General information for g13362.t12
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Acidic phospholipase A2 PA4.
Parent gene
- The parent gene g13362 is located on chr_1: 29520833..29521109 (+ 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_1 | g13362 | g13362.t12 | isoform | g13362.t12 | 29516041 | 29521109 |
| chr_1 | g13362 | g13362.t12 | exon | g13362.t12.exon1 | 29516041 | 29516378 |
| chr_1 | g13362 | g13362.t12 | exon | g13362.t12.exon2 | 29517064 | 29517375 |
| chr_1 | g13362 | g13362.t12 | cds | g13362.t12.CDS1 | 29517107 | 29517375 |
| chr_1 | g13362 | g13362.t12 | exon | g13362.t12.exon3 | 29517891 | 29518352 |
| chr_1 | g13362 | g13362.t12 | cds | g13362.t12.CDS2 | 29517891 | 29518352 |
| chr_1 | g13362 | g13362.t12 | exon | g13362.t12.exon4 | 29518532 | 29518750 |
| chr_1 | g13362 | g13362.t12 | cds | g13362.t12.CDS3 | 29518532 | 29518750 |
| chr_1 | g13362 | g13362.t12 | exon | g13362.t12.exon5 | 29520843 | 29520940 |
| chr_1 | g13362 | g13362.t12 | cds | g13362.t12.CDS4 | 29520843 | 29520940 |
| chr_1 | g13362 | g13362.t12 | exon | g13362.t12.exon6 | 29521011 | 29521109 |
| chr_1 | g13362 | g13362.t12 | cds | g13362.t12.CDS5 | 29521011 | 29521096 |
| chr_1 | g13362 | g13362.t12 | TTS | g13362.t12 | 29521376 | 29521376 |
| chr_1 | g13362 | g13362.t12 | TSS | g13362.t12 | NA | NA |
Sequences
>g13362.t12 Gene=g13362 Length=1528
ATGGTGAGAGAAATTTTCCGCAATTCTTACTCTCATTCCTCTCTTCGCAGCATGTTAAGC
ATGAGTATTTTTATCTTCTTAATTTTTTTTTCATTTCTACCTATTACTCGTACGATATAT
CCACGCGTTACGATTTGCACTCTTCAGTTCTATTTTATCGTTCAAACTATTCAGACGTGT
ATCGTTTTTGTATGATTCATTTTATGCGGTCTTATATTGCAATAGTTATGTGATGTTTAA
AAAGTTATTCAATAATAAAATTATCAAGTATTTTTATTAAAATAAAAGTGATAGTCATTA
CAATTGTGATTTATTTCAAAATAGATCTCTGTTCAAAGGAATATTGTATTACAAATATTT
AATAAACAAGTGGACAAAGTGATGACGAACATTTATCATGAAAAATATTTTTTCTTATAC
ATCATTGTCTTTATAATATGCATTATCAATCAATGTACAAGCATTAGTGATTTAAATCAT
TCAAATTATAAAAATGAAAATAAAAATTTCACACATCATCAGCAAAAAGACAATTTTCTT
ATCATTGATCATCTCAATGATAACGAACGAGAGACGAGACTAAAATGGAAAAATCTCATG
GGAAAGGAAACGACACTTGATATGGACAACAATGAAAGATTTGTTAACAGTTCTTTGAAA
TTAACGTCTCTATGGCAACTGACAGATGGCAAAGATTTTGCACAACTCATTTTTAATGGT
AATAGTCTCATCGATTGTGAAAATATTGATAATGGAAATGATATCATTGGTGATTTCGTG
AGTAAATTCATTGAAGAATATCAATTTATCCGTCATGAGAAATTAAGTAGTACAAAACAT
GCAAAGAAGCATCATCAATACCAACAGAATGCGAATCTTAATGAAGAAGTACTTAAAATG
AAGTCAAATGTAAAGTTTATTCAACTGAAAAAATTACAAGATATTCCCGAGCATTTACTC
AGGCTCATGAATTTGAAAAAATTGAAAAAACAATGCAATCGTTTGCATAAAAAAATAAAA
CAAAAATTGCAACAACAACATCATCATCATACGGTCGATGAAGAAGAAGATGAAGAAGAT
TTTAATGCCAAAAATGAAAATATGATACACAGAACAAAACGTCAAACTGACTCATGGTTT
TTGGCACCAAATTCGAAATGGTGTGGTAGTGGAAGTAGTGCTAATGGTTATAAAGAACTG
GGTCCTTCAAAAGCTGACACATGCTGTCGAAGACATGACATTTGTAAAGTTAATATACCA
CCACTTGAGAAGCGTTATAATCTTTTTAATATTAGGCCATTTACTATAAGTGCATGTCGT
TGCGATAGAAGATTCAGAACGTGCTTAAAGATTGCAGATAGTAACGACAGTCACTTAGTT
GGAAAATTATTTTTCAATATCATTCAAACTAAATGCTTCGTGCTGGTAAAAATCAGTGCA
GGAGTGTATTTTATACAGTTGGTGGGGAAAATGTTTGAAATTCAAGACCAAGAAGCAAGC
GTATCTTCGAGATAATCCAAAGTACTAA
>g13362.t12 Gene=g13362 Length=377
MTNIYHEKYFFLYIIVFIICIINQCTSISDLNHSNYKNENKNFTHHQQKDNFLIIDHLND
NERETRLKWKNLMGKETTLDMDNNERFVNSSLKLTSLWQLTDGKDFAQLIFNGNSLIDCE
NIDNGNDIIGDFVSKFIEEYQFIRHEKLSSTKHAKKHHQYQQNANLNEEVLKMKSNVKFI
QLKKLQDIPEHLLRLMNLKKLKKQCNRLHKKIKQKLQQQHHHHTVDEEEDEEDFNAKNEN
MIHRTKRQTDSWFLAPNSKWCGSGSSANGYKELGPSKADTCCRRHDICKVNIPPLEKRYN
LFNIRPFTISACRCDRRFRTCLKIADSNDSHLVGKLFFNIIQTKCFVLVKISAGVYFIQL
VGKMFEIQDQEASVSSR
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g13362.t12 | Coils | Coil | Coil | 163 | 183 | - |
| 6 | g13362.t12 | Coils | Coil | Coil | 195 | 218 | - |
| 5 | g13362.t12 | Gene3D | G3DSA:1.20.90.10 | Phospholipase A2 | 253 | 369 | 4.2E-33 |
| 13 | g13362.t12 | MobiDBLite | mobidb-lite | consensus disorder prediction | 214 | 234 | - |
| 2 | g13362.t12 | PANTHER | PTHR12253:SF33 | PHOSPHOLIPASE A2 GROUP III, ISOFORM B | 175 | 348 | 2.1E-47 |
| 3 | g13362.t12 | PANTHER | PTHR12253 | RH14732P | 175 | 348 | 2.1E-47 |
| 1 | g13362.t12 | Pfam | PF05826 | Phospholipase A2 | 255 | 347 | 1.1E-32 |
| 8 | g13362.t12 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 8 | - |
| 10 | g13362.t12 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 9 | 29 | - |
| 9 | g13362.t12 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 30 | 377 | - |
| 12 | g13362.t12 | ProSitePatterns | PS00118 | Phospholipase A2 histidine active site. | 281 | 288 | - |
| 4 | g13362.t12 | SUPERFAMILY | SSF48619 | Phospholipase A2, PLA2 | 254 | 346 | 1.71E-26 |
| 11 | g13362.t12 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 9 | 28 | - |
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:0050482 | arachidonic acid secretion | BP |
| GO:0006644 | phospholipid metabolic process | BP |
| GO:0004623 | phospholipase A2 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.
