General information for g12090.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative 1-acyl-sn-glycerol-3-phosphate acyltransferase alpha.
Parent gene
- The parent gene g12090 is located on chr_1: 20884993..20886600 (- 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 | g12090 | g12090.t1 | isoform | g12090.t1 | 20884993 | 20886600 |
| chr_1 | g12090 | g12090.t1 | exon | g12090.t1.exon1 | 20884993 | 20885288 |
| chr_1 | g12090 | g12090.t1 | cds | g12090.t1.CDS1 | 20884993 | 20885288 |
| chr_1 | g12090 | g12090.t1 | exon | g12090.t1.exon2 | 20885352 | 20885467 |
| chr_1 | g12090 | g12090.t1 | cds | g12090.t1.CDS2 | 20885352 | 20885467 |
| chr_1 | g12090 | g12090.t1 | exon | g12090.t1.exon3 | 20885764 | 20885845 |
| chr_1 | g12090 | g12090.t1 | cds | g12090.t1.CDS3 | 20885764 | 20885845 |
| chr_1 | g12090 | g12090.t1 | exon | g12090.t1.exon4 | 20886206 | 20886330 |
| chr_1 | g12090 | g12090.t1 | cds | g12090.t1.CDS4 | 20886206 | 20886330 |
| chr_1 | g12090 | g12090.t1 | exon | g12090.t1.exon5 | 20886413 | 20886600 |
| chr_1 | g12090 | g12090.t1 | cds | g12090.t1.CDS5 | 20886413 | 20886600 |
| chr_1 | g12090 | g12090.t1 | TSS | g12090.t1 | 20887418 | 20887418 |
| chr_1 | g12090 | g12090.t1 | TTS | g12090.t1 | NA | NA |
Sequences
>g12090.t1 Gene=g12090 Length=807
ATGGACTACTGCACTTTAATTGCAATTTTCTGCATCTTTTTATTATTAATATTAATTCGA
AAAGCAAATCAATCGTCCAAAGCAATTTATTATCTTAAACATATTTATTATTATGGTTTA
ACTAGTATTTGTGCATTTTTATGGATCCCATATTTTGCTTTACGAGCTAAAGACACAATG
AATTTATTAACAGCTGCAACAATTCTTGGACCAATAAGTAAAGTAATAAGTATGAAATGG
GAACTTCGTGGAAAAGAATATTTAAGCAAGAACAAAACTGTGATTATGATAGCAAATCAT
CAAAGCTCATTGGCCATTTGGCACGTGATGGGAAGAACAACCGTTATAGCAAAAAAAGAG
ATTTTTTATGTTTGGCCGTTTGGCCTTGCTGCTTGGTTATGCGGTTTAATATTCATAAAC
AAACAATCAGCAACTGAAAGTAAGAGTATAATGTATGATGCAATGGAAAGATTAAAGCGT
GAGAATATTAAACTGTGGGTTTTTCCAGAAGGCACGCGACGTAACACAAACGAAATTCAT
AAGTTCAAAAAAGGAGCATTTCATTTAGCAATTCAAACAAAGACACCTATCATGCCAATT
GTATATAGCTCATATCAAACTTTTCTTAATGATAATGAAAAAATATTAAAGCCCGGAGAA
GTAATTATAGAAGCATTGCCAGAAATAAACACAGAAAATTATACAACCGATAAAATAGAC
GAGCTCATCGATAAAACACGCAATGTCATGATCGAAGTATTCAATCGAAACTCATTAGAA
ATAAAAAATCGCATGCAATGTTCTTAA
>g12090.t1 Gene=g12090 Length=268
MDYCTLIAIFCIFLLLILIRKANQSSKAIYYLKHIYYYGLTSICAFLWIPYFALRAKDTM
NLLTAATILGPISKVISMKWELRGKEYLSKNKTVIMIANHQSSLAIWHVMGRTTVIAKKE
IFYVWPFGLAAWLCGLIFINKQSATESKSIMYDAMERLKRENIKLWVFPEGTRRNTNEIH
KFKKGAFHLAIQTKTPIMPIVYSSYQTFLNDNEKILKPGEVIIEALPEINTENYTTDKID
ELIDKTRNVMIEVFNRNSLEIKNRMQCS
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 17 | g12090.t1 | CDD | cd07989 | LPLAT_AGPAT-like | 78 | 247 | 2.03613E-41 |
| 2 | g12090.t1 | PANTHER | PTHR10434:SF50 | 1-ACYL-SN-GLYCEROL-3-PHOSPHATE ACYLTRANSFERASE | 4 | 266 | 2.6E-98 |
| 3 | g12090.t1 | PANTHER | PTHR10434 | 1-ACYL-SN-GLYCEROL-3-PHOSPHATE ACYLTRANSFERASE | 4 | 266 | 2.6E-98 |
| 1 | g12090.t1 | Pfam | PF01553 | Acyltransferase | 81 | 203 | 1.3E-26 |
| 10 | g12090.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 5 | - |
| 16 | g12090.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 6 | 23 | - |
| 6 | g12090.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 24 | 34 | - |
| 13 | g12090.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 35 | 54 | - |
| 9 | g12090.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 55 | 59 | - |
| 15 | g12090.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 60 | 82 | - |
| 8 | g12090.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 83 | 93 | - |
| 14 | g12090.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 94 | 110 | - |
| 11 | g12090.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 111 | 121 | - |
| 12 | g12090.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 122 | 139 | - |
| 7 | g12090.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 140 | 268 | - |
| 21 | g12090.t1 | SMART | SM00563 | plsc_2 | 94 | 205 | 1.2E-29 |
| 4 | g12090.t1 | SUPERFAMILY | SSF69593 | Glycerol-3-phosphate (1)-acyltransferase | 67 | 259 | 3.27E-39 |
| 5 | g12090.t1 | SignalP_EUK | SignalP-TM | SignalP-TM | 1 | 24 | - |
| 22 | g12090.t1 | TIGRFAM | TIGR00530 | AGP_acyltrn: 1-acylglycerol-3-phosphate O-acyltransferases | 79 | 202 | 1.7E-32 |
| 20 | g12090.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 5 | 22 | - |
| 18 | g12090.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 35 | 54 | - |
| 19 | g12090.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 121 | 140 | - |
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:0016020 | membrane | CC |
| GO:0008654 | phospholipid biosynthetic process | BP |
| GO:0016746 | acyltransferase activity | MF |
| GO:0003841 | 1-acylglycerol-3-phosphate O-acyltransferase activity | MF |
KEGG
Orthology
- This transcript has been annotated with K13509 (lysophosphatidate acyltransferase)
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.
