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.t11 TSS g4140.t11 30903892 30903892
chr_3 g4140 g4140.t11 isoform g4140.t11 30904128 30906789
chr_3 g4140 g4140.t11 exon g4140.t11.exon1 30904128 30904267
chr_3 g4140 g4140.t11 cds g4140.t11.CDS1 30904128 30904267
chr_3 g4140 g4140.t11 exon g4140.t11.exon2 30905882 30905939
chr_3 g4140 g4140.t11 cds g4140.t11.CDS2 30905882 30905939
chr_3 g4140 g4140.t11 exon g4140.t11.exon3 30906000 30906142
chr_3 g4140 g4140.t11 cds g4140.t11.CDS3 30906000 30906142
chr_3 g4140 g4140.t11 exon g4140.t11.exon4 30906265 30906515
chr_3 g4140 g4140.t11 cds g4140.t11.CDS4 30906265 30906515
chr_3 g4140 g4140.t11 exon g4140.t11.exon5 30906581 30906789
chr_3 g4140 g4140.t11 cds g4140.t11.CDS5 30906581 30906789
chr_3 g4140 g4140.t11 TTS g4140.t11 30906883 30906883

Sequences

>g4140.t11 Gene=g4140 Length=801
ATGCTACGAAATATAAAATCTAAAATATACATATGGATTGAAATTATTATAAGGCTTGCT
CTCTTTGTAGCTTTTTTGAAATTAGAGACATTAGAGCCTTTTCAAAGGAAAATTTTAGCT
GATGATTTATGGAATTATCGTTATCCTAATAAAAAATCATACGTTCCAGTTACATTGTTA
TGGCCAATTCTCACTCTTATCCCAACTTTTGTGTTTATTTTAAATTATATTTTTACGAGA
CATTCAAAAGATTTAAAAGCAGCTATGCTTGGTCATACTTTAGCATTTGGACTTAATGGT
GTTTTAGTAGGTGAGAAAATTCCTTTTATATTTAAATGTTTACCTGATTTTTTTGAACGA
TGTTGGCCAGACGGAATAATGAATTCTGAAATGATATGCACAGGAGAATATTGGTCAGTT
TTGGATGGCAGGAAAAGTTTCCCGAGCGGTCATTCCTCATTCTCATTCGCTAGTTTAGGA
TTTTTGACTTTTTATTTAATTGGAAAGTTGAAAATATTTTCGGATGAAGGAAGAGGAAAC
AGTTTAAAACTTATAATTTCATTTTTTCCTTTTATTGTTGCCATGTTAATAGCAATATCA
AGAACATGTGACTATCATCATTGGAAAGAAGATGTTGTCGTTGGAAGTTTAATTGGTATT
TTAATTGCATATTTATGCTATCGACAATTTTTTCCACCACTTGCGAGTAAAAAATCAAAT
TTATGCTATGAAATGCTTTACCATCTTTCTGCTACAAATGACTCAAATGATCTTCTCGAA
AAAGACATTAAATGGATCTAA

>g4140.t11 Gene=g4140 Length=266
MLRNIKSKIYIWIEIIIRLALFVAFLKLETLEPFQRKILADDLWNYRYPNKKSYVPVTLL
WPILTLIPTFVFILNYIFTRHSKDLKAAMLGHTLAFGLNGVLVGEKIPFIFKCLPDFFER
CWPDGIMNSEMICTGEYWSVLDGRKSFPSGHSSFSFASLGFLTFYLIGKLKIFSDEGRGN
SLKLIISFFPFIVAMLIAISRTCDYHHWKEDVVVGSLIGILIAYLCYRQFFPPLASKKSN
LCYEMLYHLSATNDSNDLLEKDIKWI

Protein features from InterProScan

Transcript Database ID Name Start End E.value
19 g4140.t11 CDD cd03390 PAP2_containing_1_like 44 230 2.50864E-65
5 g4140.t11 Gene3D G3DSA:1.20.144.10 - 2 245 2.0E-21
2 g4140.t11 PANTHER PTHR10165 LIPID PHOSPHATE PHOSPHATASE 10 254 7.0E-71
3 g4140.t11 PANTHER PTHR10165:SF87 PHOSPHOLIPID PHOSPHATASE 5 10 254 7.0E-71
1 g4140.t11 Pfam PF01569 PAP2 superfamily 94 231 9.3E-25
6 g4140.t11 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 8 -
14 g4140.t11 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 9 26 -
11 g4140.t11 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 27 58 -
18 g4140.t11 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 59 78 -
7 g4140.t11 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 79 89 -
17 g4140.t11 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 90 111 -
12 g4140.t11 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 112 149 -
15 g4140.t11 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 150 168 -
9 g4140.t11 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 169 179 -
13 g4140.t11 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 180 200 -
10 g4140.t11 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 201 211 -
16 g4140.t11 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 212 231 -
8 g4140.t11 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 232 266 -
25 g4140.t11 SMART SM00014 acid_phosph_2 89 227 8.1E-16
4 g4140.t11 SUPERFAMILY SSF48317 Acid phosphatase/Vanadium-dependent haloperoxidase 11 233 2.09E-27
20 g4140.t11 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 9 26 -
24 g4140.t11 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 57 79 -
23 g4140.t11 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 150 167 -
22 g4140.t11 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 182 199 -
21 g4140.t11 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 212 231 -

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: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. There were no conditions that were differentially expressed