Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative 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.t13 TSS g3018.t13 22145982 22145982
chr_3 g3018 g3018.t13 isoform g3018.t13 22146768 22147208
chr_3 g3018 g3018.t13 exon g3018.t13.exon1 22146768 22147133
chr_3 g3018 g3018.t13 cds g3018.t13.CDS1 22146796 22147133
chr_3 g3018 g3018.t13 exon g3018.t13.exon2 22147187 22147208
chr_3 g3018 g3018.t13 cds g3018.t13.CDS2 22147187 22147208
chr_3 g3018 g3018.t13 TTS g3018.t13 22148011 22148011

Sequences

>g3018.t13 Gene=g3018 Length=388
AATTCAAGTCAAATGTTTTCAAGAAATAATGCAGATTGGATTTGTTACCTATAGAGTTGA
TGAAATTCCATGGTTTCGGCATTTAACTTGGTATTTATTGACAGTCTCCAACTATTATTA
TTATGGCGAATATTTCTTCGATTATTTTGGACCACCACTCAATCGTATAGAATCACTACA
ATTCTTAATTAAATCACATCGCTTCATTTCCTATTGTCTCTATCTCTTTGCAATAATAAT
GTTTGTATTGTCACTCGTTAAGAAATACAATACTAGACAATTTCATCTGTTTGCATGGGC
GCATGTCGCTTTATTGATCACTGTCGTTCCAAGCTATCTTATCATAAGAAACACGTTCGA
TGGTGAGATTGATTTGGTTCATCATACC

>g3018.t13 Gene=g3018 Length=120
MQIGFVTYRVDEIPWFRHLTWYLLTVSNYYYYGEYFFDYFGPPLNRIESLQFLIKSHRFI
SYCLYLFAIIMFVLSLVKKYNTRQFHLFAWAHVALLITVVPSYLIIRNTFDGEIDLVHHT

Protein features from InterProScan

Transcript Database ID Name Start End E.value
1 g3018.t13 PANTHER PTHR13773:SF16 PHOSPHATIDATE CYTIDYLYLTRANSFERASE 1 2 115 5.0E-33
2 g3018.t13 PANTHER PTHR13773 PHOSPHATIDATE CYTIDYLYLTRANSFERASE 2 115 5.0E-33
8 g3018.t13 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 58 -
10 g3018.t13 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 59 77 -
6 g3018.t13 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 78 88 -
9 g3018.t13 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 89 106 -
7 g3018.t13 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 107 120 -
5 g3018.t13 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 13 32 -
4 g3018.t13 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 58 77 -
3 g3018.t13 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 84 106 -

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