General information for g4399.t8
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Phospholipase A2 group XV.
Parent gene
- The parent gene g4399 is located on chr_2: 1971798..1973006 (+ 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 | g4399 | g4399.t8 | TSS | g4399.t8 | 1970119 | 1970119 |
| chr_2 | g4399 | g4399.t8 | isoform | g4399.t8 | 1970836 | 1971798 |
| chr_2 | g4399 | g4399.t8 | exon | g4399.t8.exon1 | 1970836 | 1970868 |
| chr_2 | g4399 | g4399.t8 | exon | g4399.t8.exon2 | 1970943 | 1971141 |
| chr_2 | g4399 | g4399.t8 | cds | g4399.t8.CDS1 | 1970999 | 1971141 |
| chr_2 | g4399 | g4399.t8 | exon | g4399.t8.exon3 | 1971200 | 1971523 |
| chr_2 | g4399 | g4399.t8 | cds | g4399.t8.CDS2 | 1971200 | 1971523 |
| chr_2 | g4399 | g4399.t8 | exon | g4399.t8.exon4 | 1971582 | 1971798 |
| chr_2 | g4399 | g4399.t8 | cds | g4399.t8.CDS3 | 1971582 | 1971798 |
| chr_2 | g4399 | g4399.t8 | TTS | g4399.t8 | 1971936 | 1971936 |
Sequences
>g4399.t8 Gene=g4399 Length=773
GTGGTGCACCATATGATTTCAGAAAGGGACCATCTGAATTGGGTCAATATTTCATTGATT
TAAAACAACTCGTAGAAGAAACATATGAGATGAATTCGCAAGTGCCTGTAACTTTAATTG
CACATTCAATGGGCGCACCGATTTTGATGATTTTCTTGCAACAACAAAATGAAAAATGGA
AGGAAAAGTATATCGCTCGAATGATCACAATTGCAGGTGCTTATGGTGGAAGTGTAAAGA
CAGTAAAAGTTTTTGCTGTAGGAGATGACCTCGGTTCACTCGGGTTGTTTGCTAGTGAAA
TGAGAGAGGCACAAATTTCTATGGCTTCACTTTCATTCTTACTTCCGTTTCCGACTTTCT
GGAAGCCAAATGAAGTGCTTGTGACAACACGCAAAAGAAATTACACTCACAGTCAATTGA
ATGAATTTTTTGATGATCTGGGCTATCCTCAAGGTTGGGAAATGAGAAAAGATAATTTGA
AATTTGTTGAAAATTTCGCTGCACCAAATGTTGAAATACATTGCCTTTATTCAACAAAAA
TGCCAACTATTGAACAATTGCATTATAAAACAGATGACTTGTCGGGTTCACCATCATTAT
TGTATGGTAACGGAGATGGCTCTGTTAATATTAGAAGCTTAGAAGGCTGCACATATTGGC
GAAATTTACAGAAGCAACCTATCACAACTCTTGAAATACCAAATACTGAACATTTTGCAC
TTTTACAACATCCCAGAATTGTCTCTTATATTTTGGACGTTTTGGTCAATTAA
>g4399.t8 Gene=g4399 Length=227
MNSQVPVTLIAHSMGAPILMIFLQQQNEKWKEKYIARMITIAGAYGGSVKTVKVFAVGDD
LGSLGLFASEMREAQISMASLSFLLPFPTFWKPNEVLVTTRKRNYTHSQLNEFFDDLGYP
QGWEMRKDNLKFVENFAAPNVEIHCLYSTKMPTIEQLHYKTDDLSGSPSLLYGNGDGSVN
IRSLEGCTYWRNLQKQPITTLEIPNTEHFALLQHPRIVSYILDVLVN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 3 | g4399.t8 | PANTHER | PTHR11440:SF47 | GROUP XV PHOSPHOLIPASE A2 | 4 | 226 | 4.1E-52 |
| 4 | g4399.t8 | PANTHER | PTHR11440 | LECITHIN-CHOLESTEROL ACYLTRANSFERASE-RELATED | 4 | 226 | 4.1E-52 |
| 2 | g4399.t8 | Pfam | PF02450 | Lecithin:cholesterol acyltransferase | 3 | 117 | 2.2E-23 |
| 1 | g4399.t8 | Pfam | PF02450 | Lecithin:cholesterol acyltransferase | 137 | 212 | 8.2E-8 |
| 7 | g4399.t8 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 5 | - |
| 8 | g4399.t8 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 6 | 23 | - |
| 6 | g4399.t8 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 24 | 227 | - |
| 5 | g4399.t8 | SUPERFAMILY | SSF53474 | alpha/beta-Hydrolases | 6 | 221 | 1.03E-22 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
## Warning: Removed 1 row(s) containing missing values (geom_path).
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0008374 | O-acyltransferase activity | MF |
| GO:0006629 | lipid 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.
