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.t2 isoform g5318.t2 8706111 8707617
chr_2 g5318 g5318.t2 exon g5318.t2.exon1 8706111 8706306
chr_2 g5318 g5318.t2 exon g5318.t2.exon2 8706376 8706478
chr_2 g5318 g5318.t2 cds g5318.t2.CDS1 8706418 8706478
chr_2 g5318 g5318.t2 exon g5318.t2.exon3 8706532 8706683
chr_2 g5318 g5318.t2 cds g5318.t2.CDS2 8706532 8706683
chr_2 g5318 g5318.t2 exon g5318.t2.exon4 8706747 8706965
chr_2 g5318 g5318.t2 cds g5318.t2.CDS3 8706747 8706965
chr_2 g5318 g5318.t2 exon g5318.t2.exon5 8707130 8707304
chr_2 g5318 g5318.t2 cds g5318.t2.CDS4 8707130 8707304
chr_2 g5318 g5318.t2 exon g5318.t2.exon6 8707384 8707617
chr_2 g5318 g5318.t2 cds g5318.t2.CDS5 8707384 8707499
chr_2 g5318 g5318.t2 TTS g5318.t2 8707663 8707663
chr_2 g5318 g5318.t2 TSS g5318.t2 NA NA

Sequences

>g5318.t2 Gene=g5318 Length=1079
AGTCATACATGTGTATAAAATGCACAACATAAACAAAACAAATTACGACATGCATTTTTT
AACTTCATTGAAGGGAAATTTTCATTTAACTTTTTGTCAGTATTTTGCGGCTTTTTTTCA
TAACTGAATGATTAATTTTAAAAAATGATAAGAAAATAAATAAAAATACTCGTTATCTTA
TCAGTCAACCATGTGTTATCCATTCGAACGTCGACGTGTGAATAAGAAAAAATAAATTAT
GGAAACATCGAGTGTGAGTGCATTTAAGATTGCAGTTGACTTTGTGCTATTAGCAATACC
TGGCCTCATTGCTTTAATTTTGAATCTCTTTGTGACTCCATTTCAACGAAATTTCTTCTG
TAATGATTTGTCAATTATGTATCCATATAAACCTGATACAATCACTACATTGCAACTTGC
TCTTGTTGGTGTAATTGTGAGCGTCGTATTTGTATTTATCGTGGAATTAATTCATAAGTT
TAATAATTCATATAAATATGATGATGACGATGATAAAGAGAGCAAAATTCTGTATAAATG
GAACATTTCACCATTCATTCAGAATTTATATCAGTATATTGGCCTCCTGTTGTTTGGAAT
ATCAATCAATCAGTTTATAACTGATGGCACAAAATTTGTTGTTGGACGTTTAAGACCACA
CTTTATGGATGTCTGTCGTCCAGTTTTATCAAATGGATTAACATGCAAAGACTTAGATAA
CTGGAACACTTACATCTCTGACTACACTTGCACTAATCAGGATGTTAGTGATTGGACTCT
CACAAATGCTCGAATTTCATTTCCTTCTGGTCATGCGAGTTTCTCATTCTATTGTTCATT
TTTCTTTTTATATTCAATCGCGAATGAAATTTGGAGGGTCAAAGCTTTTGAAACATTTTA
TTCAATTAGTGTTTGTCACAGCTGCTCTTTATACTGGCTTATCACGAATTACGGACTATA
AGCATCATCCAACTGACGTAATAGCTGGCAGTATTTTAGGAATTCTTATTGCATTTGTTG
TTTGCTTTTATTTTTCTGATTTATTTAAGAGAAAAATTAATAATGTCTTACCGAGATGA

>g5318.t2 Gene=g5318 Length=240
METSSVSAFKIAVDFVLLAIPGLIALILNLFVTPFQRNFFCNDLSIMYPYKPDTITTLQL
ALVGVIVSVVFVFIVELIHKFNNSYKYDDDDDKESKILYKWNISPFIQNLYQYIGLLLFG
ISINQFITDGTKFVVGRLRPHFMDVCRPVLSNGLTCKDLDNWNTYISDYTCTNQDVSDWT
LTNARISFPSGHASFSFYCSFFFLYSIANEIWRVKAFETFYSISVCHSCSLYWLITNYGL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
10 g5318.t2 Gene3D G3DSA:1.20.144.10 - 9 235 1.0E-17
2 g5318.t2 PANTHER PTHR10165 LIPID PHOSPHATE PHOSPHATASE 9 224 2.4E-48
3 g5318.t2 PANTHER PTHR10165:SF173 FI04477P-RELATED 9 224 2.4E-48
1 g5318.t2 Pfam PF01569 PAP2 superfamily 116 225 5.6E-13
11 g5318.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 11 -
19 g5318.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 12 35 -
14 g5318.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 36 54 -
18 g5318.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 55 78 -
13 g5318.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 79 109 -
20 g5318.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 110 127 -
16 g5318.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 128 185 -
21 g5318.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 186 207 -
12 g5318.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 208 218 -
17 g5318.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 219 235 -
15 g5318.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 236 240 -
9 g5318.t2 SMART SM00014 acid_phosph_2 114 232 4.4E-4
8 g5318.t2 SUPERFAMILY SSF48317 Acid phosphatase/Vanadium-dependent haloperoxidase 26 210 4.71E-13
6 g5318.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 13 35 -
4 g5318.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 55 77 -
7 g5318.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 106 128 -
5 g5318.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 186 208 -

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g5318/g5318.t2; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5318.t2.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