Gene loci information

Transcript annotation

  • This transcript has been annotated as Phosphatidate cytidylyltransferase, photoreceptor-specific.

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_3 g3018 g3018.t5 TSS g3018.t5 22145982 22145982
chr_3 g3018 g3018.t5 isoform g3018.t5 22146023 22147970
chr_3 g3018 g3018.t5 exon g3018.t5.exon1 22146023 22146130
chr_3 g3018 g3018.t5 cds g3018.t5.CDS1 22146023 22146130
chr_3 g3018 g3018.t5 exon g3018.t5.exon2 22146382 22146465
chr_3 g3018 g3018.t5 cds g3018.t5.CDS2 22146382 22146465
chr_3 g3018 g3018.t5 exon g3018.t5.exon3 22146760 22147129
chr_3 g3018 g3018.t5 cds g3018.t5.CDS3 22146760 22147129
chr_3 g3018 g3018.t5 exon g3018.t5.exon4 22147187 22147485
chr_3 g3018 g3018.t5 cds g3018.t5.CDS4 22147187 22147485
chr_3 g3018 g3018.t5 exon g3018.t5.exon5 22147564 22147695
chr_3 g3018 g3018.t5 cds g3018.t5.CDS5 22147564 22147695
chr_3 g3018 g3018.t5 exon g3018.t5.exon6 22147749 22147970
chr_3 g3018 g3018.t5 cds g3018.t5.CDS6 22147749 22147970
chr_3 g3018 g3018.t5 TTS g3018.t5 22148819 22148819

Sequences

>g3018.t5 Gene=g3018 Length=1215
ATGAGTCGCGATAAAGTGTCAAATAAAAATCCAAATTTATTGAGAGCGAGTGGCGATATT
AGGAAGAGAGTCATTAGAAGTGATGCCTTAAACATCGATTCAGACCATATTGATTCAGAA
GCCGATGAGAATCTTTTAGAAGAGCAATATGTTAAAGAATTAGCAGAAAAGCACTCGGAA
GGAAGTAAAAAGGTCTTAGCAATTCAAGTCAAATGTTTTCAAGAAATAATGCAGATTGGA
TTTGTTACCTATAGAGTTGATGAAATTCCATGGTTTCGGCATTTAACTTGGTATTTATTG
ACAGTCTCCAACTATTATTATTATGGCGAATATTTCTTCGATTATTTTGGACCACCACTC
AATCGTATAGAATCACTACAATTCTTAATTAAATCACATCGCTTCATTTCCTATTGTCTC
TATCTCTTTGCAATAATAATGTTTGTATTGTCACTCGTTAAGAAATACAATACTAGACAA
TTTCATCTGTTTGCATGGGCGCATGTCGCTTTATTGATCACTGTCGTTCCAAGCTATCTT
ATCATAAGAAACACGTTCGATGGATTGATTTGGTTCATCATACCGGTGTCGTTAATTATT
ATCAATGATATTATGGCTTATATGTTTGGATTCTTCATTGGTAAAACGCCACTTATACAA
TTGAGCCCTAAGAAAACTTGGGAGGGATTTATCGGCGGAGGCATAACGACAGTATTGTTT
GGTTTAGTCCTCGCATACATTCTGTGTCAATATCTCTATTTCATATGTCCCATTGACTAC
TCAGAGGAAGCCGATAAAATTGTCATTCTCAATTGCCAACCGAGCTATTTGTATATACCG
CAAGAATATAAAATCAGCATTGGAAATTTCGAAACAGTTTTCAATATTCAGCCATTTGTG
CTTCATTCGTTATCATTGAGTATCTTTAGTTCAATCGTTGGTCCTTTTGGTGGATTCTTT
GCCTCAGGATTTAAACGAGCATTCAAAATTAAGGATTTTGCTAATGTTATCCCAGGACAT
GGTGGTATAATGGACAGATTTGACTGTCAAGTGTTAATGGCCTCTTTTGTATATGTTTAT
ATTAATAGTTTTATTCGAGATCCATCACCACAGAAGATTCTTAGTGCAATTTACACACTC
AGTCCCAAAGAACAACTTAATTTTTATTATCAGCTCGAAAATCATCTAAATGATTTAAAT
TTACTTAATCTTTAA

>g3018.t5 Gene=g3018 Length=404
MSRDKVSNKNPNLLRASGDIRKRVIRSDALNIDSDHIDSEADENLLEEQYVKELAEKHSE
GSKKVLAIQVKCFQEIMQIGFVTYRVDEIPWFRHLTWYLLTVSNYYYYGEYFFDYFGPPL
NRIESLQFLIKSHRFISYCLYLFAIIMFVLSLVKKYNTRQFHLFAWAHVALLITVVPSYL
IIRNTFDGLIWFIIPVSLIIINDIMAYMFGFFIGKTPLIQLSPKKTWEGFIGGGITTVLF
GLVLAYILCQYLYFICPIDYSEEADKIVILNCQPSYLYIPQEYKISIGNFETVFNIQPFV
LHSLSLSIFSSIVGPFGGFFASGFKRAFKIKDFANVIPGHGGIMDRFDCQVLMASFVYVY
INSFIRDPSPQKILSAIYTLSPKEQLNFYYQLENHLNDLNLLNL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
2 g3018.t5 PANTHER PTHR13773:SF16 PHOSPHATIDATE CYTIDYLYLTRANSFERASE 1 65 402 1.4E-134
3 g3018.t5 PANTHER PTHR13773 PHOSPHATIDATE CYTIDYLYLTRANSFERASE 65 402 1.4E-134
23 g3018.t5 PIRSF PIRSF018269 CDP-DAG_synth_e 50 403 1.4E-139
1 g3018.t5 Pfam PF01148 Cytidylyltransferase family 65 364 5.6E-72
13 g3018.t5 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 90 -
22 g3018.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 91 108 -
16 g3018.t5 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 109 134 -
19 g3018.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 135 153 -
11 g3018.t5 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 154 164 -
20 g3018.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 165 182 -
14 g3018.t5 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 183 187 -
21 g3018.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 188 209 -
12 g3018.t5 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 210 229 -
18 g3018.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 230 253 -
15 g3018.t5 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 254 298 -
17 g3018.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 299 321 -
10 g3018.t5 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 322 404 -
9 g3018.t5 ProSitePatterns PS01315 Phosphatidate cytidylyltransferase signature. 322 348 -
6 g3018.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 135 153 -
5 g3018.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 163 182 -
8 g3018.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 189 211 -
7 g3018.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 226 248 -
4 g3018.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 299 321 -

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

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. There were no conditions that were differentially expressed