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.t12 TSS g3018.t12 22145982 22145982
chr_3 g3018 g3018.t12 isoform g3018.t12 22146615 22148434
chr_3 g3018 g3018.t12 exon g3018.t12.exon1 22146615 22147129
chr_3 g3018 g3018.t12 cds g3018.t12.CDS1 22146796 22147129
chr_3 g3018 g3018.t12 exon g3018.t12.exon2 22147187 22147489
chr_3 g3018 g3018.t12 cds g3018.t12.CDS2 22147187 22147489
chr_3 g3018 g3018.t12 exon g3018.t12.exon3 22147564 22147695
chr_3 g3018 g3018.t12 cds g3018.t12.CDS3 22147564 22147631
chr_3 g3018 g3018.t12 exon g3018.t12.exon4 22147749 22148434
chr_3 g3018 g3018.t12 TTS g3018.t12 22148819 22148819

Sequences

>g3018.t12 Gene=g3018 Length=1636
GCGTGGTATTTCAATGACAGTAATGATCTCGACATTTTGCTTATTAATAGCAGGCGGTCC
GCTGGCCTTAATGATTTTAGTATGACGATCTTAGACTAAGTCAATGTGATTTCTTATAAA
ATTCTTTCTGTTTGGAAACCCTCAGGTCTTAGCAATTCAAGTCAAATGTTTTCAAGAAAT
AATGCAGATTGGATTTGTTACCTATAGAGTTGATGAAATTCCATGGTTTCGGCATTTAAC
TTGGTATTTATTGACAGTCTCCAACTATTATTATTATGGCGAATATTTCTTCGATTATTT
TGGACCACCACTCAATCGTATAGAATCACTACAATTCTTAATTAAATCACATCGCTTCAT
TTCCTATTGTCTCTATCTCTTTGCAATAATAATGTTTGTATTGTCACTCGTTAAGAAATA
CAATACTAGACAATTTCATCTGTTTGCATGGGCGCATGTCGCTTTATTGATCACTGTCGT
TCCAAGCTATCTTATCATAAGAAACACGTTCGATGGATTGATTTGGTTCATCATACCGGT
GTCGTTAATTATTATCAATGATATTATGGCTTATATGTTTGGATTCTTCATTGGTAAAAC
GCCACTTATACAATTGAGCCCTAAGAAAACTTGGGAGGGATTTATCGGCGGAGGCATAAC
GACAGTATTGTTTGGTTTAGTCCTCGCATACATTCTGTGTCAATATCTCTATTTCATATG
TCCCATTGACTACTCAGAGGAAGCCGATAAAATTGTCATTCTCAATTGCCAACCGAGCTA
TTTGTATATACCGCAAGAATATAAAATCAGCATTGTGAGGAAATTTCGAAACAGTTTTCA
ATATTCAGCCATTTGTGCTTCATTCGTTATCATTGAGTATCTTTAGTTCAATCGTTGGTC
CTTTTGGTGGATTCTTTGCCTCAGGATTTAAACGAGCATTCAAAATTAAGGATTTTGCTA
ATGTTATCCCAGGACATGGTGGTATAATGGACAGATTTGACTGTCAAGTGTTAATGGCCT
CTTTTGTATATGTTTATATTAATAGTTTTATTCGAGATCCATCACCACAGAAGATTCTTA
GTGCAATTTACACACTCAGTCCCAAAGAACAACTTAATTTTTATTATCAGCTCGAAAATC
ATCTAAATGATTTAAATTTACTTAATCTTTAAGCACAGAGAAAGACAACAATAAATCTAT
TAAAGTTGCACATGTGATCATTGATGAATTTTATCAATTTATTCCATAACTCAATATATA
GAATAAAATAAAAGGAGCAGCAACTGATGCAATGCGATGGAAGAAAGGAAGGAAGGAGAG
ACTTTGTTCATAAATATTTATTGGATAATCATACAGTTTCTGTATATATACATAGAGTAT
ATTTTCAAAAAAGAGTTACAGTCAATTATTTTAATGCAACAATTTCCTAACTGCACCTGG
TGATTTTTCTCTCTTTTTCACAAGAGAGTATATTGGTAATCGCATGCGAAACGATAGCAA
AGAAGGACGACTAAATAAAATTGAAAAATGAGAGAAAATTGCACAAATAAAGTCGAGGAA
AAATGTCGCTCGAAGGACTGTTTGTGTAGCAGTTCAAGCAAAATGATTTTTATGTTTTGG
GAGCAAGCAAGCACAC

>g3018.t12 Gene=g3018 Length=234
MQIGFVTYRVDEIPWFRHLTWYLLTVSNYYYYGEYFFDYFGPPLNRIESLQFLIKSHRFI
SYCLYLFAIIMFVLSLVKKYNTRQFHLFAWAHVALLITVVPSYLIIRNTFDGLIWFIIPV
SLIIINDIMAYMFGFFIGKTPLIQLSPKKTWEGFIGGGITTVLFGLVLAYILCQYLYFIC
PIDYSEEADKIVILNCQPSYLYIPQEYKISIVRKFRNSFQYSAICASFVIIEYL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
2 g3018.t12 PANTHER PTHR13773:SF16 PHOSPHATIDATE CYTIDYLYLTRANSFERASE 1 2 212 4.4E-78
3 g3018.t12 PANTHER PTHR13773 PHOSPHATIDATE CYTIDYLYLTRANSFERASE 2 212 4.4E-78
1 g3018.t12 Pfam PF01148 Cytidylyltransferase family 7 184 1.1E-34
12 g3018.t12 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 58 -
15 g3018.t12 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 59 77 -
9 g3018.t12 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 78 88 -
14 g3018.t12 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 89 106 -
11 g3018.t12 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 107 111 -
16 g3018.t12 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 112 133 -
8 g3018.t12 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 134 153 -
13 g3018.t12 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 154 177 -
10 g3018.t12 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 178 234 -
7 g3018.t12 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 59 77 -
5 g3018.t12 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 87 106 -
6 g3018.t12 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 113 135 -
4 g3018.t12 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 150 172 -

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.

Raw TPM values