Gene loci information

Transcript annotation

  • This transcript has been annotated as Lysophosphatidylcholine acyltransferase.

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_1 g14139 g14139.t5 isoform g14139.t5 34860675 34863760
chr_1 g14139 g14139.t5 exon g14139.t5.exon1 34860675 34861078
chr_1 g14139 g14139.t5 cds g14139.t5.CDS1 34860675 34861078
chr_1 g14139 g14139.t5 exon g14139.t5.exon2 34861934 34862151
chr_1 g14139 g14139.t5 cds g14139.t5.CDS2 34861934 34862151
chr_1 g14139 g14139.t5 exon g14139.t5.exon3 34862292 34862437
chr_1 g14139 g14139.t5 cds g14139.t5.CDS3 34862292 34862437
chr_1 g14139 g14139.t5 exon g14139.t5.exon4 34863617 34863760
chr_1 g14139 g14139.t5 cds g14139.t5.CDS4 34863617 34863760
chr_1 g14139 g14139.t5 TSS g14139.t5 34863869 34863869
chr_1 g14139 g14139.t5 TTS g14139.t5 NA NA

Sequences

>g14139.t5 Gene=g14139 Length=912
ATGAGTTTTGATGAGGAAAAACGTGAAATAAATGAAAGTCCAAGTTGTACAAAGAAAAAA
TTTAAAGAAATACCAATTAAAAATGCGTTTATTCGCGACAAGAATTATTGGGATAAAGAT
AATGAGTTGTTTGATAAAATTAAGACAGCAATATTGACAGTTTTTTTAGTACCAATTCGA
GTAATATGCATCATAGTACTCTTGTTGTTTGCTTGGAGTTTAGCTTATATTGGAATTTAT
GGTTTCACACGTGAAGAATTGAAACTTAGACCTTTGAGTGGTTGGAGAAGGAAACTGAGG
ACATTCGTTGGATGGGTCTTTAGATGGATGTTTTTTGTTGGCTCAGCTCATTTTGTGAAA
GTAAAAGGCAAATTAGCTTCACCGAAAGAGGCTAAAATTTTATTAGGTGCACCACATACT
AGCTTTTTTGATGCTCTTTCCGTGATTTTATCTGGACCTTCTGCAGTAGTAGCGAAGCAT
GAGGCAAATGACATTCCTTTTTACGGAAAAATCATTGATATGGCCCAACCTTTATATGTC
AAACGTGAAGATCACAGTTCTCGTACGACAACAATTCAAGATATTCTCACACGTGTGAAA
TCAAAAGAAGATTGGCCGAGTCTTATAATATTTCCAGAAGGAACTTGCACAAATAGGACG
AGTCTCATTAAATTTAAGCTTGGTGCATTCTATCCTGGACAACCCGTTCAACCAATTTTA
ATTCGATATCCGAACAAAATTGACACATTTACTTGGACTTGGAAAGGGCCTCATGTTATG
TTATTGATATGGAGAACTTTGGCTCAATTTCACACATTTGTGGAAATTGAATATTTACCC
GTTTATACCCCGAGTGAAGAAGAGAAACAAAATCCAAAACTGTTTGCTCAAAATGTACAA
AATTTAATGTCG

>g14139.t5 Gene=g14139 Length=304
MSFDEEKREINESPSCTKKKFKEIPIKNAFIRDKNYWDKDNELFDKIKTAILTVFLVPIR
VICIIVLLLFAWSLAYIGIYGFTREELKLRPLSGWRRKLRTFVGWVFRWMFFVGSAHFVK
VKGKLASPKEAKILLGAPHTSFFDALSVILSGPSAVVAKHEANDIPFYGKIIDMAQPLYV
KREDHSSRTTTIQDILTRVKSKEDWPSLIIFPEGTCTNRTSLIKFKLGAFYPGQPVQPIL
IRYPNKIDTFTWTWKGPHVMLLIWRTLAQFHTFVEIEYLPVYTPSEEEKQNPKLFAQNVQ
NLMS

Protein features from InterProScan

Transcript Database ID Name Start End E.value
12 g14139.t5 CDD cd07991 LPLAT_LPCAT1-like 107 304 1.19319E-73
2 g14139.t5 PANTHER PTHR23063 PHOSPHOLIPID ACYLTRANSFERASE 19 304 8.9E-90
3 g14139.t5 PANTHER PTHR23063:SF21 LYSOPHOSPHATIDYLCHOLINE ACYLTRANSFERASE 2 19 304 8.9E-90
1 g14139.t5 Pfam PF01553 Acyltransferase 119 232 4.1E-12
7 g14139.t5 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 48 -
10 g14139.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 49 82 -
9 g14139.t5 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 83 101 -
11 g14139.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 102 119 -
8 g14139.t5 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 120 304 -
6 g14139.t5 SMART SM00563 plsc_2 133 244 1.5E-18
5 g14139.t5 SUPERFAMILY SSF69593 Glycerol-3-phosphate (1)-acyltransferase 26 302 6.28E-22
4 g14139.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 56 78 -

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.

Raw TPM values