General information for g12089.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 g12089 is located on chr_1: 20883607..20884841 (- 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 | g12089 | g12089.t1 | TTS | g12089.t1 | 20883568 | 20883568 |
| chr_1 | g12089 | g12089.t1 | isoform | g12089.t1 | 20883607 | 20884841 |
| chr_1 | g12089 | g12089.t1 | exon | g12089.t1.exon1 | 20883607 | 20883902 |
| chr_1 | g12089 | g12089.t1 | cds | g12089.t1.CDS1 | 20883607 | 20883902 |
| chr_1 | g12089 | g12089.t1 | exon | g12089.t1.exon2 | 20883962 | 20884077 |
| chr_1 | g12089 | g12089.t1 | cds | g12089.t1.CDS2 | 20883962 | 20884077 |
| chr_1 | g12089 | g12089.t1 | exon | g12089.t1.exon3 | 20884137 | 20884233 |
| chr_1 | g12089 | g12089.t1 | cds | g12089.t1.CDS3 | 20884137 | 20884233 |
| chr_1 | g12089 | g12089.t1 | exon | g12089.t1.exon4 | 20884298 | 20884306 |
| chr_1 | g12089 | g12089.t1 | cds | g12089.t1.CDS4 | 20884298 | 20884306 |
| chr_1 | g12089 | g12089.t1 | exon | g12089.t1.exon5 | 20884410 | 20884442 |
| chr_1 | g12089 | g12089.t1 | cds | g12089.t1.CDS5 | 20884410 | 20884442 |
| chr_1 | g12089 | g12089.t1 | exon | g12089.t1.exon6 | 20884512 | 20884612 |
| chr_1 | g12089 | g12089.t1 | cds | g12089.t1.CDS6 | 20884512 | 20884612 |
| chr_1 | g12089 | g12089.t1 | exon | g12089.t1.exon7 | 20884672 | 20884841 |
| chr_1 | g12089 | g12089.t1 | cds | g12089.t1.CDS7 | 20884672 | 20884841 |
| chr_1 | g12089 | g12089.t1 | TSS | g12089.t1 | 20884883 | 20884883 |
Sequences
>g12089.t1 Gene=g12089 Length=822
ATGTTCCTGATCATTCTAACTTTATTAATAATTTCTACAATTTTATATAAGAACAATCAT
GTGTTTAAATATAATGTTAAATATCTTTTTTACATACTCGCATCATCAATTTTAGGGACA
CTTTCAATTCCTTATTTGATGCTACGACCAAGAAATCCGATAAATTTTAGAGGAGTTTGT
AAAATGTTTAGATTGATGTCACCTGTTTTGGGTTTGAGTTACGAATTAAGAGGAATAAAT
AATTTAGAAAAAGACTATGCATGTGTAATCGCTTCTAACCATCAAAGCAGTTTAGATTTT
CTCTGCATGTATGAAATTTGGTATGCAATGCGAAGACATCCAATATTTCGAGTTACAGCA
GTTGCAAGAATGTTATTGCTATTTGCTGGACCATATGGAATTGGTGCATGGTTGTCTGGA
TTAATTTTCATCAATAAAGATTCACCAGATCGTGGGATCAAAAAAATGAATGAAAGCATG
GAATATTTAAAGAAAAATAAAATTCATTTGTGGATGTATGTGGAAGGCTATCGAAATCAT
TCGGGAAAGATTGATGAATTTAAGAAAGGAGCTTTTAGATTGGCAATTCAATCTCAAGTT
CCAATTATACCTCTTGTTATCTCGTCATACAATTATTTTCTTGACCCAAAAAAGATGATT
TTCAATTCTGGGAAAATTATAATTGAAGTCCTTCCCGAAATACCAACTAAAGGATTAAAA
TTGAGTGATTTGGATACATTAATGGAGAAAACTAGAAATGTGATGGTGAAAAAATTTGAT
GAATTAAATAATGAATTAAGATTGAATAATAATTTAAAATAA
>g12089.t1 Gene=g12089 Length=273
MFLIILTLLIISTILYKNNHVFKYNVKYLFYILASSILGTLSIPYLMLRPRNPINFRGVC
KMFRLMSPVLGLSYELRGINNLEKDYACVIASNHQSSLDFLCMYEIWYAMRRHPIFRVTA
VARMLLLFAGPYGIGAWLSGLIFINKDSPDRGIKKMNESMEYLKKNKIHLWMYVEGYRNH
SGKIDEFKKGAFRLAIQSQVPIIPLVISSYNYFLDPKKMIFNSGKIIIEVLPEIPTKGLK
LSDLDTLMEKTRNVMVKKFDELNNELRLNNNLK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 19 | g12089.t1 | CDD | cd07989 | LPLAT_AGPAT-like | 63 | 252 | 2.58672E-37 |
| 2 | g12089.t1 | PANTHER | PTHR10434:SF50 | 1-ACYL-SN-GLYCEROL-3-PHOSPHATE ACYLTRANSFERASE | 3 | 267 | 8.6E-84 |
| 3 | g12089.t1 | PANTHER | PTHR10434 | 1-ACYL-SN-GLYCEROL-3-PHOSPHATE ACYLTRANSFERASE | 3 | 267 | 8.6E-84 |
| 1 | g12089.t1 | Pfam | PF01553 | Acyltransferase | 76 | 208 | 6.9E-24 |
| 13 | g12089.t1 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 13 | - |
| 14 | g12089.t1 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 1 | - |
| 15 | g12089.t1 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 2 | 9 | - |
| 18 | g12089.t1 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 10 | 13 | - |
| 11 | g12089.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 14 | 28 | - |
| 16 | g12089.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 29 | 48 | - |
| 10 | g12089.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 49 | 119 | - |
| 17 | g12089.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 120 | 144 | - |
| 12 | g12089.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 145 | 273 | - |
| 9 | g12089.t1 | SMART | SM00563 | plsc_2 | 88 | 210 | 1.6E-22 |
| 8 | g12089.t1 | SUPERFAMILY | SSF69593 | Glycerol-3-phosphate (1)-acyltransferase | 14 | 266 | 3.66E-42 |
| 4 | g12089.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 2 | 16 | - |
| 7 | g12089.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 26 | 48 | - |
| 6 | g12089.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 120 | 142 | - |
| 5 | g12089.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 195 | 214 | - |
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:0016746 | acyltransferase 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.
