General information for g4140.t10
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Phospholipid phosphatase 5.
Parent gene
- The parent gene g4140 is located on chr_3: 30906000..30906789 (+ 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_3 | g4140 | g4140.t10 | TSS | g4140.t10 | 30903892 | 30903892 |
| chr_3 | g4140 | g4140.t10 | isoform | g4140.t10 | 30904128 | 30906789 |
| chr_3 | g4140 | g4140.t10 | exon | g4140.t10.exon1 | 30904128 | 30904267 |
| chr_3 | g4140 | g4140.t10 | exon | g4140.t10.exon2 | 30905882 | 30905939 |
| chr_3 | g4140 | g4140.t10 | exon | g4140.t10.exon3 | 30906000 | 30906111 |
| chr_3 | g4140 | g4140.t10 | exon | g4140.t10.exon4 | 30906242 | 30906515 |
| chr_3 | g4140 | g4140.t10 | cds | g4140.t10.CDS1 | 30906302 | 30906515 |
| chr_3 | g4140 | g4140.t10 | exon | g4140.t10.exon5 | 30906581 | 30906789 |
| chr_3 | g4140 | g4140.t10 | cds | g4140.t10.CDS2 | 30906581 | 30906789 |
| chr_3 | g4140 | g4140.t10 | TTS | g4140.t10 | 30906883 | 30906883 |
Sequences
>g4140.t10 Gene=g4140 Length=793
ATGCTACGAAATATAAAATCTAAAATATACATATGGATTGAAATTATTATAAGGCTTGCT
CTCTTTGTAGCTTTTTTGAAATTAGAGACATTAGAGCCTTTTCAAAGGAAAATTTTAGCT
GATGATTTATGGAATTATCGTTATCCTAATAAAAAATCATACGTTCCAGTTACATTGTTA
TGGCCAATTCTCACTCTTATCCCAACTTTTGTGTTTATTTTAAATTATATTTTTACGAGA
CATTCAAAAGATTTAAAAGCAGCTATGCTTGGTCATACTTTAGCATTTGGACTTAATGGT
GTTTTAGTAGAACGATATGTTAACTATACACAGACCTGATTTTTTTGAACGATGTTGGCC
AGACGGAATAATGAATTCTGAAATGATATGCACAGGAGAATATTGGTCAGTTTTGGATGG
CAGGAAAAGTTTCCCGAGCGGTCATTCCTCATTCTCATTCGCTAGTTTAGGATTTTTGAC
TTTTTATTTAATTGGAAAGTTGAAAATATTTTCGGATGAAGGAAGAGGAAACAGTTTAAA
ACTTATAATTTCATTTTTTCCTTTTATTGTTGCCATGTTAATAGCAATATCAAGAACATG
TGACTATCATCATTGGAAAGAAGATGTTGTCGTTGGAAGTTTAATTGGTATTTTAATTGC
ATATTTATGCTATCGACAATTTTTTCCACCACTTGCGAGTAAAAAATCAAATTTATGCTA
TGAAATGCTTTACCATCTTTCTGCTACAAATGACTCAAATGATCTTCTCGAAAAAGACAT
TAAATGGATCTAA
>g4140.t10 Gene=g4140 Length=140
MNSEMICTGEYWSVLDGRKSFPSGHSSFSFASLGFLTFYLIGKLKIFSDEGRGNSLKLII
SFFPFIVAMLIAISRTCDYHHWKEDVVVGSLIGILIAYLCYRQFFPPLASKKSNLCYEML
YHLSATNDSNDLLEKDIKWI
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g4140.t10 | Gene3D | G3DSA:1.20.144.10 | - | 6 | 125 | 2.7E-24 |
| 2 | g4140.t10 | PANTHER | PTHR10165 | LIPID PHOSPHATE PHOSPHATASE | 1 | 128 | 6.8E-45 |
| 3 | g4140.t10 | PANTHER | PTHR10165:SF87 | PHOSPHOLIPID PHOSPHATASE 5 | 1 | 128 | 6.8E-45 |
| 1 | g4140.t10 | Pfam | PF01569 | PAP2 superfamily | 16 | 105 | 4.6E-24 |
| 13 | g4140.t10 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 23 | - |
| 14 | g4140.t10 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 24 | 42 | - |
| 10 | g4140.t10 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 43 | 53 | - |
| 16 | g4140.t10 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 54 | 74 | - |
| 12 | g4140.t10 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 75 | 85 | - |
| 15 | g4140.t10 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 86 | 105 | - |
| 11 | g4140.t10 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 106 | 140 | - |
| 8 | g4140.t10 | SMART | SM00014 | acid_phosph_2 | 1 | 101 | 4.1E-4 |
| 7 | g4140.t10 | SUPERFAMILY | SSF48317 | Acid phosphatase/Vanadium-dependent haloperoxidase | 3 | 107 | 1.31E-22 |
| 4 | g4140.t10 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 20 | 42 | - |
| 5 | g4140.t10 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 54 | 76 | - |
| 6 | g4140.t10 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 86 | 105 | - |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0042577 | lipid phosphatase activity | MF |
| GO:0046839 | phospholipid dephosphorylation | BP |
| GO:0006644 | phospholipid metabolic process | BP |
| GO:0008195 | phosphatidate phosphatase activity | MF |
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