General information for g5318.t1
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.t1 | TSS | g5318.t1 | 8706373 | 8706373 |
| chr_2 | g5318 | g5318.t1 | isoform | g5318.t1 | 8706418 | 8707617 |
| chr_2 | g5318 | g5318.t1 | exon | g5318.t1.exon1 | 8706418 | 8706478 |
| chr_2 | g5318 | g5318.t1 | cds | g5318.t1.CDS1 | 8706418 | 8706478 |
| chr_2 | g5318 | g5318.t1 | exon | g5318.t1.exon2 | 8706532 | 8706683 |
| chr_2 | g5318 | g5318.t1 | cds | g5318.t1.CDS2 | 8706532 | 8706683 |
| chr_2 | g5318 | g5318.t1 | exon | g5318.t1.exon3 | 8706747 | 8706965 |
| chr_2 | g5318 | g5318.t1 | cds | g5318.t1.CDS3 | 8706747 | 8706965 |
| chr_2 | g5318 | g5318.t1 | exon | g5318.t1.exon4 | 8707130 | 8707309 |
| chr_2 | g5318 | g5318.t1 | cds | g5318.t1.CDS4 | 8707130 | 8707309 |
| chr_2 | g5318 | g5318.t1 | exon | g5318.t1.exon5 | 8707384 | 8707617 |
| chr_2 | g5318 | g5318.t1 | cds | g5318.t1.CDS5 | 8707384 | 8707617 |
| chr_2 | g5318 | g5318.t1 | TTS | g5318.t1 | 8707663 | 8707663 |
Sequences
>g5318.t1 Gene=g5318 Length=846
ATGGAAACATCGAGTGTGAGTGCATTTAAGATTGCAGTTGACTTTGTGCTATTAGCAATA
CCTGGCCTCATTGCTTTAATTTTGAATCTCTTTGTGACTCCATTTCAACGAAATTTCTTC
TGTAATGATTTGTCAATTATGTATCCATATAAACCTGATACAATCACTACATTGCAACTT
GCTCTTGTTGGTGTAATTGTGAGCGTCGTATTTGTATTTATCGTGGAATTAATTCATAAG
TTTAATAATTCATATAAATATGATGATGACGATGATAAAGAGAGCAAAATTCTGTATAAA
TGGAACATTTCACCATTCATTCAGAATTTATATCAGTATATTGGCCTCCTGTTGTTTGGA
ATATCAATCAATCAGTTTATAACTGATGGCACAAAATTTGTTGTTGGACGTTTAAGACCA
CACTTTATGGATGTCTGTCGTCCAGTTTTATCAAATGGATTAACATGCAAAGACTTAGAT
AACTGGAACACTTACATCTCTGACTACACTTGCACTAATCAGGATGTTAGTGATTGGACT
CTCACAAATGCTCGAATTTCATTTCCTTCTGGTCATGCGAGTTTCTCATTCTATTGTTCA
TTTTTCTGTGCATTTTATATTCAATCGCGAATGAAATTTGGAGGGTCAAAGCTTTTGAAA
CATTTTATTCAATTAGTGTTTGTCACAGCTGCTCTTTATACTGGCTTATCACGAATTACG
GACTATAAGCATCATCCAACTGACGTAATAGCTGGCAGTATTTTAGGAATTCTTATTGCA
TTTGTTGTTTGCTTTTATTTTTCTGATTTATTTAAGAGAAAAATTAATAATGTCTTACCG
AGATGA
>g5318.t1 Gene=g5318 Length=281
METSSVSAFKIAVDFVLLAIPGLIALILNLFVTPFQRNFFCNDLSIMYPYKPDTITTLQL
ALVGVIVSVVFVFIVELIHKFNNSYKYDDDDDKESKILYKWNISPFIQNLYQYIGLLLFG
ISINQFITDGTKFVVGRLRPHFMDVCRPVLSNGLTCKDLDNWNTYISDYTCTNQDVSDWT
LTNARISFPSGHASFSFYCSFFCAFYIQSRMKFGGSKLLKHFIQLVFVTAALYTGLSRIT
DYKHHPTDVIAGSILGILIAFVVCFYFSDLFKRKINNVLPR
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 19 | g5318.t1 | CDD | cd03384 | PAP2_wunen | 110 | 264 | 2.68837E-57 |
| 5 | g5318.t1 | Gene3D | G3DSA:1.20.144.10 | - | 9 | 279 | 5.5E-38 |
| 2 | g5318.t1 | PANTHER | PTHR10165 | LIPID PHOSPHATE PHOSPHATASE | 9 | 274 | 7.7E-78 |
| 3 | g5318.t1 | PANTHER | PTHR10165:SF173 | FI04477P-RELATED | 9 | 274 | 7.7E-78 |
| 1 | g5318.t1 | Pfam | PF01569 | PAP2 superfamily | 116 | 268 | 3.9E-27 |
| 6 | g5318.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 11 | - |
| 16 | g5318.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 12 | 35 | - |
| 10 | g5318.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 36 | 54 | - |
| 14 | g5318.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 55 | 78 | - |
| 8 | g5318.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 79 | 109 | - |
| 17 | g5318.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 110 | 127 | - |
| 12 | g5318.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 128 | 185 | - |
| 18 | g5318.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 186 | 207 | - |
| 7 | g5318.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 208 | 218 | - |
| 15 | g5318.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 219 | 237 | - |
| 11 | g5318.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 238 | 248 | - |
| 13 | g5318.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 249 | 271 | - |
| 9 | g5318.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 272 | 281 | - |
| 26 | g5318.t1 | SMART | SM00014 | acid_phosph_2 | 114 | 264 | 7.7E-38 |
| 4 | g5318.t1 | SUPERFAMILY | SSF48317 | Acid phosphatase/Vanadium-dependent haloperoxidase | 27 | 267 | 4.06E-28 |
| 23 | g5318.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 13 | 35 | - |
| 20 | g5318.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 55 | 77 | - |
| 24 | g5318.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 106 | 128 | - |
| 21 | g5318.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 186 | 208 | - |
| 25 | g5318.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 221 | 239 | - |
| 22 | g5318.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 249 | 271 | - |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5318/g5318.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5318.t1.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 transcript has been annotated with K01080 (phosphatidate phosphatase)
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.
