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.t7 TSS g3018.t7 22145982 22145982
chr_3 g3018 g3018.t7 isoform g3018.t7 22146023 22148801
chr_3 g3018 g3018.t7 exon g3018.t7.exon1 22146023 22146130
chr_3 g3018 g3018.t7 exon g3018.t7.exon2 22146382 22146509
chr_3 g3018 g3018.t7 exon g3018.t7.exon3 22146597 22147129
chr_3 g3018 g3018.t7 cds g3018.t7.CDS1 22146796 22147129
chr_3 g3018 g3018.t7 exon g3018.t7.exon4 22147187 22147485
chr_3 g3018 g3018.t7 cds g3018.t7.CDS2 22147187 22147485
chr_3 g3018 g3018.t7 exon g3018.t7.exon5 22147564 22147695
chr_3 g3018 g3018.t7 cds g3018.t7.CDS3 22147564 22147695
chr_3 g3018 g3018.t7 exon g3018.t7.exon6 22147749 22148801
chr_3 g3018 g3018.t7 cds g3018.t7.CDS4 22147749 22147970
chr_3 g3018 g3018.t7 TTS g3018.t7 22148819 22148819

Sequences

>g3018.t7 Gene=g3018 Length=2253
ATGAGTCGCGATAAAGTGTCAAATAAAAATCCAAATTTATTGAGAGCGAGTGGCGATATT
AGGAAGAGAGTCATTAGAAGTGATGCCTTAAACATCGATTCAGACCATATTGATTCAGAA
GCCGATGAGAATCTTTTAGAAGAGCAATATGTTAAAGAATTAGCAGAAAAGCACTCGGAA
GGAAGTAAAAAGGTACCGAAATTCCTATCATCAGCTTTAAAAGGTCTACCCGAAAGATGG
AAAAATTGGGTTGTGCGTGGTATTTCAATGACAGTAATGATCTCGACATTTTGCTTATTA
ATAGCAGGCGGTCCGCTGGCCTTAATGATTTTAGTATGACGATCTTAGACTAAGTCAATG
TGATTTCTTATAAAATTCTTTCTGTTTGGAAACCCTCAGGTCTTAGCAATTCAAGTCAAA
TGTTTTCAAGAAATAATGCAGATTGGATTTGTTACCTATAGAGTTGATGAAATTCCATGG
TTTCGGCATTTAACTTGGTATTTATTGACAGTCTCCAACTATTATTATTATGGCGAATAT
TTCTTCGATTATTTTGGACCACCACTCAATCGTATAGAATCACTACAATTCTTAATTAAA
TCACATCGCTTCATTTCCTATTGTCTCTATCTCTTTGCAATAATAATGTTTGTATTGTCA
CTCGTTAAGAAATACAATACTAGACAATTTCATCTGTTTGCATGGGCGCATGTCGCTTTA
TTGATCACTGTCGTTCCAAGCTATCTTATCATAAGAAACACGTTCGATGGATTGATTTGG
TTCATCATACCGGTGTCGTTAATTATTATCAATGATATTATGGCTTATATGTTTGGATTC
TTCATTGGTAAAACGCCACTTATACAATTGAGCCCTAAGAAAACTTGGGAGGGATTTATC
GGCGGAGGCATAACGACAGTATTGTTTGGTTTAGTCCTCGCATACATTCTGTGTCAATAT
CTCTATTTCATATGTCCCATTGACTACTCAGAGGAAGCCGATAAAATTGTCATTCTCAAT
TGCCAACCGAGCTATTTGTATATACCGCAAGAATATAAAATCAGCATTGGAAATTTCGAA
ACAGTTTTCAATATTCAGCCATTTGTGCTTCATTCGTTATCATTGAGTATCTTTAGTTCA
ATCGTTGGTCCTTTTGGTGGATTCTTTGCCTCAGGATTTAAACGAGCATTCAAAATTAAG
GATTTTGCTAATGTTATCCCAGGACATGGTGGTATAATGGACAGATTTGACTGTCAAGTG
TTAATGGCCTCTTTTGTATATGTTTATATTAATAGTTTTATTCGAGATCCATCACCACAG
AAGATTCTTAGTGCAATTTACACACTCAGTCCCAAAGAACAACTTAATTTTTATTATCAG
CTCGAAAATCATCTAAATGATTTAAATTTACTTAATCTTTAAGCACAGAGAAAGACAACA
ATAAATCTATTAAAGTTGCACATGTGATCATTGATGAATTTTATCAATTTATTCCATAAC
TCAATATATAGAATAAAATAAAAGGAGCAGCAACTGATGCAATGCGATGGAAGAAAGGAA
GGAAGGAGAGACTTTGTTCATAAATATTTATTGGATAATCATACAGTTTCTGTATATATA
CATAGAGTATATTTTCAAAAAAGAGTTACAGTCAATTATTTTAATGCAACAATTTCCTAA
CTGCACCTGGTGATTTTTCTCTCTTTTTCACAAGAGAGTATATTGGTAATCGCATGCGAA
ACGATAGCAAAGAAGGACGACTAAATAAAATTGAAAAATGAGAGAAAATTGCACAAATAA
AGTCGAGGAAAAATGTCGCTCGAAGGACTGTTTGTGTAGCAGTTCAAGCAAAATGATTTT
TATGTTTTGGGAGCAAGCAAGCACACGAGAAAAAGAAAAAGGAAGAAAGAAATTGTCGTG
ACATTAAAAGACGGTGATAAAAAGCATATGAGAGCGCAGGAAATGTTCATTCTTTTTTCT
TCGACATAATCTCAAGACTGCAATGCTCTTTATGGTTTTATTAAATAAAGGAAAAAACTA
CTTTCACCATTGCTGCTGCTTCTGTTAGCTCTATGAAATGTATATATTGAAAAGCGGCAC
CATCGTCAATTGCTCTATGTGTGTATGCTATCATACATGTGAAATTTTTCTTTGATGTGA
CATAATGTGGAAATAAGTTGATAGAAAAAACAAGTTTTTATAATTTCTTTGTGCTATATA
AAGGAGCTCTTTTTTATAAGCAAAAGAGGAAGG

>g3018.t7 Gene=g3018 Length=328
MQIGFVTYRVDEIPWFRHLTWYLLTVSNYYYYGEYFFDYFGPPLNRIESLQFLIKSHRFI
SYCLYLFAIIMFVLSLVKKYNTRQFHLFAWAHVALLITVVPSYLIIRNTFDGLIWFIIPV
SLIIINDIMAYMFGFFIGKTPLIQLSPKKTWEGFIGGGITTVLFGLVLAYILCQYLYFIC
PIDYSEEADKIVILNCQPSYLYIPQEYKISIGNFETVFNIQPFVLHSLSLSIFSSIVGPF
GGFFASGFKRAFKIKDFANVIPGHGGIMDRFDCQVLMASFVYVYINSFIRDPSPQKILSA
IYTLSPKEQLNFYYQLENHLNDLNLLNL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
2 g3018.t7 PANTHER PTHR13773:SF16 PHOSPHATIDATE CYTIDYLYLTRANSFERASE 1 2 326 4.0E-127
3 g3018.t7 PANTHER PTHR13773 PHOSPHATIDATE CYTIDYLYLTRANSFERASE 2 326 4.0E-127
1 g3018.t7 Pfam PF01148 Cytidylyltransferase family 7 288 4.7E-68
15 g3018.t7 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 58 -
19 g3018.t7 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 59 77 -
11 g3018.t7 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 78 88 -
18 g3018.t7 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 89 106 -
14 g3018.t7 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 107 111 -
20 g3018.t7 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 112 133 -
10 g3018.t7 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 134 153 -
17 g3018.t7 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 154 177 -
13 g3018.t7 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 178 222 -
16 g3018.t7 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 223 245 -
12 g3018.t7 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 246 328 -
9 g3018.t7 ProSitePatterns PS01315 Phosphatidate cytidylyltransferase signature. 246 272 -
8 g3018.t7 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 59 77 -
6 g3018.t7 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 87 106 -
7 g3018.t7 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 113 135 -
5 g3018.t7 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 150 172 -
4 g3018.t7 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 223 245 -

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.

Raw TPM values