Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Phospholipid phosphatase 4.

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 g4140 g4140.t3 TSS g4140.t3 30903892 30903892
chr_3 g4140 g4140.t3 isoform g4140.t3 30904128 30906789
chr_3 g4140 g4140.t3 exon g4140.t3.exon1 30904128 30904267
chr_3 g4140 g4140.t3 cds g4140.t3.CDS1 30904249 30904267
chr_3 g4140 g4140.t3 exon g4140.t3.exon2 30905911 30905939
chr_3 g4140 g4140.t3 cds g4140.t3.CDS2 30905911 30905939
chr_3 g4140 g4140.t3 exon g4140.t3.exon3 30906000 30906111
chr_3 g4140 g4140.t3 cds g4140.t3.CDS3 30906000 30906111
chr_3 g4140 g4140.t3 exon g4140.t3.exon4 30906179 30906209
chr_3 g4140 g4140.t3 cds g4140.t3.CDS4 30906179 30906209
chr_3 g4140 g4140.t3 exon g4140.t3.exon5 30906265 30906515
chr_3 g4140 g4140.t3 cds g4140.t3.CDS5 30906265 30906515
chr_3 g4140 g4140.t3 exon g4140.t3.exon6 30906581 30906789
chr_3 g4140 g4140.t3 cds g4140.t3.CDS6 30906581 30906789
chr_3 g4140 g4140.t3 TTS g4140.t3 30906883 30906883

Sequences

>g4140.t3 Gene=g4140 Length=772
ATGCTACGAAATATAAAATCTAAAATATACATATGGATTGAAATTATTATAAGGCTTGCT
CTCTTTGTAGCTTTTTTGAAATTAGAGACATTAGAGCCTTTTCAAAGGAAAATTTTAGCT
GATGATTTATGGAATTATCGTTACATTGTTATGGCCAATTCTCACTCTTATCCCAACTTT
TGTGTTTATTTTAAATTATATTTTTACGAGACATTCAAAAGATTTAAAAGCAGCTATGCT
TGGTCATACTTTAGCATTTGGACTTAATGGTGTTTTAGTAGATATTATCAAACTTACTGT
CGGTCGACCAAGACCTGATTTTTTTGAACGATGTTGGCCAGACGGAATAATGAATTCTGA
AATGATATGCACAGGAGAATATTGGTCAGTTTTGGATGGCAGGAAAAGTTTCCCGAGCGG
TCATTCCTCATTCTCATTCGCTAGTTTAGGATTTTTGACTTTTTATTTAATTGGAAAGTT
GAAAATATTTTCGGATGAAGGAAGAGGAAACAGTTTAAAACTTATAATTTCATTTTTTCC
TTTTATTGTTGCCATGTTAATAGCAATATCAAGAACATGTGACTATCATCATTGGAAAGA
AGATGTTGTCGTTGGAAGTTTAATTGGTATTTTAATTGCATATTTATGCTATCGACAATT
TTTTCCACCACTTGCGAGTAAAAAATCAAATTTATGCTATGAAATGCTTTACCATCTTTC
TGCTACAAATGACTCAAATGATCTTCTCGAAAAAGACATTAAATGGATCTAA

>g4140.t3 Gene=g4140 Length=216
MIYGIIVTLLWPILTLIPTFVFILNYIFTRHSKDLKAAMLGHTLAFGLNGVLVDIIKLTV
GRPRPDFFERCWPDGIMNSEMICTGEYWSVLDGRKSFPSGHSSFSFASLGFLTFYLIGKL
KIFSDEGRGNSLKLIISFFPFIVAMLIAISRTCDYHHWKEDVVVGSLIGILIAYLCYRQF
FPPLASKKSNLCYEMLYHLSATNDSNDLLEKDIKWI

Protein features from InterProScan

Transcript Database ID Name Start End E.value
17 g4140.t3 CDD cd03390 PAP2_containing_1_like 7 180 6.79176E-71
5 g4140.t3 Gene3D G3DSA:1.20.144.10 - 1 199 2.4E-32
2 g4140.t3 PANTHER PTHR10165 LIPID PHOSPHATE PHOSPHATASE 11 204 2.3E-69
3 g4140.t3 PANTHER PTHR10165:SF87 PHOSPHOLIPID PHOSPHATASE 5 11 204 2.3E-69
1 g4140.t3 Pfam PF01569 PAP2 superfamily 43 181 1.1E-31
9 g4140.t3 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 5 -
13 g4140.t3 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 6 28 -
8 g4140.t3 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 29 39 -
14 g4140.t3 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 40 60 -
11 g4140.t3 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 61 99 -
12 g4140.t3 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 100 118 -
7 g4140.t3 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 119 129 -
16 g4140.t3 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 130 150 -
10 g4140.t3 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 151 161 -
15 g4140.t3 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 162 181 -
6 g4140.t3 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 182 216 -
23 g4140.t3 SMART SM00014 acid_phosph_2 39 177 9.0E-23
4 g4140.t3 SUPERFAMILY SSF48317 Acid phosphatase/Vanadium-dependent haloperoxidase 13 183 1.31E-34
18 g4140.t3 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 7 29 -
19 g4140.t3 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 39 61 -
21 g4140.t3 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 100 117 -
20 g4140.t3 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 132 149 -
22 g4140.t3 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 162 181 -

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:0042577 lipid phosphatase activity MF
GO:0046839 phospholipid dephosphorylation BP
GO:0006644 phospholipid metabolic process BP
GO:0008195 phosphatidate phosphatase activity 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