Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Putative phosphatidate phosphatase.

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_2 g5318 g5318.t11 TSS g5318.t11 8706373 8706373
chr_2 g5318 g5318.t11 isoform g5318.t11 8706418 8707617
chr_2 g5318 g5318.t11 exon g5318.t11.exon1 8706418 8706482
chr_2 g5318 g5318.t11 cds g5318.t11.CDS1 8706418 8706482
chr_2 g5318 g5318.t11 exon g5318.t11.exon2 8706545 8706683
chr_2 g5318 g5318.t11 cds g5318.t11.CDS2 8706545 8706683
chr_2 g5318 g5318.t11 exon g5318.t11.exon3 8706747 8706965
chr_2 g5318 g5318.t11 cds g5318.t11.CDS3 8706747 8706965
chr_2 g5318 g5318.t11 exon g5318.t11.exon4 8707130 8707362
chr_2 g5318 g5318.t11 cds g5318.t11.CDS4 8707130 8707362
chr_2 g5318 g5318.t11 exon g5318.t11.exon5 8707530 8707617
chr_2 g5318 g5318.t11 cds g5318.t11.CDS5 8707530 8707617
chr_2 g5318 g5318.t11 TTS g5318.t11 8707663 8707663

Sequences

>g5318.t11 Gene=g5318 Length=744
ATGGAAACATCGAGTGTGAGTGCATTTAAGATTGCAGTTGACTTTGTGCTATTAGCAATA
CGTGATTTAATTTTGAATCTCTTTGTGACTCCATTTCAACGAAATTTCTTCTGTAATGAT
TTGTCAATTATGTATCCATATAAACCTGATACAATCACTACATTGCAACTTGCTCTTGTT
GGTGTAATTGTGAGCGTCGTATTTGTATTTATCGTGGAATTAATTCATAAGTTTAATAAT
TCATATAAATATGATGATGACGATGATAAAGAGAGCAAAATTCTGTATAAATGGAACATT
TCACCATTCATTCAGAATTTATATCAGTATATTGGCCTCCTGTTGTTTGGAATATCAATC
AATCAGTTTATAACTGATGGCACAAAATTTGTTGTTGGACGTTTAAGACCACACTTTATG
GATGTCTGTCGTCCAGTTTTATCAAATGGATTAACATGCAAAGACTTAGATAACTGGAAC
ACTTACATCTCTGACTACACTTGCACTAATCAGGATGTTAGTGATTGGACTCTCACAAAT
GCTCGAATTTCATTTCCTTCTGGTCATGCGAGTTTCTCATTCTATTGTTCATTTTTCTGT
GCAGTGAGTATCAATTATTTCGCGCGTAAAATCACGTATGAATCATTATACAAATTTATT
TTAGGAATTCTTATTGCATTTGTTGTTTGCTTTTATTTTTCTGATTTATTTAAGAGAAAA
ATTAATAATGTCTTACCGAGATGA

>g5318.t11 Gene=g5318 Length=247
METSSVSAFKIAVDFVLLAIRDLILNLFVTPFQRNFFCNDLSIMYPYKPDTITTLQLALV
GVIVSVVFVFIVELIHKFNNSYKYDDDDDKESKILYKWNISPFIQNLYQYIGLLLFGISI
NQFITDGTKFVVGRLRPHFMDVCRPVLSNGLTCKDLDNWNTYISDYTCTNQDVSDWTLTN
ARISFPSGHASFSFYCSFFCAVSINYFARKITYESLYKFILGILIAFVVCFYFSDLFKRK
INNVLPR

Protein features from InterProScan

Transcript Database ID Name Start End E.value
11 g5318.t11 Gene3D G3DSA:1.20.144.10 - 13 239 3.1E-18
2 g5318.t11 PANTHER PTHR10165 LIPID PHOSPHATE PHOSPHATASE 10 224 1.6E-46
3 g5318.t11 PANTHER PTHR10165:SF173 FI04477P-RELATED 10 224 1.6E-46
1 g5318.t11 Pfam PF01569 PAP2 superfamily 113 229 9.4E-14
12 g5318.t11 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 11 -
18 g5318.t11 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 12 32 -
15 g5318.t11 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 33 51 -
19 g5318.t11 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 52 75 -
14 g5318.t11 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 76 106 -
21 g5318.t11 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 107 124 -
17 g5318.t11 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 125 191 -
20 g5318.t11 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 192 208 -
13 g5318.t11 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 209 214 -
22 g5318.t11 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 215 234 -
16 g5318.t11 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 235 247 -
10 g5318.t11 SMART SM00014 acid_phosph_2 111 234 1.3E-6
9 g5318.t11 SUPERFAMILY SSF48317 Acid phosphatase/Vanadium-dependent haloperoxidase 12 229 1.83E-13
8 g5318.t11 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 13 32 -
6 g5318.t11 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 52 74 -
4 g5318.t11 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 103 125 -
5 g5318.t11 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 186 208 -
7 g5318.t11 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 215 237 -

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g5318/g5318.t11; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5318.t11.fa.iupred3.txt does not exist

GO terms from InterProScan

GOID TERM ONTOLOGY
GO:0042577 lipid phosphatase activity MF
GO:0006644 phospholipid metabolic process BP

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