General information for g5318.t12
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Putative phosphatidate phosphatase.
Parent gene
- The parent gene g5318 is located on chr_2: 8706747..8708069 (+ strand)
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.t12 | TSS | g5318.t12 | 8706373 | 8706373 |
| chr_2 | g5318 | g5318.t12 | isoform | g5318.t12 | 8706418 | 8707617 |
| chr_2 | g5318 | g5318.t12 | exon | g5318.t12.exon1 | 8706418 | 8706478 |
| chr_2 | g5318 | g5318.t12 | cds | g5318.t12.CDS1 | 8706418 | 8706478 |
| chr_2 | g5318 | g5318.t12 | exon | g5318.t12.exon2 | 8706532 | 8706683 |
| chr_2 | g5318 | g5318.t12 | cds | g5318.t12.CDS2 | 8706532 | 8706683 |
| chr_2 | g5318 | g5318.t12 | exon | g5318.t12.exon3 | 8706747 | 8706965 |
| chr_2 | g5318 | g5318.t12 | cds | g5318.t12.CDS3 | 8706747 | 8706965 |
| chr_2 | g5318 | g5318.t12 | exon | g5318.t12.exon4 | 8707130 | 8707292 |
| chr_2 | g5318 | g5318.t12 | cds | g5318.t12.CDS4 | 8707130 | 8707292 |
| chr_2 | g5318 | g5318.t12 | exon | g5318.t12.exon5 | 8707384 | 8707617 |
| chr_2 | g5318 | g5318.t12 | cds | g5318.t12.CDS5 | 8707384 | 8707499 |
| chr_2 | g5318 | g5318.t12 | TTS | g5318.t12 | 8707663 | 8707663 |
Sequences
>g5318.t12 Gene=g5318 Length=829
ATGGAAACATCGAGTGTGAGTGCATTTAAGATTGCAGTTGACTTTGTGCTATTAGCAATA
CCTGGCCTCATTGCTTTAATTTTGAATCTCTTTGTGACTCCATTTCAACGAAATTTCTTC
TGTAATGATTTGTCAATTATGTATCCATATAAACCTGATACAATCACTACATTGCAACTT
GCTCTTGTTGGTGTAATTGTGAGCGTCGTATTTGTATTTATCGTGGAATTAATTCATAAG
TTTAATAATTCATATAAATATGATGATGACGATGATAAAGAGAGCAAAATTCTGTATAAA
TGGAACATTTCACCATTCATTCAGAATTTATATCAGTATATTGGCCTCCTGTTGTTTGGA
ATATCAATCAATCAGTTTATAACTGATGGCACAAAATTTGTTGTTGGACGTTTAAGACCA
CACTTTATGGATGTCTGTCGTCCAGTTTTATCAAATGGATTAACATGCAAAGACTTAGAT
AACTGGAACACTTACATCTCTGACTACACTTGCACTAATCAGGATGTTAGTGATTGGACT
CTCACAAATGCTCGAATTTCATTTCCTTCTGGTCATGCGAGTTTCTCATTCTATTTTTTA
TATTCAATCGCGAATGAAATTTGGAGGGTCAAAGCTTTTGAAACATTTTATTCAATTAGT
GTTTGTCACAGCTGCTCTTTATACTGGCTTATCACGAATTACGGACTATAAGCATCATCC
AACTGACGTAATAGCTGGCAGTATTTTAGGAATTCTTATTGCATTTGTTGTTTGCTTTTA
TTTTTCTGATTTATTTAAGAGAAAAATTAATAATGTCTTACCGAGATGA
>g5318.t12 Gene=g5318 Length=236
METSSVSAFKIAVDFVLLAIPGLIALILNLFVTPFQRNFFCNDLSIMYPYKPDTITTLQL
ALVGVIVSVVFVFIVELIHKFNNSYKYDDDDDKESKILYKWNISPFIQNLYQYIGLLLFG
ISINQFITDGTKFVVGRLRPHFMDVCRPVLSNGLTCKDLDNWNTYISDYTCTNQDVSDWT
LTNARISFPSGHASFSFYFLYSIANEIWRVKAFETFYSISVCHSCSLYWLITNYGL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g5318.t12 | Gene3D | G3DSA:1.20.144.10 | - | 10 | 231 | 2.7E-16 |
| 2 | g5318.t12 | PANTHER | PTHR10165 | LIPID PHOSPHATE PHOSPHATASE | 9 | 201 | 1.8E-47 |
| 3 | g5318.t12 | PANTHER | PTHR10165:SF173 | FI04477P-RELATED | 9 | 201 | 1.8E-47 |
| 1 | g5318.t12 | Pfam | PF01569 | PAP2 superfamily | 116 | 218 | 1.8E-11 |
| 10 | g5318.t12 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 11 | - |
| 14 | g5318.t12 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 12 | 35 | - |
| 12 | g5318.t12 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 36 | 54 | - |
| 13 | g5318.t12 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 55 | 78 | - |
| 11 | g5318.t12 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 79 | 236 | - |
| 8 | g5318.t12 | SMART | SM00014 | acid_phosph_2 | 114 | 230 | 4.5E-5 |
| 7 | g5318.t12 | SUPERFAMILY | SSF48317 | Acid phosphatase/Vanadium-dependent haloperoxidase | 26 | 220 | 1.57E-13 |
| 5 | g5318.t12 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 13 | 35 | - |
| 4 | g5318.t12 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 55 | 77 | - |
| 6 | g5318.t12 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 106 | 128 | - |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5318/g5318.t12; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5318.t12.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