General information for g3018.t1
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.t1 | TSS | g3018.t1 | 22145982 | 22145982 |
| chr_3 | g3018 | g3018.t1 | isoform | g3018.t1 | 22146023 | 22147970 |
| chr_3 | g3018 | g3018.t1 | exon | g3018.t1.exon1 | 22146023 | 22146130 |
| chr_3 | g3018 | g3018.t1 | cds | g3018.t1.CDS1 | 22146023 | 22146130 |
| chr_3 | g3018 | g3018.t1 | exon | g3018.t1.exon2 | 22146382 | 22146509 |
| chr_3 | g3018 | g3018.t1 | cds | g3018.t1.CDS2 | 22146382 | 22146509 |
| chr_3 | g3018 | g3018.t1 | exon | g3018.t1.exon3 | 22146597 | 22146693 |
| chr_3 | g3018 | g3018.t1 | cds | g3018.t1.CDS3 | 22146597 | 22146693 |
| chr_3 | g3018 | g3018.t1 | exon | g3018.t1.exon4 | 22146760 | 22147129 |
| chr_3 | g3018 | g3018.t1 | cds | g3018.t1.CDS4 | 22146760 | 22147129 |
| chr_3 | g3018 | g3018.t1 | exon | g3018.t1.exon5 | 22147187 | 22147485 |
| chr_3 | g3018 | g3018.t1 | cds | g3018.t1.CDS5 | 22147187 | 22147485 |
| chr_3 | g3018 | g3018.t1 | exon | g3018.t1.exon6 | 22147564 | 22147695 |
| chr_3 | g3018 | g3018.t1 | cds | g3018.t1.CDS6 | 22147564 | 22147695 |
| chr_3 | g3018 | g3018.t1 | exon | g3018.t1.exon7 | 22147749 | 22147970 |
| chr_3 | g3018 | g3018.t1 | cds | g3018.t1.CDS7 | 22147749 | 22147970 |
| chr_3 | g3018 | g3018.t1 | TTS | g3018.t1 | 22148819 | 22148819 |
Sequences
>g3018.t1 Gene=g3018 Length=1356
ATGAGTCGCGATAAAGTGTCAAATAAAAATCCAAATTTATTGAGAGCGAGTGGCGATATT
AGGAAGAGAGTCATTAGAAGTGATGCCTTAAACATCGATTCAGACCATATTGATTCAGAA
GCCGATGAGAATCTTTTAGAAGAGCAATATGTTAAAGAATTAGCAGAAAAGCACTCGGAA
GGAAGTAAAAAGGTACCGAAATTCCTATCATCAGCTTTAAAAGGTCTACCCGAAAGATGG
AAAAATTGGGTTGTGCGTGGTATTTCAATGACAGTAATGATCTCGACATTTTGCTTATTA
ATAGCAGGCGGTCCGCTGGCCTTAATGATTTTAGTCTTAGCAATTCAAGTCAAATGTTTT
CAAGAAATAATGCAGATTGGATTTGTTACCTATAGAGTTGATGAAATTCCATGGTTTCGG
CATTTAACTTGGTATTTATTGACAGTCTCCAACTATTATTATTATGGCGAATATTTCTTC
GATTATTTTGGACCACCACTCAATCGTATAGAATCACTACAATTCTTAATTAAATCACAT
CGCTTCATTTCCTATTGTCTCTATCTCTTTGCAATAATAATGTTTGTATTGTCACTCGTT
AAGAAATACAATACTAGACAATTTCATCTGTTTGCATGGGCGCATGTCGCTTTATTGATC
ACTGTCGTTCCAAGCTATCTTATCATAAGAAACACGTTCGATGGATTGATTTGGTTCATC
ATACCGGTGTCGTTAATTATTATCAATGATATTATGGCTTATATGTTTGGATTCTTCATT
GGTAAAACGCCACTTATACAATTGAGCCCTAAGAAAACTTGGGAGGGATTTATCGGCGGA
GGCATAACGACAGTATTGTTTGGTTTAGTCCTCGCATACATTCTGTGTCAATATCTCTAT
TTCATATGTCCCATTGACTACTCAGAGGAAGCCGATAAAATTGTCATTCTCAATTGCCAA
CCGAGCTATTTGTATATACCGCAAGAATATAAAATCAGCATTGGAAATTTCGAAACAGTT
TTCAATATTCAGCCATTTGTGCTTCATTCGTTATCATTGAGTATCTTTAGTTCAATCGTT
GGTCCTTTTGGTGGATTCTTTGCCTCAGGATTTAAACGAGCATTCAAAATTAAGGATTTT
GCTAATGTTATCCCAGGACATGGTGGTATAATGGACAGATTTGACTGTCAAGTGTTAATG
GCCTCTTTTGTATATGTTTATATTAATAGTTTTATTCGAGATCCATCACCACAGAAGATT
CTTAGTGCAATTTACACACTCAGTCCCAAAGAACAACTTAATTTTTATTATCAGCTCGAA
AATCATCTAAATGATTTAAATTTACTTAATCTTTAA
>g3018.t1 Gene=g3018 Length=451
MSRDKVSNKNPNLLRASGDIRKRVIRSDALNIDSDHIDSEADENLLEEQYVKELAEKHSE
GSKKVPKFLSSALKGLPERWKNWVVRGISMTVMISTFCLLIAGGPLALMILVLAIQVKCF
QEIMQIGFVTYRVDEIPWFRHLTWYLLTVSNYYYYGEYFFDYFGPPLNRIESLQFLIKSH
RFISYCLYLFAIIMFVLSLVKKYNTRQFHLFAWAHVALLITVVPSYLIIRNTFDGLIWFI
IPVSLIIINDIMAYMFGFFIGKTPLIQLSPKKTWEGFIGGGITTVLFGLVLAYILCQYLY
FICPIDYSEEADKIVILNCQPSYLYIPQEYKISIGNFETVFNIQPFVLHSLSLSIFSSIV
GPFGGFFASGFKRAFKIKDFANVIPGHGGIMDRFDCQVLMASFVYVYINSFIRDPSPQKI
LSAIYTLSPKEQLNFYYQLENHLNDLNLLNL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 2 | g3018.t1 | PANTHER | PTHR13773:SF16 | PHOSPHATIDATE CYTIDYLYLTRANSFERASE 1 | 47 | 449 | 1.8E-155 |
| 3 | g3018.t1 | PANTHER | PTHR13773 | PHOSPHATIDATE CYTIDYLYLTRANSFERASE | 47 | 449 | 1.8E-155 |
| 26 | g3018.t1 | PIRSF | PIRSF018269 | CDP-DAG_synth_e | 26 | 450 | 1.0E-157 |
| 1 | g3018.t1 | Pfam | PF01148 | Cytidylyltransferase family | 85 | 411 | 1.4E-77 |
| 15 | g3018.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 87 | - |
| 21 | g3018.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 88 | 117 | - |
| 14 | g3018.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 118 | 137 | - |
| 23 | g3018.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 138 | 155 | - |
| 18 | g3018.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 156 | 181 | - |
| 22 | g3018.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 182 | 200 | - |
| 12 | g3018.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 201 | 211 | - |
| 24 | g3018.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 212 | 229 | - |
| 17 | g3018.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 230 | 234 | - |
| 20 | g3018.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 235 | 256 | - |
| 11 | g3018.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 257 | 276 | - |
| 19 | g3018.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 277 | 300 | - |
| 16 | g3018.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 301 | 345 | - |
| 25 | g3018.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 346 | 368 | - |
| 13 | g3018.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 369 | 451 | - |
| 10 | g3018.t1 | ProSitePatterns | PS01315 | Phosphatidate cytidylyltransferase signature. | 369 | 395 | - |
| 5 | g3018.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 93 | 115 | - |
| 7 | g3018.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 182 | 200 | - |
| 8 | g3018.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 210 | 229 | - |
| 6 | g3018.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 236 | 258 | - |
| 4 | g3018.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 273 | 295 | - |
| 9 | g3018.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 346 | 368 | - |
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.
