Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative 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.t6 isoform g14139.t6 34860996 34863760
chr_1 g14139 g14139.t6 exon g14139.t6.exon1 34860996 34861078
chr_1 g14139 g14139.t6 cds g14139.t6.CDS1 34860996 34861078
chr_1 g14139 g14139.t6 exon g14139.t6.exon2 34861398 34861606
chr_1 g14139 g14139.t6 cds g14139.t6.CDS2 34861398 34861606
chr_1 g14139 g14139.t6 exon g14139.t6.exon3 34862292 34862437
chr_1 g14139 g14139.t6 cds g14139.t6.CDS3 34862292 34862437
chr_1 g14139 g14139.t6 exon g14139.t6.exon4 34863617 34863760
chr_1 g14139 g14139.t6 cds g14139.t6.CDS4 34863617 34863760
chr_1 g14139 g14139.t6 TSS g14139.t6 34863869 34863869
chr_1 g14139 g14139.t6 TTS g14139.t6 NA NA

Sequences

>g14139.t6 Gene=g14139 Length=582
ATGAGTTTTGATGAGGAAAAACGTGAAATAAATGAAAGTCCAAGTTGTACAAAGAAAAAA
TTTAAAGAAATACCAATTAAAAATGCGTTTATTCGCGACAAGAATTATTGGGATAAAGAT
AATGAGTTGTTTGATAAAATTAAGACAGCAATATTGACAGTTTTTTTAGTACCAATTCGA
GTAATATGCATCATAGTACTCTTGTTGTTTGCTTGGAGTTTAGCTTATATTGGAATTTAT
GGTTTCACACGTGAAGAATTGAAACTTAGACCTTTGAGTGGTTGGAGAAGACAATTAAAA
TTCATAATAAGTCAAATTGCTTTATCCATGTGGATGCTTTGCGGAATCGGAGTAATTGTT
CGAGGTGAAAAAAAGGCAAGTCGTGGTGAAGCTCCAATAATAGTTGCAGCGCCACATTCA
ACGTTTTTCGATGCAATAATTATCTTTATTACTCATATGGGCTCGCCATTAGTGCGTGAT
GAGGACAAGCGTTTGGGCAAAATCATTGATATGGCCCAACCTTTATATGTCAAACGTGAA
GATCACAGTTCTCGTACGACAACAATTCAAGATATTCTCACA

>g14139.t6 Gene=g14139 Length=194
MSFDEEKREINESPSCTKKKFKEIPIKNAFIRDKNYWDKDNELFDKIKTAILTVFLVPIR
VICIIVLLLFAWSLAYIGIYGFTREELKLRPLSGWRRQLKFIISQIALSMWMLCGIGVIV
RGEKKASRGEAPIIVAAPHSTFFDAIIIFITHMGSPLVRDEDKRLGKIIDMAQPLYVKRE
DHSSRTTTIQDILT

Protein features from InterProScan

Transcript Database ID Name Start End E.value
1 g14139.t6 PANTHER PTHR23063 PHOSPHOLIPID ACYLTRANSFERASE 19 192 1.8E-32
2 g14139.t6 PANTHER PTHR23063:SF21 LYSOPHOSPHATIDYLCHOLINE ACYLTRANSFERASE 2 19 192 1.8E-32
7 g14139.t6 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 48 -
11 g14139.t6 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 49 82 -
9 g14139.t6 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 83 101 -
10 g14139.t6 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 102 120 -
8 g14139.t6 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 121 194 -
6 g14139.t6 SUPERFAMILY SSF69593 Glycerol-3-phosphate (1)-acyltransferase 26 182 2.35E-8
3 g14139.t6 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 50 72 -
5 g14139.t6 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 101 120 -
4 g14139.t6 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 133 155 -

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

GO terms from InterProScan

There are no GO annotations for this transcript.

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