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.t9 TSS g3018.t9 22145982 22145982
chr_3 g3018 g3018.t9 isoform g3018.t9 22146023 22148833
chr_3 g3018 g3018.t9 exon g3018.t9.exon1 22146023 22146130
chr_3 g3018 g3018.t9 cds g3018.t9.CDS1 22146023 22146130
chr_3 g3018 g3018.t9 exon g3018.t9.exon2 22146382 22146465
chr_3 g3018 g3018.t9 cds g3018.t9.CDS2 22146382 22146465
chr_3 g3018 g3018.t9 exon g3018.t9.exon3 22147030 22147129
chr_3 g3018 g3018.t9 cds g3018.t9.CDS3 22147030 22147129
chr_3 g3018 g3018.t9 exon g3018.t9.exon4 22147187 22147485
chr_3 g3018 g3018.t9 cds g3018.t9.CDS4 22147187 22147485
chr_3 g3018 g3018.t9 exon g3018.t9.exon5 22147564 22147695
chr_3 g3018 g3018.t9 cds g3018.t9.CDS5 22147564 22147695
chr_3 g3018 g3018.t9 exon g3018.t9.exon6 22147749 22148833
chr_3 g3018 g3018.t9 cds g3018.t9.CDS6 22147749 22147970
chr_3 g3018 g3018.t9 TTS g3018.t9 22148819 22148819

Sequences

>g3018.t9 Gene=g3018 Length=1808
ATGAGTCGCGATAAAGTGTCAAATAAAAATCCAAATTTATTGAGAGCGAGTGGCGATATT
AGGAAGAGAGTCATTAGAAGTGATGCCTTAAACATCGATTCAGACCATATTGATTCAGAA
GCCGATGAGAATCTTTTAGAAGAGCAATATGTTAAAGAATTAGCAGAAAAGCACTCGGAA
GGAAGTAAAAAGAAATACAATACTAGACAATTTCATCTGTTTGCATGGGCGCATGTCGCT
TTATTGATCACTGTCGTTCCAAGCTATCTTATCATAAGAAACACGTTCGATGGATTGATT
TGGTTCATCATACCGGTGTCGTTAATTATTATCAATGATATTATGGCTTATATGTTTGGA
TTCTTCATTGGTAAAACGCCACTTATACAATTGAGCCCTAAGAAAACTTGGGAGGGATTT
ATCGGCGGAGGCATAACGACAGTATTGTTTGGTTTAGTCCTCGCATACATTCTGTGTCAA
TATCTCTATTTCATATGTCCCATTGACTACTCAGAGGAAGCCGATAAAATTGTCATTCTC
AATTGCCAACCGAGCTATTTGTATATACCGCAAGAATATAAAATCAGCATTGGAAATTTC
GAAACAGTTTTCAATATTCAGCCATTTGTGCTTCATTCGTTATCATTGAGTATCTTTAGT
TCAATCGTTGGTCCTTTTGGTGGATTCTTTGCCTCAGGATTTAAACGAGCATTCAAAATT
AAGGATTTTGCTAATGTTATCCCAGGACATGGTGGTATAATGGACAGATTTGACTGTCAA
GTGTTAATGGCCTCTTTTGTATATGTTTATATTAATAGTTTTATTCGAGATCCATCACCA
CAGAAGATTCTTAGTGCAATTTACACACTCAGTCCCAAAGAACAACTTAATTTTTATTAT
CAGCTCGAAAATCATCTAAATGATTTAAATTTACTTAATCTTTAAGCACAGAGAAAGACA
ACAATAAATCTATTAAAGTTGCACATGTGATCATTGATGAATTTTATCAATTTATTCCAT
AACTCAATATATAGAATAAAATAAAAGGAGCAGCAACTGATGCAATGCGATGGAAGAAAG
GAAGGAAGGAGAGACTTTGTTCATAAATATTTATTGGATAATCATACAGTTTCTGTATAT
ATACATAGAGTATATTTTCAAAAAAGAGTTACAGTCAATTATTTTAATGCAACAATTTCC
TAACTGCACCTGGTGATTTTTCTCTCTTTTTCACAAGAGAGTATATTGGTAATCGCATGC
GAAACGATAGCAAAGAAGGACGACTAAATAAAATTGAAAAATGAGAGAAAATTGCACAAA
TAAAGTCGAGGAAAAATGTCGCTCGAAGGACTGTTTGTGTAGCAGTTCAAGCAAAATGAT
TTTTATGTTTTGGGAGCAAGCAAGCACACGAGAAAAAGAAAAAGGAAGAAAGAAATTGTC
GTGACATTAAAAGACGGTGATAAAAAGCATATGAGAGCGCAGGAAATGTTCATTCTTTTT
TCTTCGACATAATCTCAAGACTGCAATGCTCTTTATGGTTTTATTAAATAAAGGAAAAAA
CTACTTTCACCATTGCTGCTGCTTCTGTTAGCTCTATGAAATGTATATATTGAAAAGCGG
CACCATCGTCAATTGCTCTATGTGTGTATGCTATCATACATGTGAAATTTTTCTTTGATG
TGACATAATGTGGAAATAAGTTGATAGAAAAAACAAGTTTTTATAATTTCTTTGTGCTAT
ATAAAGGAGCTCTTTTTTATAAGCAAAAGAGGAAGGAAATAAAGAGAGAATTTTTATTGT
TTGATTTA

>g3018.t9 Gene=g3018 Length=314
MSRDKVSNKNPNLLRASGDIRKRVIRSDALNIDSDHIDSEADENLLEEQYVKELAEKHSE
GSKKKYNTRQFHLFAWAHVALLITVVPSYLIIRNTFDGLIWFIIPVSLIIINDIMAYMFG
FFIGKTPLIQLSPKKTWEGFIGGGITTVLFGLVLAYILCQYLYFICPIDYSEEADKIVIL
NCQPSYLYIPQEYKISIGNFETVFNIQPFVLHSLSLSIFSSIVGPFGGFFASGFKRAFKI
KDFANVIPGHGGIMDRFDCQVLMASFVYVYINSFIRDPSPQKILSAIYTLSPKEQLNFYY
QLENHLNDLNLLNL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
2 g3018.t9 PANTHER PTHR13773 PHOSPHATIDATE CYTIDYLYLTRANSFERASE 63 307 6.5E-104
3 g3018.t9 PANTHER PTHR13773:SF8 PHOSPHATIDATE CYTIDYLYLTRANSFERASE, PHOTORECEPTOR-SPECIFIC 63 307 6.5E-104
1 g3018.t9 Pfam PF01148 Cytidylyltransferase family 59 274 1.4E-64
10 g3018.t9 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 72 -
16 g3018.t9 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 73 92 -
12 g3018.t9 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 93 97 -
14 g3018.t9 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 98 119 -
11 g3018.t9 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 120 139 -
15 g3018.t9 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 140 163 -
13 g3018.t9 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 164 208 -
17 g3018.t9 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 209 231 -
9 g3018.t9 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 232 314 -
8 g3018.t9 ProSitePatterns PS01315 Phosphatidate cytidylyltransferase signature. 232 258 -
5 g3018.t9 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 73 92 -
4 g3018.t9 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 102 124 -
6 g3018.t9 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 137 159 -
7 g3018.t9 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 209 231 -

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.

Raw TPM values