General information for g3018.t10
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.t10 | TSS | g3018.t10 | 22145982 | 22145982 |
| chr_3 | g3018 | g3018.t10 | isoform | g3018.t10 | 22146605 | 22147970 |
| chr_3 | g3018 | g3018.t10 | exon | g3018.t10.exon1 | 22146605 | 22146693 |
| chr_3 | g3018 | g3018.t10 | cds | g3018.t10.CDS1 | 22146628 | 22146693 |
| chr_3 | g3018 | g3018.t10 | exon | g3018.t10.exon2 | 22146760 | 22147129 |
| chr_3 | g3018 | g3018.t10 | cds | g3018.t10.CDS2 | 22146760 | 22147129 |
| chr_3 | g3018 | g3018.t10 | exon | g3018.t10.exon3 | 22147187 | 22147485 |
| chr_3 | g3018 | g3018.t10 | cds | g3018.t10.CDS3 | 22147187 | 22147485 |
| chr_3 | g3018 | g3018.t10 | exon | g3018.t10.exon4 | 22147564 | 22147695 |
| chr_3 | g3018 | g3018.t10 | cds | g3018.t10.CDS4 | 22147564 | 22147695 |
| chr_3 | g3018 | g3018.t10 | exon | g3018.t10.exon5 | 22147749 | 22147970 |
| chr_3 | g3018 | g3018.t10 | cds | g3018.t10.CDS5 | 22147749 | 22147970 |
| chr_3 | g3018 | g3018.t10 | TTS | g3018.t10 | 22148819 | 22148819 |
Sequences
>g3018.t10 Gene=g3018 Length=1112
ATTGGGTTGTGCGTGGTATTTCAATGACAGTAATGATCTCGACATTTTGCTTATTAATAG
CAGGCGGTCCGCTGGCCTTAATGATTTTAGTCTTAGCAATTCAAGTCAAATGTTTTCAAG
AAATAATGCAGATTGGATTTGTTACCTATAGAGTTGATGAAATTCCATGGTTTCGGCATT
TAACTTGGTATTTATTGACAGTCTCCAACTATTATTATTATGGCGAATATTTCTTCGATT
ATTTTGGACCACCACTCAATCGTATAGAATCACTACAATTCTTAATTAAATCACATCGCT
TCATTTCCTATTGTCTCTATCTCTTTGCAATAATAATGTTTGTATTGTCACTCGTTAAGA
AATACAATACTAGACAATTTCATCTGTTTGCATGGGCGCATGTCGCTTTATTGATCACTG
TCGTTCCAAGCTATCTTATCATAAGAAACACGTTCGATGGATTGATTTGGTTCATCATAC
CGGTGTCGTTAATTATTATCAATGATATTATGGCTTATATGTTTGGATTCTTCATTGGTA
AAACGCCACTTATACAATTGAGCCCTAAGAAAACTTGGGAGGGATTTATCGGCGGAGGCA
TAACGACAGTATTGTTTGGTTTAGTCCTCGCATACATTCTGTGTCAATATCTCTATTTCA
TATGTCCCATTGACTACTCAGAGGAAGCCGATAAAATTGTCATTCTCAATTGCCAACCGA
GCTATTTGTATATACCGCAAGAATATAAAATCAGCATTGGAAATTTCGAAACAGTTTTCA
ATATTCAGCCATTTGTGCTTCATTCGTTATCATTGAGTATCTTTAGTTCAATCGTTGGTC
CTTTTGGTGGATTCTTTGCCTCAGGATTTAAACGAGCATTCAAAATTAAGGATTTTGCTA
ATGTTATCCCAGGACATGGTGGTATAATGGACAGATTTGACTGTCAAGTGTTAATGGCCT
CTTTTGTATATGTTTATATTAATAGTTTTATTCGAGATCCATCACCACAGAAGATTCTTA
GTGCAATTTACACACTCAGTCCCAAAGAACAACTTAATTTTTATTATCAGCTCGAAAATC
ATCTAAATGATTTAAATTTACTTAATCTTTAA
>g3018.t10 Gene=g3018 Length=362
MTVMISTFCLLIAGGPLALMILVLAIQVKCFQEIMQIGFVTYRVDEIPWFRHLTWYLLTV
SNYYYYGEYFFDYFGPPLNRIESLQFLIKSHRFISYCLYLFAIIMFVLSLVKKYNTRQFH
LFAWAHVALLITVVPSYLIIRNTFDGLIWFIIPVSLIIINDIMAYMFGFFIGKTPLIQLS
PKKTWEGFIGGGITTVLFGLVLAYILCQYLYFICPIDYSEEADKIVILNCQPSYLYIPQE
YKISIGNFETVFNIQPFVLHSLSLSIFSSIVGPFGGFFASGFKRAFKIKDFANVIPGHGG
IMDRFDCQVLMASFVYVYINSFIRDPSPQKILSAIYTLSPKEQLNFYYQLENHLNDLNLL
NL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 2 | g3018.t10 | PANTHER | PTHR13773:SF16 | PHOSPHATIDATE CYTIDYLYLTRANSFERASE 1 | 3 | 360 | 8.2E-141 |
| 3 | g3018.t10 | PANTHER | PTHR13773 | PHOSPHATIDATE CYTIDYLYLTRANSFERASE | 3 | 360 | 8.2E-141 |
| 1 | g3018.t10 | Pfam | PF01148 | Cytidylyltransferase family | 2 | 322 | 2.3E-76 |
| 17 | g3018.t10 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 30 | - |
| 18 | g3018.t10 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 7 | - |
| 19 | g3018.t10 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 8 | 26 | - |
| 25 | g3018.t10 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 27 | 30 | - |
| 15 | g3018.t10 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 31 | 92 | - |
| 22 | g3018.t10 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 93 | 111 | - |
| 12 | g3018.t10 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 112 | 122 | - |
| 23 | g3018.t10 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 123 | 140 | - |
| 16 | g3018.t10 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 141 | 145 | - |
| 21 | g3018.t10 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 146 | 167 | - |
| 13 | g3018.t10 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 168 | 187 | - |
| 20 | g3018.t10 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 188 | 211 | - |
| 14 | g3018.t10 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 212 | 256 | - |
| 24 | g3018.t10 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 257 | 279 | - |
| 11 | g3018.t10 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 280 | 362 | - |
| 10 | g3018.t10 | ProSitePatterns | PS01315 | Phosphatidate cytidylyltransferase signature. | 280 | 306 | - |
| 5 | g3018.t10 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 4 | 26 | - |
| 6 | g3018.t10 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 93 | 111 | - |
| 7 | g3018.t10 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 121 | 140 | - |
| 8 | g3018.t10 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 147 | 169 | - |
| 4 | g3018.t10 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 184 | 206 | - |
| 9 | g3018.t10 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 257 | 279 | - |
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.
