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.t2 TSS g4140.t2 30903892 30903892
chr_3 g4140 g4140.t2 isoform g4140.t2 30904128 30906515
chr_3 g4140 g4140.t2 exon g4140.t2.exon1 30904128 30904267
chr_3 g4140 g4140.t2 cds g4140.t2.CDS1 30904128 30904267
chr_3 g4140 g4140.t2 exon g4140.t2.exon2 30905882 30905939
chr_3 g4140 g4140.t2 cds g4140.t2.CDS2 30905882 30905939
chr_3 g4140 g4140.t2 exon g4140.t2.exon3 30906000 30906111
chr_3 g4140 g4140.t2 cds g4140.t2.CDS3 30906000 30906111
chr_3 g4140 g4140.t2 exon g4140.t2.exon4 30906246 30906515
chr_3 g4140 g4140.t2 cds g4140.t2.CDS4 30906246 30906514
chr_3 g4140 g4140.t2 TTS g4140.t2 30906883 30906883

Sequences

>g4140.t2 Gene=g4140 Length=580
ATGCTACGAAATATAAAATCTAAAATATACATATGGATTGAAATTATTATAAGGCTTGCT
CTCTTTGTAGCTTTTTTGAAATTAGAGACATTAGAGCCTTTTCAAAGGAAAATTTTAGCT
GATGATTTATGGAATTATCGTTATCCTAATAAAAAATCATACGTTCCAGTTACATTGTTA
TGGCCAATTCTCACTCTTATCCCAACTTTTGTGTTTATTTTAAATTATATTTTTACGAGA
CATTCAAAAGATTTAAAAGCAGCTATGCTTGGTCATACTTTAGCATTTGGACTTAATGGT
GTTTTAGTAGATATGTTAACTATACACAGACCTGATTTTTTTGAACGATGTTGGCCAGAC
GGAATAATGAATTCTGAAATGATATGCACAGGAGAATATTGGTCAGTTTTGGATGGCAGG
AAAAGTTTCCCGAGCGGTCATTCCTCATTCTCATTCGCTAGTTTAGGATTTTTGACTTTT
TATTTAATTGGAAAGTTGAAAATATTTTCGGATGAAGGAAGAGGAAACAGTTTAAAACTT
ATAATTTCATTTTTTCCTTTTATTGTTGCCATGTTAATAG

>g4140.t2 Gene=g4140 Length=193
MLRNIKSKIYIWIEIIIRLALFVAFLKLETLEPFQRKILADDLWNYRYPNKKSYVPVTLL
WPILTLIPTFVFILNYIFTRHSKDLKAAMLGHTLAFGLNGVLVDMLTIHRPDFFERCWPD
GIMNSEMICTGEYWSVLDGRKSFPSGHSSFSFASLGFLTFYLIGKLKIFSDEGRGNSLKL
IISFFPFIVAMLI

Protein features from InterProScan

Transcript Database ID Name Start End E.value
7 g4140.t2 Gene3D G3DSA:1.20.144.10 - 2 193 1.8E-8
2 g4140.t2 PANTHER PTHR10165 LIPID PHOSPHATE PHOSPHATASE 10 193 1.2E-47
3 g4140.t2 PANTHER PTHR10165:SF87 PHOSPHOLIPID PHOSPHATASE 5 10 193 1.2E-47
1 g4140.t2 Pfam PF01569 PAP2 superfamily 87 193 1.5E-12
8 g4140.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 8 -
14 g4140.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 9 26 -
11 g4140.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 27 58 -
17 g4140.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 59 78 -
10 g4140.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 79 89 -
18 g4140.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 90 108 -
13 g4140.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 109 145 -
15 g4140.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 146 164 -
9 g4140.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 165 175 -
16 g4140.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 176 192 -
12 g4140.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 193 193 -
6 g4140.t2 SUPERFAMILY SSF48317 Acid phosphatase/Vanadium-dependent haloperoxidase 11 164 6.02E-15
4 g4140.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 9 26 -
5 g4140.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 57 79 -

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

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