General information for g4399.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as 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.t2 | TSS | g4399.t2 | 1966834 | 1966834 |
| chr_2 | g4399 | g4399.t2 | isoform | g4399.t2 | 1967482 | 1973006 |
| chr_2 | g4399 | g4399.t2 | exon | g4399.t2.exon1 | 1967482 | 1968081 |
| chr_2 | g4399 | g4399.t2 | cds | g4399.t2.CDS1 | 1967961 | 1968081 |
| chr_2 | g4399 | g4399.t2 | exon | g4399.t2.exon2 | 1970436 | 1970679 |
| chr_2 | g4399 | g4399.t2 | cds | g4399.t2.CDS2 | 1970436 | 1970679 |
| chr_2 | g4399 | g4399.t2 | exon | g4399.t2.exon3 | 1970738 | 1970868 |
| chr_2 | g4399 | g4399.t2 | cds | g4399.t2.CDS3 | 1970738 | 1970868 |
| chr_2 | g4399 | g4399.t2 | exon | g4399.t2.exon4 | 1970943 | 1971141 |
| chr_2 | g4399 | g4399.t2 | cds | g4399.t2.CDS4 | 1970943 | 1971141 |
| chr_2 | g4399 | g4399.t2 | exon | g4399.t2.exon5 | 1971200 | 1971523 |
| chr_2 | g4399 | g4399.t2 | cds | g4399.t2.CDS5 | 1971200 | 1971523 |
| chr_2 | g4399 | g4399.t2 | exon | g4399.t2.exon6 | 1971582 | 1973006 |
| chr_2 | g4399 | g4399.t2 | cds | g4399.t2.CDS6 | 1971582 | 1971798 |
| chr_2 | g4399 | g4399.t2 | TTS | g4399.t2 | 1972983 | 1972983 |
Sequences
>g4399.t2 Gene=g4399 Length=2923
ATTAAACAACTAAAAATTATTTTTATTTCTTTTCTTTCATTTAAATGAATCATGAACCTT
TTACTTTTCACCACCACAATCGTGTAGATTCACTATTTTTCGATTTTATTTTTTTTTTAA
ATTTAATTTTTTATAAGCATCAAATTTTTTTAAGAAATTTTTTAAAAAAATTTTATTATT
TTTTTAATTTAACCTAATTTATATTATACATAATCCATCATATTTAAAAAGTTTAAATTG
GTGAATTTAGGGTGTGCATAACGGTGTTAAAGTTCAAAAATATTTAGTCTCTTCGGTAAC
CATCATCAATCAGTTGTTTTCATTGTTTGTTATATGACATCTATAAAAAAATCGTTTTAG
TGAAAAACACTGCAATTATTGACATAGTGAAATTTTAAAACAATAGAGAAATAAATTCGT
AAAATTTTAAGTTGAAAAGACTCGTTTATCATTTATAATTTTATTTAAAAAAAGAGAAAA
TGATGCGAGTGTTTATTTCTTTTTTTTGTATTCTTATCATTTTTGCAAATTATGATAAAA
TTAATGCTGCCTTTGTTGTGAAGAAAGGACCCCAAAAGCCAATTTCACCCGTTATTTTTG
TTCCGGGAGATGGTGGTACACAAGTGGATGCAAAGCTCAATAAACCATCAACTAGGCATA
TTTTCTGTACAAAAACGACAAAAGACTATTTCAATGTATGGCTTAATTTAGAACTTATGG
CACCATTAATTATTGACTGCTGGACAGATAATGTAAAACTTTATTACAATAATGAAACTC
GAACAACAAGTAACTCGCCAGGTGTTGAATTAAGAATCCCAAGATGGGGTGATCCTGAAG
TTGTTGAATGGATCGATCCATCAAAAAACCATATTGGTGCATATTTCAAATCTATTGCAA
ATGGTCTCGTTCAAAATGGCTACGTCAGAAATGTTTCAATTCGTGGTGCACCATATGATT
TCAGAAAGGGACCATCTGAATTGGGTCAATATTTCATTGATTTAAAACAACTCGTAGAAG
AAACATATGAGATGAATTCGCAAGTGCCTGTAACTTTAATTGCACATTCAATGGGCGCAC
CGATTTTGATGATTTTCTTGCAACAACAAAATGAAAAATGGAAGGAAAAGTATATCGCTC
GAATGATCACAATTGCAGGTGCTTATGGTGGAAGTGTAAAGACAGTAAAAGTTTTTGCTG
TAGGAGATGACCTCGGTTCACTCGGGTTGTTTGCTAGTGAAATGAGAGAGGCACAAATTT
CTATGGCTTCACTTTCATTCTTACTTCCGTTTCCGACTTTCTGGAAGCCAAATGAAGTGC
TTGTGACAACACGCAAAAGAAATTACACTCACAGTCAATTGAATGAATTTTTTGATGATC
TGGGCTATCCTCAAGGTTGGGAAATGAGAAAAGATAATTTGAAATTTGTTGAAAATTTCG
CTGCACCAAATGTTGAAATACATTGCCTTTATTCAACAAAAATGCCAACTATTGAACAAT
TGCATTATAAAACAGATGACTTGTCGGGTTCACCATCATTATTGTATGGTAACGGAGATG
GCTCTGTTAATATTAGAAGCTTAGAAGGCTGCACATATTGGCGAAATTTACAGAAGCAAC
CTATCACAACTCTTGAAATACCAAATACTGAACATTTTGCACTTTTACAACATCCCAGAA
TTGTCTCTTATATTTTGGACGTTTTGGTCAATTAATTTTAAGATCTGTTATGACTCTATT
CAATGTGATGAAACGAATTTCGAAAAAAATTGATATTATCAGACTTTTATCCCAATACCA
AAATTGAAATTATCAACAAATTATTAAATTTATTATAAGCTTAAAATTTATTTCATTCAA
TATCTTTAAATATTTACAAAAAATTTCTAACAATAACTAACTAAATTTTTAAGTTTTCTT
CTCTTTCATACAAATTGGTCTCTTTCTCTCATTCTTTCATACAGTCATTAACTTTTTTTA
TTCTTTAAAAAAATACACATTACTAAATACTTTTTGGACAAAATAGCAAATACGACTGGA
AATTATAATGAGCGTAAAAATAATGTTTTCTTCTATCTCACGCTGATTCCATTTATTGTA
ATGATATTTCCTCTATTCGGTTCTGGCTCATACATTTCTTCATTCACTCTCATTTCATAT
GGTTGATCGTAAATGGTCGTCTCGTTGGGTATTTGATCGTAAATATTTTCTGACCTAAGG
CTGTTAACACTACTTAAATTACTATTATTTATGACTGGTGATTGAAATGTATTAAATGTT
GCTGATCTATTATGTAAATCAAAGTTTGCACGCTGATTCTCGATACTCGAGTATGACATC
ACAGCAGCATTTTGATCTTCTTTTCGCTCAGCTGCTTGCACATTTTCTGAATTCTTTACT
GGTCTCGATTTGTTTCTAAAATTTGATATACTGGCGCTGAGAAATTGTTTTCTTTAATCA
AATATTTACATCAAGCAAATAATCAAAAAAGTTTTTTTACTTACCGATGAAGGAACACAA
TGAGAATAAAAATAAGCAATATAACAATAACAGCTGCTGAAATTGCAACTCCAGTTCCAA
AATTGTCTTCATTTTGAGCATCATTCACAGCCACTAAAATTTTTTTTTTAAAAAAATTAG
AATCAATTAAAAATTAATATCATTATTACTCACATTCACATCGTGGTTCATCACCACTCC
ATTTTCCATCTTCCATACACTTTCTCAAATATGGGCCAATTCGATTATAATTTGGTATGC
AATGATATTCTGCTGATCCTCCATAGGTTGTTATATCATTAACAATTATCACACGACCAT
TTTCAACTTCATTTGGTCGTTCGCAATCAACAGCTGTGAAAAATTAAGTTTGTCAAATAA
AAAATTCTATTTAGAAAAATTAATTTTCTGTGTTTTTCTTACG
>g4399.t2 Gene=g4399 Length=411
MMRVFISFFCILIIFANYDKINAAFVVKKGPQKPISPVIFVPGDGGTQVDAKLNKPSTRH
IFCTKTTKDYFNVWLNLELMAPLIIDCWTDNVKLYYNNETRTTSNSPGVELRIPRWGDPE
VVEWIDPSKNHIGAYFKSIANGLVQNGYVRNVSIRGAPYDFRKGPSELGQYFIDLKQLVE
ETYEMNSQVPVTLIAHSMGAPILMIFLQQQNEKWKEKYIARMITIAGAYGGSVKTVKVFA
VGDDLGSLGLFASEMREAQISMASLSFLLPFPTFWKPNEVLVTTRKRNYTHSQLNEFFDD
LGYPQGWEMRKDNLKFVENFAAPNVEIHCLYSTKMPTIEQLHYKTDDLSGSPSLLYGNGD
GSVNIRSLEGCTYWRNLQKQPITTLEIPNTEHFALLQHPRIVSYILDVLVN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 3 | g4399.t2 | PANTHER | PTHR11440:SF47 | GROUP XV PHOSPHOLIPASE A2 | 12 | 410 | 5.2E-115 |
| 4 | g4399.t2 | PANTHER | PTHR11440 | LECITHIN-CHOLESTEROL ACYLTRANSFERASE-RELATED | 12 | 410 | 5.2E-115 |
| 1 | g4399.t2 | Pfam | PF02450 | Lecithin:cholesterol acyltransferase | 70 | 301 | 1.9E-56 |
| 2 | g4399.t2 | Pfam | PF02450 | Lecithin:cholesterol acyltransferase | 321 | 396 | 2.2E-7 |
| 8 | g4399.t2 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 23 | - |
| 9 | g4399.t2 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 3 | - |
| 10 | g4399.t2 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 4 | 15 | - |
| 11 | g4399.t2 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 16 | 23 | - |
| 7 | g4399.t2 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 24 | 411 | - |
| 5 | g4399.t2 | SUPERFAMILY | SSF53474 | alpha/beta-Hydrolases | 37 | 405 | 2.38E-28 |
| 6 | g4399.t2 | SignalP_EUK | SignalP-noTM | SignalP-noTM | 1 | 23 | - |
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 transcript has been annotated with K06129 (lysophospholipase III)
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.
