Gene loci information

Transcript annotation

  • This transcript has been annotated as Acyl-CoA:lysophosphatidylglycerol acyltransferase 1.

Parent gene

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.t1 TSS g3442.t1 25483296 25483296
chr_3 g3442 g3442.t1 isoform g3442.t1 25483377 25485504
chr_3 g3442 g3442.t1 exon g3442.t1.exon1 25483377 25483396
chr_3 g3442 g3442.t1 cds g3442.t1.CDS1 25483377 25483396
chr_3 g3442 g3442.t1 exon g3442.t1.exon2 25483482 25483627
chr_3 g3442 g3442.t1 cds g3442.t1.CDS2 25483482 25483627
chr_3 g3442 g3442.t1 exon g3442.t1.exon3 25483937 25484136
chr_3 g3442 g3442.t1 cds g3442.t1.CDS3 25483937 25484136
chr_3 g3442 g3442.t1 exon g3442.t1.exon4 25484199 25484276
chr_3 g3442 g3442.t1 cds g3442.t1.CDS4 25484199 25484276
chr_3 g3442 g3442.t1 exon g3442.t1.exon5 25484366 25484433
chr_3 g3442 g3442.t1 cds g3442.t1.CDS5 25484366 25484433
chr_3 g3442 g3442.t1 exon g3442.t1.exon6 25484570 25484601
chr_3 g3442 g3442.t1 cds g3442.t1.CDS6 25484570 25484601
chr_3 g3442 g3442.t1 exon g3442.t1.exon7 25484669 25485201
chr_3 g3442 g3442.t1 cds g3442.t1.CDS7 25484669 25485201
chr_3 g3442 g3442.t1 exon g3442.t1.exon8 25485262 25485504
chr_3 g3442 g3442.t1 cds g3442.t1.CDS8 25485262 25485504
chr_3 g3442 g3442.t1 TTS g3442.t1 25485585 25485585

Sequences

>g3442.t1 Gene=g3442 Length=1320
ATGCCATCTGAATGTTTTGAAAATATTATTAAATATCCGCGAGCAATTTTGCGGGTACTT
TTTGTGATAGTGAATAATATATATTGTATTCCAACTTATTTGATATGGATGTTTCTATTA
TTACCACTGAAGAAATTACATCCCGATACGTTTTATTGGATTGAAGGTAAATTTTTCCAT
TGGTTACTCGCAAATGTGACAATGTGGAGTTATACTGCGGGCTATGACATAGTTGAGCTA
GGAGATGACATAACACCGACTTTAGATCAACGTACTTTGGTACTAGTCAATCATCAATCA
ACTGCTGATGTGCCTATGCTTATGTCAACTTTTAATACCAAGCAAGAAGTGTTACCGAAC
ATAATGTGGATAATGGACAAAATTTTTATGTACACAAATTTTGGTATTGTCAGTTTGATT
CATCAAGATTTTTTTATTGGTTCTGGACCGAAACAACGTGATTTGGCGTTAGTTCAATTG
AGAGAACATATAGAAAAATCATATATTCCGAGACGGAGGGAGTGGATGGTACTCTTTCCT
GAAGGCGGATTTTTAAGAAAGAGACGTGAAGCAAGTCAGCGGTATGCTCAAAAGAACAAT
TTACCATTACTTCATAATGTGACACTGCCACGTATCGGCGCCATGAAAACTATTATTGAT
CAACTCGGTAGTTCAGACGAAGATCGTCCCTCTCAACAAACCACAACTCCACCACATTCA
ATAAAAAATATCAATAAAGTGATTAATGGTGATGGAGATGAATTCTATATCGATAATGAA
TATACAAATCAAACATCAACACCGCCAGACACACCACTAAGAAATGCTTACAATGTAAGC
AATAATCGCAACAATGAGAATAATAATAGACAAACCCAGAGAATAATTGATGACGATGAG
AACCTAAAGGAGAAAATTGGCGAAGCTGAAGTTAGTTCTCGAAAAACGCTCAAATATATT
GTCGATATAACGGTGGCATATGCTAATGGCAAACCACTTGATTTGGCAGATATAGTGACG
GGCATAAGGAAGGCATGTCAAACACATATGCTGTATAGAGTATATCGATGTTCAGAGGTC
CCAAGAGATGAAGAATCTTTAACAAAATGGCTGTATGATCGATTTGTAGAGAAAGAGGAA
CTATTAGAAAATTTTTACAATACCGGCTCATTTGCTTATCCATCAGAAGTTCAACCAACT
GTAGTGTCGCAAGATCTTTTGCGTTTCTTCCTAATTCATCTTTTCTTTATAACATCCTCA
TATTTACATTTTCAAATGCTTAGTATGCTTTATACAGCAATTTTTCCATTTGACACTTAA

>g3442.t1 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.t1 CDD cd07990 LPLAT_LCLAT1-like 66 223 2.03806E-25
3 g3442.t1 PANTHER PTHR10983:SF2 ACYL-COA:LYSOPHOSPHATIDYLGLYCEROL ACYLTRANSFERASE 1 8 424 6.1E-134
4 g3442.t1 PANTHER PTHR10983 1-ACYLGLYCEROL-3-PHOSPHATE ACYLTRANSFERASE-RELATED 8 424 6.1E-134
2 g3442.t1 Pfam PF01553 Acyltransferase 89 189 2.4E-6
1 g3442.t1 Pfam PF16076 Acyltransferase C-terminus 341 396 1.4E-14
9 g3442.t1 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 18 -
12 g3442.t1 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 19 41 -
10 g3442.t1 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 42 405 -
11 g3442.t1 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 406 424 -
8 g3442.t1 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 425 439 -
7 g3442.t1 SMART SM00563 plsc_2 92 208 8.1E-7
6 g3442.t1 SUPERFAMILY SSF69593 Glycerol-3-phosphate (1)-acyltransferase 16 190 8.37E-6
5 g3442.t1 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

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.

Raw TPM values