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.t5 isoform g5318.t5 8706369 8707617
chr_2 g5318 g5318.t5 exon g5318.t5.exon1 8706369 8706478
chr_2 g5318 g5318.t5 TSS g5318.t5 8706373 8706373
chr_2 g5318 g5318.t5 cds g5318.t5.CDS1 8706418 8706478
chr_2 g5318 g5318.t5 exon g5318.t5.exon2 8706532 8706677
chr_2 g5318 g5318.t5 cds g5318.t5.CDS2 8706532 8706677
chr_2 g5318 g5318.t5 exon g5318.t5.exon3 8706747 8706965
chr_2 g5318 g5318.t5 cds g5318.t5.CDS3 8706747 8706965
chr_2 g5318 g5318.t5 exon g5318.t5.exon4 8707130 8707309
chr_2 g5318 g5318.t5 cds g5318.t5.CDS4 8707130 8707309
chr_2 g5318 g5318.t5 exon g5318.t5.exon5 8707384 8707617
chr_2 g5318 g5318.t5 cds g5318.t5.CDS5 8707384 8707617
chr_2 g5318 g5318.t5 TTS g5318.t5 8707663 8707663

Sequences

>g5318.t5 Gene=g5318 Length=889
ATTTCAGTATCCATTCGAACGTCGACGTGTGAATAAGAAAAAATAAATTATGGAAACATC
GAGTGTGAGTGCATTTAAGATTGCAGTTGACTTTGTGCTATTAGCAATACCTGGCCTCAT
TGCTTTAATTTTGAATCTCTTTGTGACTCCATTTCAACGAAATTTCTTCTGTAATGATTT
GTCAATTATGTATCCATATAAACCTGATACAATCACTACATTGCAACTTGCTCTTGTTGG
TGTAATTGTGAGCGTCGTATTTATCGTGGAATTAATTCATAAGTTTAATAATTCATATAA
ATATGATGATGACGATGATAAAGAGAGCAAAATTCTGTATAAATGGAACATTTCACCATT
CATTCAGAATTTATATCAGTATATTGGCCTCCTGTTGTTTGGAATATCAATCAATCAGTT
TATAACTGATGGCACAAAATTTGTTGTTGGACGTTTAAGACCACACTTTATGGATGTCTG
TCGTCCAGTTTTATCAAATGGATTAACATGCAAAGACTTAGATAACTGGAACACTTACAT
CTCTGACTACACTTGCACTAATCAGGATGTTAGTGATTGGACTCTCACAAATGCTCGAAT
TTCATTTCCTTCTGGTCATGCGAGTTTCTCATTCTATTGTTCATTTTTCTGTGCATTTTA
TATTCAATCGCGAATGAAATTTGGAGGGTCAAAGCTTTTGAAACATTTTATTCAATTAGT
GTTTGTCACAGCTGCTCTTTATACTGGCTTATCACGAATTACGGACTATAAGCATCATCC
AACTGACGTAATAGCTGGCAGTATTTTAGGAATTCTTATTGCATTTGTTGTTTGCTTTTA
TTTTTCTGATTTATTTAAGAGAAAAATTAATAATGTCTTACCGAGATGA

>g5318.t5 Gene=g5318 Length=279
METSSVSAFKIAVDFVLLAIPGLIALILNLFVTPFQRNFFCNDLSIMYPYKPDTITTLQL
ALVGVIVSVVFIVELIHKFNNSYKYDDDDDKESKILYKWNISPFIQNLYQYIGLLLFGIS
INQFITDGTKFVVGRLRPHFMDVCRPVLSNGLTCKDLDNWNTYISDYTCTNQDVSDWTLT
NARISFPSGHASFSFYCSFFCAFYIQSRMKFGGSKLLKHFIQLVFVTAALYTGLSRITDY
KHHPTDVIAGSILGILIAFVVCFYFSDLFKRKINNVLPR

Protein features from InterProScan

Transcript Database ID Name Start End E.value
19 g5318.t5 CDD cd03384 PAP2_wunen 108 262 6.41837E-57
5 g5318.t5 Gene3D G3DSA:1.20.144.10 - 8 277 5.7E-38
2 g5318.t5 PANTHER PTHR10165 LIPID PHOSPHATE PHOSPHATASE 9 272 8.2E-76
3 g5318.t5 PANTHER PTHR10165:SF173 FI04477P-RELATED 9 272 8.2E-76
1 g5318.t5 Pfam PF01569 PAP2 superfamily 114 266 3.9E-27
6 g5318.t5 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 11 -
17 g5318.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 12 35 -
11 g5318.t5 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 36 54 -
16 g5318.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 55 76 -
9 g5318.t5 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 77 107 -
15 g5318.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 108 125 -
12 g5318.t5 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 126 183 -
13 g5318.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 184 205 -
8 g5318.t5 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 206 216 -
18 g5318.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 217 235 -
10 g5318.t5 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 236 246 -
14 g5318.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 247 269 -
7 g5318.t5 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 270 279 -
26 g5318.t5 SMART SM00014 acid_phosph_2 112 262 7.7E-38
4 g5318.t5 SUPERFAMILY SSF48317 Acid phosphatase/Vanadium-dependent haloperoxidase 32 265 1.02E-27
22 g5318.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 13 35 -
20 g5318.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 55 77 -
25 g5318.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 104 126 -
21 g5318.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 184 206 -
24 g5318.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 219 237 -
23 g5318.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 247 269 -

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g5318/g5318.t5; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5318.t5.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

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