General information for g3018.t16
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Phosphatidate cytidylyltransferase, photoreceptor-specific.
Parent gene
- The parent gene g3018 is located on chr_3: 22146942..22148833 (+ 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_3 | g3018 | g3018.t16 | TSS | g3018.t16 | 22145982 | 22145982 |
| chr_3 | g3018 | g3018.t16 | isoform | g3018.t16 | 22146942 | 22147970 |
| chr_3 | g3018 | g3018.t16 | exon | g3018.t16.exon1 | 22146942 | 22147129 |
| chr_3 | g3018 | g3018.t16 | cds | g3018.t16.CDS1 | 22147006 | 22147129 |
| chr_3 | g3018 | g3018.t16 | exon | g3018.t16.exon2 | 22147187 | 22147485 |
| chr_3 | g3018 | g3018.t16 | cds | g3018.t16.CDS2 | 22147187 | 22147485 |
| chr_3 | g3018 | g3018.t16 | exon | g3018.t16.exon3 | 22147564 | 22147695 |
| chr_3 | g3018 | g3018.t16 | cds | g3018.t16.CDS3 | 22147564 | 22147695 |
| chr_3 | g3018 | g3018.t16 | exon | g3018.t16.exon4 | 22147749 | 22147970 |
| chr_3 | g3018 | g3018.t16 | cds | g3018.t16.CDS4 | 22147749 | 22147970 |
| chr_3 | g3018 | g3018.t16 | TTS | g3018.t16 | 22148819 | 22148819 |
Sequences
>g3018.t16 Gene=g3018 Length=841
ACTACAATTCTTAATTAAATCACATCGCTTCATTTCCTATTGTCTCTATCTCTTTGCAAT
AATAATGTTTGTATTGTCACTCGTTAAGAAATACAATACTAGACAATTTCATCTGTTTGC
ATGGGCGCATGTCGCTTTATTGATCACTGTCGTTCCAAGCTATCTTATCATAAGAAACAC
GTTCGATGGATTGATTTGGTTCATCATACCGGTGTCGTTAATTATTATCAATGATATTAT
GGCTTATATGTTTGGATTCTTCATTGGTAAAACGCCACTTATACAATTGAGCCCTAAGAA
AACTTGGGAGGGATTTATCGGCGGAGGCATAACGACAGTATTGTTTGGTTTAGTCCTCGC
ATACATTCTGTGTCAATATCTCTATTTCATATGTCCCATTGACTACTCAGAGGAAGCCGA
TAAAATTGTCATTCTCAATTGCCAACCGAGCTATTTGTATATACCGCAAGAATATAAAAT
CAGCATTGGAAATTTCGAAACAGTTTTCAATATTCAGCCATTTGTGCTTCATTCGTTATC
ATTGAGTATCTTTAGTTCAATCGTTGGTCCTTTTGGTGGATTCTTTGCCTCAGGATTTAA
ACGAGCATTCAAAATTAAGGATTTTGCTAATGTTATCCCAGGACATGGTGGTATAATGGA
CAGATTTGACTGTCAAGTGTTAATGGCCTCTTTTGTATATGTTTATATTAATAGTTTTAT
TCGAGATCCATCACCACAGAAGATTCTTAGTGCAATTTACACACTCAGTCCCAAAGAACA
ACTTAATTTTTATTATCAGCTCGAAAATCATCTAAATGATTTAAATTTACTTAATCTTTA
A
>g3018.t16 Gene=g3018 Length=258
MFVLSLVKKYNTRQFHLFAWAHVALLITVVPSYLIIRNTFDGLIWFIIPVSLIIINDIMA
YMFGFFIGKTPLIQLSPKKTWEGFIGGGITTVLFGLVLAYILCQYLYFICPIDYSEEADK
IVILNCQPSYLYIPQEYKISIGNFETVFNIQPFVLHSLSLSIFSSIVGPFGGFFASGFKR
AFKIKDFANVIPGHGGIMDRFDCQVLMASFVYVYINSFIRDPSPQKILSAIYTLSPKEQL
NFYYQLENHLNDLNLLNL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 2 | g3018.t16 | PANTHER | PTHR13773 | PHOSPHATIDATE CYTIDYLYLTRANSFERASE | 1 | 251 | 1.1E-106 |
| 3 | g3018.t16 | PANTHER | PTHR13773:SF8 | PHOSPHATIDATE CYTIDYLYLTRANSFERASE, PHOTORECEPTOR-SPECIFIC | 1 | 251 | 1.1E-106 |
| 1 | g3018.t16 | Pfam | PF01148 | Cytidylyltransferase family | 7 | 218 | 9.6E-63 |
| 10 | g3018.t16 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 16 | - |
| 16 | g3018.t16 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 17 | 36 | - |
| 12 | g3018.t16 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 37 | 41 | - |
| 14 | g3018.t16 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 42 | 63 | - |
| 11 | g3018.t16 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 64 | 83 | - |
| 15 | g3018.t16 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 84 | 107 | - |
| 13 | g3018.t16 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 108 | 152 | - |
| 17 | g3018.t16 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 153 | 175 | - |
| 9 | g3018.t16 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 176 | 258 | - |
| 8 | g3018.t16 | ProSitePatterns | PS01315 | Phosphatidate cytidylyltransferase signature. | 176 | 202 | - |
| 7 | g3018.t16 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 15 | 36 | - |
| 5 | g3018.t16 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 43 | 65 | - |
| 4 | g3018.t16 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 80 | 102 | - |
| 6 | g3018.t16 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 153 | 175 | - |
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:0016020 | membrane | CC |
| GO:0004605 | phosphatidate cytidylyltransferase activity | MF |
| GO:0016772 | transferase activity, transferring phosphorus-containing groups | MF |
KEGG
Orthology
- This transcript has been annotated with K00981 (phosphatidate cytidylyltransferase)
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.
