General information for g3442.t11
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Acyl-CoA:lysophosphatidylglycerol acyltransferase 1.
Parent gene
- The parent gene g3442 is located on chr_3: 25485261..25486662 (+ 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_3 | g3442 | g3442.t11 | TSS | g3442.t11 | 25479721 | 25479721 |
| chr_3 | g3442 | g3442.t11 | isoform | g3442.t11 | 25479793 | 25486138 |
| chr_3 | g3442 | g3442.t11 | exon | g3442.t11.exon1 | 25479793 | 25479869 |
| chr_3 | g3442 | g3442.t11 | exon | g3442.t11.exon2 | 25483297 | 25483396 |
| chr_3 | g3442 | g3442.t11 | cds | g3442.t11.CDS1 | 25483377 | 25483396 |
| chr_3 | g3442 | g3442.t11 | exon | g3442.t11.exon3 | 25483482 | 25483627 |
| chr_3 | g3442 | g3442.t11 | cds | g3442.t11.CDS2 | 25483482 | 25483627 |
| chr_3 | g3442 | g3442.t11 | exon | g3442.t11.exon4 | 25483937 | 25484136 |
| chr_3 | g3442 | g3442.t11 | cds | g3442.t11.CDS3 | 25483937 | 25484136 |
| chr_3 | g3442 | g3442.t11 | exon | g3442.t11.exon5 | 25484199 | 25484276 |
| chr_3 | g3442 | g3442.t11 | cds | g3442.t11.CDS4 | 25484199 | 25484276 |
| chr_3 | g3442 | g3442.t11 | exon | g3442.t11.exon6 | 25484366 | 25484433 |
| chr_3 | g3442 | g3442.t11 | cds | g3442.t11.CDS5 | 25484366 | 25484433 |
| chr_3 | g3442 | g3442.t11 | exon | g3442.t11.exon7 | 25484570 | 25484601 |
| chr_3 | g3442 | g3442.t11 | cds | g3442.t11.CDS6 | 25484570 | 25484601 |
| chr_3 | g3442 | g3442.t11 | exon | g3442.t11.exon8 | 25484669 | 25485201 |
| chr_3 | g3442 | g3442.t11 | cds | g3442.t11.CDS7 | 25484669 | 25485201 |
| chr_3 | g3442 | g3442.t11 | exon | g3442.t11.exon9 | 25485262 | 25486138 |
| chr_3 | g3442 | g3442.t11 | cds | g3442.t11.CDS8 | 25485262 | 25485504 |
| chr_3 | g3442 | g3442.t11 | TTS | g3442.t11 | 25486916 | 25486916 |
Sequences
>g3442.t11 Gene=g3442 Length=2111
AGTACCAATATTTTTTATTTACTACTAATTTTAGTGCTTTAAAGTCGACGAGTGTTTGAT
GAATGAATAAAATAAAGAACGAAGTCCACTTTTAACATCATCAGACTCTGAAAAAGACTT
ATATGAATGTGAAAGACAAATTGCAGGAGTGAACAAAATGCCATCTGAATGTTTTGAAAA
TATTATTAAATATCCGCGAGCAATTTTGCGGGTACTTTTTGTGATAGTGAATAATATATA
TTGTATTCCAACTTATTTGATATGGATGTTTCTATTATTACCACTGAAGAAATTACATCC
CGATACGTTTTATTGGATTGAAGGTAAATTTTTCCATTGGTTACTCGCAAATGTGACAAT
GTGGAGTTATACTGCGGGCTATGACATAGTTGAGCTAGGAGATGACATAACACCGACTTT
AGATCAACGTACTTTGGTACTAGTCAATCATCAATCAACTGCTGATGTGCCTATGCTTAT
GTCAACTTTTAATACCAAGCAAGAAGTGTTACCGAACATAATGTGGATAATGGACAAAAT
TTTTATGTACACAAATTTTGGTATTGTCAGTTTGATTCATCAAGATTTTTTTATTGGTTC
TGGACCGAAACAACGTGATTTGGCGTTAGTTCAATTGAGAGAACATATAGAAAAATCATA
TATTCCGAGACGGAGGGAGTGGATGGTACTCTTTCCTGAAGGCGGATTTTTAAGAAAGAG
ACGTGAAGCAAGTCAGCGGTATGCTCAAAAGAACAATTTACCATTACTTCATAATGTGAC
ACTGCCACGTATCGGCGCCATGAAAACTATTATTGATCAACTCGGTAGTTCAGACGAAGA
TCGTCCCTCTCAACAAACCACAACTCCACCACATTCAATAAAAAATATCAATAAAGTGAT
TAATGGTGATGGAGATGAATTCTATATCGATAATGAATATACAAATCAAACATCAACACC
GCCAGACACACCACTAAGAAATGCTTACAATGTAAGCAATAATCGCAACAATGAGAATAA
TAATAGACAAACCCAGAGAATAATTGATGACGATGAGAACCTAAAGGAGAAAATTGGCGA
AGCTGAAGTTAGTTCTCGAAAAACGCTCAAATATATTGTCGATATAACGGTGGCATATGC
TAATGGCAAACCACTTGATTTGGCAGATATAGTGACGGGCATAAGGAAGGCATGTCAAAC
ACATATGCTGTATAGAGTATATCGATGTTCAGAGGTCCCAAGAGATGAAGAATCTTTAAC
AAAATGGCTGTATGATCGATTTGTAGAGAAAGAGGAACTATTAGAAAATTTTTACAATAC
CGGCTCATTTGCTTATCCATCAGAAGTTCAACCAACTGTAGTGTCGCAAGATCTTTTGCG
TTTCTTCCTAATTCATCTTTTCTTTATAACATCCTCATATTTACATTTTCAAATGCTTAG
TATGCTTTATACAGCAATTTTTCCATTTGACACTTAAATCTATAAAACGATTTTCGATTA
AATTTATTTTTCGTTTTACTTATTATTCCTCGTCGTTGCCGTTGTTGCTCGTCGATATAA
AAAAGAAAAAAAAAGCATTAATTATTAAAATTCACATACCGTCAATAAGAGTTGCTCGCT
TGACGGGAACGCGCGCTGACAAGATGTGGATCTCATTTAAGATAATAATAATTATTTTTA
TGATAAAAATATCTTTAAACATGTATCACCCCCTTCAGAATAACATATAAATATATTTTT
TCCTCAATGTTTTATTCAAAAACACTTTTAAATGTGAAAAAGTATCTGAAATAATGGCAG
CGAATCAGTAACAAAAACAAAGTGACACATTTTTGTGTAAAAAAAATCTTTTTTAAATAG
AGGCATAAATGAAGAAAACAAAATTGAGAAGATGTTTTGAATGAAGATTTATAGCCTTTG
TTGCTTTACTGATTGTTTATCAATTTTACTCACAGTATTAAAAGAAAACATTTCAATTCA
CCCTATATAAATTTTTTCTTTTTCCCTAATTCTGGTTGTAAAATTGATCACAAACTGACG
TAAAAAAGTGACTTTTATTTATTTGATTTGATAATAATTTTGAGAAAGATAACAAGAAAC
AATTATAAAAC
>g3442.t11 Gene=g3442 Length=439
MPSECFENIIKYPRAILRVLFVIVNNIYCIPTYLIWMFLLLPLKKLHPDTFYWIEGKFFH
WLLANVTMWSYTAGYDIVELGDDITPTLDQRTLVLVNHQSTADVPMLMSTFNTKQEVLPN
IMWIMDKIFMYTNFGIVSLIHQDFFIGSGPKQRDLALVQLREHIEKSYIPRRREWMVLFP
EGGFLRKRREASQRYAQKNNLPLLHNVTLPRIGAMKTIIDQLGSSDEDRPSQQTTTPPHS
IKNINKVINGDGDEFYIDNEYTNQTSTPPDTPLRNAYNVSNNRNNENNNRQTQRIIDDDE
NLKEKIGEAEVSSRKTLKYIVDITVAYANGKPLDLADIVTGIRKACQTHMLYRVYRCSEV
PRDEESLTKWLYDRFVEKEELLENFYNTGSFAYPSEVQPTVVSQDLLRFFLIHLFFITSS
YLHFQMLSMLYTAIFPFDT
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 13 | g3442.t11 | CDD | cd07990 | LPLAT_LCLAT1-like | 66 | 223 | 2.03806E-25 |
| 3 | g3442.t11 | PANTHER | PTHR10983:SF2 | ACYL-COA:LYSOPHOSPHATIDYLGLYCEROL ACYLTRANSFERASE 1 | 8 | 424 | 6.1E-134 |
| 4 | g3442.t11 | PANTHER | PTHR10983 | 1-ACYLGLYCEROL-3-PHOSPHATE ACYLTRANSFERASE-RELATED | 8 | 424 | 6.1E-134 |
| 2 | g3442.t11 | Pfam | PF01553 | Acyltransferase | 89 | 189 | 2.4E-6 |
| 1 | g3442.t11 | Pfam | PF16076 | Acyltransferase C-terminus | 341 | 396 | 1.4E-14 |
| 9 | g3442.t11 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 18 | - |
| 12 | g3442.t11 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 19 | 41 | - |
| 10 | g3442.t11 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 42 | 405 | - |
| 11 | g3442.t11 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 406 | 424 | - |
| 8 | g3442.t11 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 425 | 439 | - |
| 7 | g3442.t11 | SMART | SM00563 | plsc_2 | 92 | 208 | 8.1E-7 |
| 6 | g3442.t11 | SUPERFAMILY | SSF69593 | Glycerol-3-phosphate (1)-acyltransferase | 16 | 190 | 8.37E-6 |
| 5 | g3442.t11 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 19 | 41 | - |
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 transcript has been annotated with K13514 (lysophosphatidylglycerol acyltransferase 1 [EC:2.3.1.-])
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.
