Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Phospholipid phosphatase 5.

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.t9 TSS g4140.t9 30903892 30903892
chr_3 g4140 g4140.t9 isoform g4140.t9 30904128 30906789
chr_3 g4140 g4140.t9 exon g4140.t9.exon1 30904128 30904267
chr_3 g4140 g4140.t9 exon g4140.t9.exon2 30905882 30905939
chr_3 g4140 g4140.t9 exon g4140.t9.exon3 30906000 30906111
chr_3 g4140 g4140.t9 exon g4140.t9.exon4 30906179 30906515
chr_3 g4140 g4140.t9 cds g4140.t9.CDS1 30906302 30906515
chr_3 g4140 g4140.t9 exon g4140.t9.exon5 30906581 30906789
chr_3 g4140 g4140.t9 cds g4140.t9.CDS2 30906581 30906789
chr_3 g4140 g4140.t9 TTS g4140.t9 30906883 30906883

Sequences

>g4140.t9 Gene=g4140 Length=856
ATGCTACGAAATATAAAATCTAAAATATACATATGGATTGAAATTATTATAAGGCTTGCT
CTCTTTGTAGCTTTTTTGAAATTAGAGACATTAGAGCCTTTTCAAAGGAAAATTTTAGCT
GATGATTTATGGAATTATCGTTATCCTAATAAAAAATCATACGTTCCAGTTACATTGTTA
TGGCCAATTCTCACTCTTATCCCAACTTTTGTGTTTATTTTAAATTATATTTTTACGAGA
CATTCAAAAGATTTAAAAGCAGCTATGCTTGGTCATACTTTAGCATTTGGACTTAATGGT
GTTTTAGTAGATATTATCAAACTTACTGTCGGTCGACCAAGGTAATAAATTAAAAATTTA
TTTTTCACACACTAACGATATGTTAACTATACACAGACCTGATTTTTTTGAACGATGTTG
GCCAGACGGAATAATGAATTCTGAAATGATATGCACAGGAGAATATTGGTCAGTTTTGGA
TGGCAGGAAAAGTTTCCCGAGCGGTCATTCCTCATTCTCATTCGCTAGTTTAGGATTTTT
GACTTTTTATTTAATTGGAAAGTTGAAAATATTTTCGGATGAAGGAAGAGGAAACAGTTT
AAAACTTATAATTTCATTTTTTCCTTTTATTGTTGCCATGTTAATAGCAATATCAAGAAC
ATGTGACTATCATCATTGGAAAGAAGATGTTGTCGTTGGAAGTTTAATTGGTATTTTAAT
TGCATATTTATGCTATCGACAATTTTTTCCACCACTTGCGAGTAAAAAATCAAATTTATG
CTATGAAATGCTTTACCATCTTTCTGCTACAAATGACTCAAATGATCTTCTCGAAAAAGA
CATTAAATGGATCTAA

>g4140.t9 Gene=g4140 Length=140
MNSEMICTGEYWSVLDGRKSFPSGHSSFSFASLGFLTFYLIGKLKIFSDEGRGNSLKLII
SFFPFIVAMLIAISRTCDYHHWKEDVVVGSLIGILIAYLCYRQFFPPLASKKSNLCYEML
YHLSATNDSNDLLEKDIKWI

Protein features from InterProScan

Transcript Database ID Name Start End E.value
9 g4140.t9 Gene3D G3DSA:1.20.144.10 - 6 125 2.7E-24
2 g4140.t9 PANTHER PTHR10165 LIPID PHOSPHATE PHOSPHATASE 1 128 6.8E-45
3 g4140.t9 PANTHER PTHR10165:SF87 PHOSPHOLIPID PHOSPHATASE 5 1 128 6.8E-45
1 g4140.t9 Pfam PF01569 PAP2 superfamily 16 105 4.6E-24
13 g4140.t9 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 23 -
14 g4140.t9 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 24 42 -
10 g4140.t9 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 43 53 -
16 g4140.t9 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 54 74 -
12 g4140.t9 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 75 85 -
15 g4140.t9 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 86 105 -
11 g4140.t9 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 106 140 -
8 g4140.t9 SMART SM00014 acid_phosph_2 1 101 4.1E-4
7 g4140.t9 SUPERFAMILY SSF48317 Acid phosphatase/Vanadium-dependent haloperoxidase 3 107 1.31E-22
4 g4140.t9 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 20 42 -
5 g4140.t9 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 54 76 -
6 g4140.t9 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 86 105 -

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