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.t11 TSS g3018.t11 22145982 22145982
chr_3 g3018 g3018.t11 isoform g3018.t11 22146611 22147478
chr_3 g3018 g3018.t11 exon g3018.t11.exon1 22146611 22146693
chr_3 g3018 g3018.t11 cds g3018.t11.CDS1 22146628 22146693
chr_3 g3018 g3018.t11 exon g3018.t11.exon2 22146760 22147129
chr_3 g3018 g3018.t11 cds g3018.t11.CDS2 22146760 22147129
chr_3 g3018 g3018.t11 exon g3018.t11.exon3 22147187 22147478
chr_3 g3018 g3018.t11 cds g3018.t11.CDS3 22147187 22147476
chr_3 g3018 g3018.t11 TTS g3018.t11 22148011 22148011

Sequences

>g3018.t11 Gene=g3018 Length=745
TTGTGCGTGGTATTTCAATGACAGTAATGATCTCGACATTTTGCTTATTAATAGCAGGCG
GTCCGCTGGCCTTAATGATTTTAGTCTTAGCAATTCAAGTCAAATGTTTTCAAGAAATAA
TGCAGATTGGATTTGTTACCTATAGAGTTGATGAAATTCCATGGTTTCGGCATTTAACTT
GGTATTTATTGACAGTCTCCAACTATTATTATTATGGCGAATATTTCTTCGATTATTTTG
GACCACCACTCAATCGTATAGAATCACTACAATTCTTAATTAAATCACATCGCTTCATTT
CCTATTGTCTCTATCTCTTTGCAATAATAATGTTTGTATTGTCACTCGTTAAGAAATACA
ATACTAGACAATTTCATCTGTTTGCATGGGCGCATGTCGCTTTATTGATCACTGTCGTTC
CAAGCTATCTTATCATAAGAAACACGTTCGATGGATTGATTTGGTTCATCATACCGGTGT
CGTTAATTATTATCAATGATATTATGGCTTATATGTTTGGATTCTTCATTGGTAAAACGC
CACTTATACAATTGAGCCCTAAGAAAACTTGGGAGGGATTTATCGGCGGAGGCATAACGA
CAGTATTGTTTGGTTTAGTCCTCGCATACATTCTGTGTCAATATCTCTATTTCATATGTC
CCATTGACTACTCAGAGGAAGCCGATAAAATTGTCATTCTCAATTGCCAACCGAGCTATT
TGTATATACCGCAAGAATATAAAAT

>g3018.t11 Gene=g3018 Length=242
MTVMISTFCLLIAGGPLALMILVLAIQVKCFQEIMQIGFVTYRVDEIPWFRHLTWYLLTV
SNYYYYGEYFFDYFGPPLNRIESLQFLIKSHRFISYCLYLFAIIMFVLSLVKKYNTRQFH
LFAWAHVALLITVVPSYLIIRNTFDGLIWFIIPVSLIIINDIMAYMFGFFIGKTPLIQLS
PKKTWEGFIGGGITTVLFGLVLAYILCQYLYFICPIDYSEEADKIVILNCQPSYLYIPQE
YK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
2 g3018.t11 PANTHER PTHR13773:SF16 PHOSPHATIDATE CYTIDYLYLTRANSFERASE 1 3 241 2.5E-91
3 g3018.t11 PANTHER PTHR13773 PHOSPHATIDATE CYTIDYLYLTRANSFERASE 3 241 2.5E-91
1 g3018.t11 Pfam PF01148 Cytidylyltransferase family 2 210 6.5E-43
14 g3018.t11 Phobius SIGNAL_PEPTIDE Signal peptide region 1 30 -
15 g3018.t11 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 7 -
16 g3018.t11 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 8 26 -
21 g3018.t11 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 27 30 -
11 g3018.t11 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 31 92 -
19 g3018.t11 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 93 111 -
9 g3018.t11 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 112 122 -
20 g3018.t11 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 123 140 -
12 g3018.t11 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 141 145 -
18 g3018.t11 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 146 167 -
10 g3018.t11 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 168 187 -
17 g3018.t11 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 188 211 -
13 g3018.t11 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 212 242 -
5 g3018.t11 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 4 26 -
6 g3018.t11 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 93 111 -
7 g3018.t11 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 121 140 -
8 g3018.t11 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 147 169 -
4 g3018.t11 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 184 206 -

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:0004605 phosphatidate cytidylyltransferase activity MF

KEGG

Orthology

This gene did not have any KEGG ortholog annotations (KAAS, GHOSTZ).

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