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.t12 isoform g4140.t12 30905865 30906789
chr_3 g4140 g4140.t12 exon g4140.t12.exon1 30905865 30905939
chr_3 g4140 g4140.t12 exon g4140.t12.exon2 30906000 30906111
chr_3 g4140 g4140.t12 cds g4140.t12.CDS1 30906066 30906111
chr_3 g4140 g4140.t12 exon g4140.t12.exon3 30906179 30906209
chr_3 g4140 g4140.t12 cds g4140.t12.CDS2 30906179 30906209
chr_3 g4140 g4140.t12 exon g4140.t12.exon4 30906265 30906515
chr_3 g4140 g4140.t12 cds g4140.t12.CDS3 30906265 30906515
chr_3 g4140 g4140.t12 exon g4140.t12.exon5 30906581 30906789
chr_3 g4140 g4140.t12 cds g4140.t12.CDS4 30906581 30906789
chr_3 g4140 g4140.t12 TTS g4140.t12 30906883 30906883
chr_3 g4140 g4140.t12 TSS g4140.t12 NA NA

Sequences

>g4140.t12 Gene=g4140 Length=678
ATTAATTTAAATTTCAGTTATCCTAATAAAAAATCATACGTTCCAGTTACATTGTTATGG
CCAATTCTCACTCTTATCCCAACTTTTGTGTTTATTTTAAATTATATTTTTACGAGACAT
TCAAAAGATTTAAAAGCAGCTATGCTTGGTCATACTTTAGCATTTGGACTTAATGGTGTT
TTAGTAGATATTATCAAACTTACTGTCGGTCGACCAAGACCTGATTTTTTTGAACGATGT
TGGCCAGACGGAATAATGAATTCTGAAATGATATGCACAGGAGAATATTGGTCAGTTTTG
GATGGCAGGAAAAGTTTCCCGAGCGGTCATTCCTCATTCTCATTCGCTAGTTTAGGATTT
TTGACTTTTTATTTAATTGGAAAGTTGAAAATATTTTCGGATGAAGGAAGAGGAAACAGT
TTAAAACTTATAATTTCATTTTTTCCTTTTATTGTTGCCATGTTAATAGCAATATCAAGA
ACATGTGACTATCATCATTGGAAAGAAGATGTTGTCGTTGGAAGTTTAATTGGTATTTTA
ATTGCATATTTATGCTATCGACAATTTTTTCCACCACTTGCGAGTAAAAAATCAAATTTA
TGCTATGAAATGCTTTACCATCTTTCTGCTACAAATGACTCAAATGATCTTCTCGAAAAA
GACATTAAATGGATCTAA

>g4140.t12 Gene=g4140 Length=178
MLGHTLAFGLNGVLVDIIKLTVGRPRPDFFERCWPDGIMNSEMICTGEYWSVLDGRKSFP
SGHSSFSFASLGFLTFYLIGKLKIFSDEGRGNSLKLIISFFPFIVAMLIAISRTCDYHHW
KEDVVVGSLIGILIAYLCYRQFFPPLASKKSNLCYEMLYHLSATNDSNDLLEKDIKWI

Protein features from InterProScan

Transcript Database ID Name Start End E.value
13 g4140.t12 CDD cd03390 PAP2_containing_1_like 1 142 1.05332E-65
5 g4140.t12 Gene3D G3DSA:1.20.144.10 - 1 160 5.7E-30
2 g4140.t12 PANTHER PTHR10165 LIPID PHOSPHATE PHOSPHATASE 2 166 3.5E-65
3 g4140.t12 PANTHER PTHR10165:SF87 PHOSPHOLIPID PHOSPHATASE 5 2 166 3.5E-65
1 g4140.t12 Pfam PF01569 PAP2 superfamily 5 143 6.2E-32
8 g4140.t12 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 61 -
12 g4140.t12 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 62 80 -
7 g4140.t12 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 81 91 -
11 g4140.t12 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 92 112 -
9 g4140.t12 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 113 123 -
10 g4140.t12 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 124 143 -
6 g4140.t12 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 144 178 -
17 g4140.t12 SMART SM00014 acid_phosph_2 1 139 9.0E-23
4 g4140.t12 SUPERFAMILY SSF48317 Acid phosphatase/Vanadium-dependent haloperoxidase 3 145 7.85E-32
16 g4140.t12 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 58 80 -
15 g4140.t12 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 92 114 -
14 g4140.t12 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 124 143 -

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