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.t6 TSS g3018.t6 22145982 22145982
chr_3 g3018 g3018.t6 isoform g3018.t6 22146023 22147970
chr_3 g3018 g3018.t6 exon g3018.t6.exon1 22146023 22146130
chr_3 g3018 g3018.t6 cds g3018.t6.CDS1 22146023 22146130
chr_3 g3018 g3018.t6 exon g3018.t6.exon2 22147030 22147129
chr_3 g3018 g3018.t6 cds g3018.t6.CDS2 22147030 22147129
chr_3 g3018 g3018.t6 exon g3018.t6.exon3 22147187 22147485
chr_3 g3018 g3018.t6 cds g3018.t6.CDS3 22147187 22147485
chr_3 g3018 g3018.t6 exon g3018.t6.exon4 22147564 22147695
chr_3 g3018 g3018.t6 cds g3018.t6.CDS4 22147564 22147695
chr_3 g3018 g3018.t6 exon g3018.t6.exon5 22147749 22147970
chr_3 g3018 g3018.t6 cds g3018.t6.CDS5 22147749 22147970
chr_3 g3018 g3018.t6 TTS g3018.t6 22148819 22148819

Sequences

>g3018.t6 Gene=g3018 Length=861
ATGAGTCGCGATAAAGTGTCAAATAAAAATCCAAATTTATTGAGAGCGAGTGGCGATATT
AGGAAGAGAGTCATTAGAAGTGATGCCTTAAACATCGATTCAGACCATAAATACAATACT
AGACAATTTCATCTGTTTGCATGGGCGCATGTCGCTTTATTGATCACTGTCGTTCCAAGC
TATCTTATCATAAGAAACACGTTCGATGGATTGATTTGGTTCATCATACCGGTGTCGTTA
ATTATTATCAATGATATTATGGCTTATATGTTTGGATTCTTCATTGGTAAAACGCCACTT
ATACAATTGAGCCCTAAGAAAACTTGGGAGGGATTTATCGGCGGAGGCATAACGACAGTA
TTGTTTGGTTTAGTCCTCGCATACATTCTGTGTCAATATCTCTATTTCATATGTCCCATT
GACTACTCAGAGGAAGCCGATAAAATTGTCATTCTCAATTGCCAACCGAGCTATTTGTAT
ATACCGCAAGAATATAAAATCAGCATTGGAAATTTCGAAACAGTTTTCAATATTCAGCCA
TTTGTGCTTCATTCGTTATCATTGAGTATCTTTAGTTCAATCGTTGGTCCTTTTGGTGGA
TTCTTTGCCTCAGGATTTAAACGAGCATTCAAAATTAAGGATTTTGCTAATGTTATCCCA
GGACATGGTGGTATAATGGACAGATTTGACTGTCAAGTGTTAATGGCCTCTTTTGTATAT
GTTTATATTAATAGTTTTATTCGAGATCCATCACCACAGAAGATTCTTAGTGCAATTTAC
ACACTCAGTCCCAAAGAACAACTTAATTTTTATTATCAGCTCGAAAATCATCTAAATGAT
TTAAATTTACTTAATCTTTAA

>g3018.t6 Gene=g3018 Length=286
MSRDKVSNKNPNLLRASGDIRKRVIRSDALNIDSDHKYNTRQFHLFAWAHVALLITVVPS
YLIIRNTFDGLIWFIIPVSLIIINDIMAYMFGFFIGKTPLIQLSPKKTWEGFIGGGITTV
LFGLVLAYILCQYLYFICPIDYSEEADKIVILNCQPSYLYIPQEYKISIGNFETVFNIQP
FVLHSLSLSIFSSIVGPFGGFFASGFKRAFKIKDFANVIPGHGGIMDRFDCQVLMASFVY
VYINSFIRDPSPQKILSAIYTLSPKEQLNFYYQLENHLNDLNLLNL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
2 g3018.t6 PANTHER PTHR13773 PHOSPHATIDATE CYTIDYLYLTRANSFERASE 37 279 2.7E-103
3 g3018.t6 PANTHER PTHR13773:SF8 PHOSPHATIDATE CYTIDYLYLTRANSFERASE, PHOTORECEPTOR-SPECIFIC 37 279 2.7E-103
1 g3018.t6 Pfam PF01148 Cytidylyltransferase family 39 246 3.4E-63
9 g3018.t6 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 44 -
15 g3018.t6 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 45 64 -
13 g3018.t6 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 65 69 -
16 g3018.t6 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 70 91 -
10 g3018.t6 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 92 111 -
17 g3018.t6 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 112 135 -
12 g3018.t6 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 136 180 -
14 g3018.t6 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 181 203 -
11 g3018.t6 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 204 286 -
8 g3018.t6 ProSitePatterns PS01315 Phosphatidate cytidylyltransferase signature. 204 230 -
5 g3018.t6 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 45 64 -
6 g3018.t6 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 74 96 -
7 g3018.t6 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 109 131 -
4 g3018.t6 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 181 203 -

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