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.t2 TSS g3018.t2 22145982 22145982
chr_3 g3018 g3018.t2 isoform g3018.t2 22146023 22147208
chr_3 g3018 g3018.t2 exon g3018.t2.exon1 22146023 22146141
chr_3 g3018 g3018.t2 exon g3018.t2.exon2 22146392 22146465
chr_3 g3018 g3018.t2 exon g3018.t2.exon3 22146597 22146693
chr_3 g3018 g3018.t2 cds g3018.t2.CDS1 22146637 22146693
chr_3 g3018 g3018.t2 exon g3018.t2.exon4 22146760 22147129
chr_3 g3018 g3018.t2 cds g3018.t2.CDS2 22146760 22147129
chr_3 g3018 g3018.t2 exon g3018.t2.exon5 22147187 22147208
chr_3 g3018 g3018.t2 cds g3018.t2.CDS3 22147187 22147206
chr_3 g3018 g3018.t2 TTS g3018.t2 22148011 22148011

Sequences

>g3018.t2 Gene=g3018 Length=682
ATGAGTCGCGATAAAGTGTCAAATAAAAATCCAAATTTATTGAGAGCGAGTGGCGATATT
AGGAAGAGAGTCATTAGAAGTGATGCCTTAAACATCGATTCAGACCATGTATGTTGTGGA
AGCCGATGAGAATCTTTTAGAAGAGCAATATGTTAAAGAATTAGCAGAAAAGCACTCGGA
AGGAAGTAAAAAGATGGAAAAATTGGGTTGTGCGTGGTATTTCAATGACAGTAATGATCT
CGACATTTTGCTTATTAATAGCAGGCGGTCCGCTGGCCTTAATGATTTTAGTCTTAGCAA
TTCAAGTCAAATGTTTTCAAGAAATAATGCAGATTGGATTTGTTACCTATAGAGTTGATG
AAATTCCATGGTTTCGGCATTTAACTTGGTATTTATTGACAGTCTCCAACTATTATTATT
ATGGCGAATATTTCTTCGATTATTTTGGACCACCACTCAATCGTATAGAATCACTACAAT
TCTTAATTAAATCACATCGCTTCATTTCCTATTGTCTCTATCTCTTTGCAATAATAATGT
TTGTATTGTCACTCGTTAAGAAATACAATACTAGACAATTTCATCTGTTTGCATGGGCGC
ATGTCGCTTTATTGATCACTGTCGTTCCAAGCTATCTTATCATAAGAAACACGTTCGATG
GATTGATTTGGTTCATCATACC

>g3018.t2 Gene=g3018 Length=149
MISTFCLLIAGGPLALMILVLAIQVKCFQEIMQIGFVTYRVDEIPWFRHLTWYLLTVSNY
YYYGEYFFDYFGPPLNRIESLQFLIKSHRFISYCLYLFAIIMFVLSLVKKYNTRQFHLFA
WAHVALLITVVPSYLIIRNTFDGLIWFII

Protein features from InterProScan

Transcript Database ID Name Start End E.value
2 g3018.t2 PANTHER PTHR13773:SF16 PHOSPHATIDATE CYTIDYLYLTRANSFERASE 1 1 149 3.4E-49
3 g3018.t2 PANTHER PTHR13773 PHOSPHATIDATE CYTIDYLYLTRANSFERASE 1 149 3.4E-49
1 g3018.t2 Pfam PF01148 Cytidylyltransferase family 1 149 5.7E-14
11 g3018.t2 Phobius SIGNAL_PEPTIDE Signal peptide region 1 27 -
12 g3018.t2 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 4 -
13 g3018.t2 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 5 23 -
16 g3018.t2 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 24 27 -
9 g3018.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 28 89 -
15 g3018.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 90 108 -
8 g3018.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 109 119 -
14 g3018.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 120 137 -
10 g3018.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 138 149 -
5 g3018.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 4 23 -
6 g3018.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 44 63 -
7 g3018.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 89 108 -
4 g3018.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 115 137 -

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