAAACAACTGCGGATTAAAAAGT
ATTTTTCATAAAGTACATTTTTAACACAATCTTTTTTTTTTCGTAACTACATAACTTTAT
ATTTTTATGGGTTTTCGAAACATTCTTCAAATATGTTACTTATACATTTAATCTTCATTT
AAAATTCGAATTTTTATATCTTAATTAATTTTAACTATCTATACATATATATGTTATGTG
TGTGTCATAATCTCAGGTTGAACTAATGATTATTTTATTTTAAATCAAATCACTCGCCTG
ATGCTCAAACATTTTTTAAAATATTTATTAAAATTTACCTAATATTTTTTAATTAAAATC
AAAAATGTCTATATAAAGTGCTAATTTCAACCATATTCACGATTTAGAATTTTTTAAAAA
AAATTTCTAGTGTTGAGTAATTCTATACATCTATTTAAAAAGAATCAAGTGATTGACTAA
AAGTAGAAACTTTAAAAGCAAAAATTTTTAAATGGACTTAAAATTATACCTATTAATAAT
GATTATATTGTATTTAGAGAGCACTATAAGCTTTTTGCACTTTTAATGTGTAATTAAAAA
TTATGAAGGAATTTTATACGAAAAAACCAAAATTTTTATTGGGAAACAAGTAAAAATTAA
AGCAAATTGTTGAT
>g7656.t15 Gene=g7656 Length=172
MEIYWRDNFLCPEESDYKLMTIRKTGGLFMLAIRLMLLFSDNERDFTKLTALLGLYFQIR
DDYCNLSLKEYSENKSFCEDLTEGKFSFPIIHAIQSQSEDKQVLHILRQRTRDIEVKKYC
VSLLEKMGSFRYTRETLDALDKEARKEVAQLGPNPIMEELLDELLSWKTTAD
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g7656.t15 | Gene3D | G3DSA:1.10.600.10 | Farnesyl Diphosphate Synthase | 1 | 171 | 2.3E-58 |
| 2 | g7656.t15 | PANTHER | PTHR12001:SF44 | GERANYLGERANYL PYROPHOSPHATE SYNTHASE | 1 | 167 | 5.7E-74 |
| 3 | g7656.t15 | PANTHER | PTHR12001 | GERANYLGERANYL PYROPHOSPHATE SYNTHASE | 1 | 167 | 5.7E-74 |
| 1 | g7656.t15 | Pfam | PF00348 | Polyprenyl synthetase | 2 | 123 | 1.6E-28 |
| 8 | g7656.t15 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 19 | - |
| 9 | g7656.t15 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 20 | 39 | - |
| 7 | g7656.t15 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 40 | 172 | - |
| 5 | g7656.t15 | ProSitePatterns | PS00444 | Polyprenyl synthases signature 2. | 53 | 65 | - |
| 4 | g7656.t15 | SUPERFAMILY | SSF48576 | Terpenoid synthases | 1 | 162 | 1.73E-38 |
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 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.
