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.t4 TSS g3018.t4 22145982 22145982
chr_3 g3018 g3018.t4 isoform g3018.t4 22146023 22147970
chr_3 g3018 g3018.t4 exon g3018.t4.exon1 22146023 22146130
chr_3 g3018 g3018.t4 exon g3018.t4.exon2 22146382 22146465
chr_3 g3018 g3018.t4 exon g3018.t4.exon3 22146597 22146693
chr_3 g3018 g3018.t4 exon g3018.t4.exon4 22146760 22147129
chr_3 g3018 g3018.t4 cds g3018.t4.CDS1 22147006 22147129
chr_3 g3018 g3018.t4 exon g3018.t4.exon5 22147187 22147485
chr_3 g3018 g3018.t4 cds g3018.t4.CDS2 22147187 22147485
chr_3 g3018 g3018.t4 exon g3018.t4.exon6 22147564 22147695
chr_3 g3018 g3018.t4 cds g3018.t4.CDS3 22147564 22147695
chr_3 g3018 g3018.t4 exon g3018.t4.exon7 22147749 22147970
chr_3 g3018 g3018.t4 cds g3018.t4.CDS4 22147749 22147970
chr_3 g3018 g3018.t4 TTS g3018.t4 22148819 22148819

Sequences

>g3018.t4 Gene=g3018 Length=1312
ATGAGTCGCGATAAAGTGTCAAATAAAAATCCAAATTTATTGAGAGCGAGTGGCGATATT
AGGAAGAGAGTCATTAGAAGTGATGCCTTAAACATCGATTCAGACCATATTGATTCAGAA
GCCGATGAGAATCTTTTAGAAGAGCAATATGTTAAAGAATTAGCAGAAAAGCACTCGGAA
GGAAGTAAAAAGATGGAAAAATTGGGTTGTGCGTGGTATTTCAATGACAGTAATGATCTC
GACATTTTGCTTATTAATAGCAGGCGGTCCGCTGGCCTTAATGATTTTAGTCTTAGCAAT
TCAAGTCAAATGTTTTCAAGAAATAATGCAGATTGGATTTGTTACCTATAGAGTTGATGA
AATTCCATGGTTTCGGCATTTAACTTGGTATTTATTGACAGTCTCCAACTATTATTATTA
TGGCGAATATTTCTTCGATTATTTTGGACCACCACTCAATCGTATAGAATCACTACAATT
CTTAATTAAATCACATCGCTTCATTTCCTATTGTCTCTATCTCTTTGCAATAATAATGTT
TGTATTGTCACTCGTTAAGAAATACAATACTAGACAATTTCATCTGTTTGCATGGGCGCA
TGTCGCTTTATTGATCACTGTCGTTCCAAGCTATCTTATCATAAGAAACACGTTCGATGG
ATTGATTTGGTTCATCATACCGGTGTCGTTAATTATTATCAATGATATTATGGCTTATAT
GTTTGGATTCTTCATTGGTAAAACGCCACTTATACAATTGAGCCCTAAGAAAACTTGGGA
GGGATTTATCGGCGGAGGCATAACGACAGTATTGTTTGGTTTAGTCCTCGCATACATTCT
GTGTCAATATCTCTATTTCATATGTCCCATTGACTACTCAGAGGAAGCCGATAAAATTGT
CATTCTCAATTGCCAACCGAGCTATTTGTATATACCGCAAGAATATAAAATCAGCATTGG
AAATTTCGAAACAGTTTTCAATATTCAGCCATTTGTGCTTCATTCGTTATCATTGAGTAT
CTTTAGTTCAATCGTTGGTCCTTTTGGTGGATTCTTTGCCTCAGGATTTAAACGAGCATT
CAAAATTAAGGATTTTGCTAATGTTATCCCAGGACATGGTGGTATAATGGACAGATTTGA
CTGTCAAGTGTTAATGGCCTCTTTTGTATATGTTTATATTAATAGTTTTATTCGAGATCC
ATCACCACAGAAGATTCTTAGTGCAATTTACACACTCAGTCCCAAAGAACAACTTAATTT
TTATTATCAGCTCGAAAATCATCTAAATGATTTAAATTTACTTAATCTTTAA

>g3018.t4 Gene=g3018 Length=258
MFVLSLVKKYNTRQFHLFAWAHVALLITVVPSYLIIRNTFDGLIWFIIPVSLIIINDIMA
YMFGFFIGKTPLIQLSPKKTWEGFIGGGITTVLFGLVLAYILCQYLYFICPIDYSEEADK
IVILNCQPSYLYIPQEYKISIGNFETVFNIQPFVLHSLSLSIFSSIVGPFGGFFASGFKR
AFKIKDFANVIPGHGGIMDRFDCQVLMASFVYVYINSFIRDPSPQKILSAIYTLSPKEQL
NFYYQLENHLNDLNLLNL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
2 g3018.t4 PANTHER PTHR13773 PHOSPHATIDATE CYTIDYLYLTRANSFERASE 1 251 1.1E-106
3 g3018.t4 PANTHER PTHR13773:SF8 PHOSPHATIDATE CYTIDYLYLTRANSFERASE, PHOTORECEPTOR-SPECIFIC 1 251 1.1E-106
1 g3018.t4 Pfam PF01148 Cytidylyltransferase family 7 218 9.6E-63
10 g3018.t4 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 16 -
16 g3018.t4 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 17 36 -
12 g3018.t4 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 37 41 -
14 g3018.t4 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 42 63 -
11 g3018.t4 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 64 83 -
15 g3018.t4 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 84 107 -
13 g3018.t4 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 108 152 -
17 g3018.t4 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 153 175 -
9 g3018.t4 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 176 258 -
8 g3018.t4 ProSitePatterns PS01315 Phosphatidate cytidylyltransferase signature. 176 202 -
7 g3018.t4 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 15 36 -
5 g3018.t4 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 43 65 -
4 g3018.t4 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 80 102 -
6 g3018.t4 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

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