General information for g5318.t17
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.t17 | TSS | g5318.t17 | 8706373 | 8706373 |
| chr_2 | g5318 | g5318.t17 | isoform | g5318.t17 | 8706418 | 8707617 |
| chr_2 | g5318 | g5318.t17 | exon | g5318.t17.exon1 | 8706418 | 8706482 |
| chr_2 | g5318 | g5318.t17 | exon | g5318.t17.exon2 | 8706532 | 8706683 |
| chr_2 | g5318 | g5318.t17 | cds | g5318.t17.CDS1 | 8706609 | 8706683 |
| chr_2 | g5318 | g5318.t17 | exon | g5318.t17.exon3 | 8706747 | 8706965 |
| chr_2 | g5318 | g5318.t17 | cds | g5318.t17.CDS2 | 8706747 | 8706965 |
| chr_2 | g5318 | g5318.t17 | exon | g5318.t17.exon4 | 8707130 | 8707309 |
| chr_2 | g5318 | g5318.t17 | cds | g5318.t17.CDS3 | 8707130 | 8707309 |
| chr_2 | g5318 | g5318.t17 | exon | g5318.t17.exon5 | 8707384 | 8707617 |
| chr_2 | g5318 | g5318.t17 | cds | g5318.t17.CDS4 | 8707384 | 8707617 |
| chr_2 | g5318 | g5318.t17 | TTS | g5318.t17 | 8707663 | 8707663 |
Sequences
>g5318.t17 Gene=g5318 Length=850
ATGGAAACATCGAGTGTGAGTGCATTTAAGATTGCAGTTGACTTTGTGCTATTAGCAATA
CGTGACTGGCCTCATTGCTTTAATTTTGAATCTCTTTGTGACTCCATTTCAACGAAATTT
CTTCTGTAATGATTTGTCAATTATGTATCCATATAAACCTGATACAATCACTACATTGCA
ACTTGCTCTTGTTGGTGTAATTGTGAGCGTCGTATTTGTATTTATCGTGGAATTAATTCA
TAAGTTTAATAATTCATATAAATATGATGATGACGATGATAAAGAGAGCAAAATTCTGTA
TAAATGGAACATTTCACCATTCATTCAGAATTTATATCAGTATATTGGCCTCCTGTTGTT
TGGAATATCAATCAATCAGTTTATAACTGATGGCACAAAATTTGTTGTTGGACGTTTAAG
ACCACACTTTATGGATGTCTGTCGTCCAGTTTTATCAAATGGATTAACATGCAAAGACTT
AGATAACTGGAACACTTACATCTCTGACTACACTTGCACTAATCAGGATGTTAGTGATTG
GACTCTCACAAATGCTCGAATTTCATTTCCTTCTGGTCATGCGAGTTTCTCATTCTATTG
TTCATTTTTCTGTGCATTTTATATTCAATCGCGAATGAAATTTGGAGGGTCAAAGCTTTT
GAAACATTTTATTCAATTAGTGTTTGTCACAGCTGCTCTTTATACTGGCTTATCACGAAT
TACGGACTATAAGCATCATCCAACTGACGTAATAGCTGGCAGTATTTTAGGAATTCTTAT
TGCATTTGTTGTTTGCTTTTATTTTTCTGATTTATTTAAGAGAAAAATTAATAATGTCTT
ACCGAGATGA
>g5318.t17 Gene=g5318 Length=235
MYPYKPDTITTLQLALVGVIVSVVFVFIVELIHKFNNSYKYDDDDDKESKILYKWNISPF
IQNLYQYIGLLLFGISINQFITDGTKFVVGRLRPHFMDVCRPVLSNGLTCKDLDNWNTYI
SDYTCTNQDVSDWTLTNARISFPSGHASFSFYCSFFCAFYIQSRMKFGGSKLLKHFIQLV
FVTAALYTGLSRITDYKHHPTDVIAGSILGILIAFVVCFYFSDLFKRKINNVLPR
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 17 | g5318.t17 | CDD | cd03384 | PAP2_wunen | 64 | 218 | 2.43795E-58 |
| 5 | g5318.t17 | Gene3D | G3DSA:1.20.144.10 | - | 9 | 233 | 1.5E-38 |
| 2 | g5318.t17 | PANTHER | PTHR10165 | LIPID PHOSPHATE PHOSPHATASE | 1 | 228 | 4.9E-66 |
| 3 | g5318.t17 | PANTHER | PTHR10165:SF173 | FI04477P-RELATED | 1 | 228 | 4.9E-66 |
| 1 | g5318.t17 | Pfam | PF01569 | PAP2 superfamily | 70 | 222 | 2.4E-27 |
| 9 | g5318.t17 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 11 | - |
| 14 | g5318.t17 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 12 | 32 | - |
| 6 | g5318.t17 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 33 | 63 | - |
| 12 | g5318.t17 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 64 | 81 | - |
| 11 | g5318.t17 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 82 | 139 | - |
| 13 | g5318.t17 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 140 | 161 | - |
| 7 | g5318.t17 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 162 | 172 | - |
| 15 | g5318.t17 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 173 | 191 | - |
| 10 | g5318.t17 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 192 | 202 | - |
| 16 | g5318.t17 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 203 | 225 | - |
| 8 | g5318.t17 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 226 | 235 | - |
| 23 | g5318.t17 | SMART | SM00014 | acid_phosph_2 | 68 | 218 | 7.7E-38 |
| 4 | g5318.t17 | SUPERFAMILY | SSF48317 | Acid phosphatase/Vanadium-dependent haloperoxidase | 64 | 221 | 9.94E-28 |
| 22 | g5318.t17 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 10 | 32 | - |
| 19 | g5318.t17 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 60 | 82 | - |
| 20 | g5318.t17 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 140 | 162 | - |
| 18 | g5318.t17 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 175 | 193 | - |
| 21 | g5318.t17 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 203 | 225 | - |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5318/g5318.t17; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5318.t17.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