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.t1 TTS g14139.t1 34859249 34859249
chr_1 g14139 g14139.t1 isoform g14139.t1 34859869 34863760
chr_1 g14139 g14139.t1 exon g14139.t1.exon1 34859869 34860099
chr_1 g14139 g14139.t1 cds g14139.t1.CDS1 34859869 34860099
chr_1 g14139 g14139.t1 exon g14139.t1.exon2 34860168 34860423
chr_1 g14139 g14139.t1 cds g14139.t1.CDS2 34860168 34860423
chr_1 g14139 g14139.t1 exon g14139.t1.exon3 34860477 34860602
chr_1 g14139 g14139.t1 cds g14139.t1.CDS3 34860477 34860602
chr_1 g14139 g14139.t1 exon g14139.t1.exon4 34860673 34861078
chr_1 g14139 g14139.t1 cds g14139.t1.CDS4 34860673 34861078
chr_1 g14139 g14139.t1 exon g14139.t1.exon5 34861934 34862151
chr_1 g14139 g14139.t1 cds g14139.t1.CDS5 34861934 34862151
chr_1 g14139 g14139.t1 exon g14139.t1.exon6 34862292 34862437
chr_1 g14139 g14139.t1 cds g14139.t1.CDS6 34862292 34862437
chr_1 g14139 g14139.t1 exon g14139.t1.exon7 34863617 34863760
chr_1 g14139 g14139.t1 cds g14139.t1.CDS7 34863617 34863760
chr_1 g14139 g14139.t1 TSS g14139.t1 34863869 34863869

Sequences

>g14139.t1 Gene=g14139 Length=1527
ATGAGTTTTGATGAGGAAAAACGTGAAATAAATGAAAGTCCAAGTTGTACAAAGAAAAAA
TTTAAAGAAATACCAATTAAAAATGCGTTTATTCGCGACAAGAATTATTGGGATAAAGAT
AATGAGTTGTTTGATAAAATTAAGACAGCAATATTGACAGTTTTTTTAGTACCAATTCGA
GTAATATGCATCATAGTACTCTTGTTGTTTGCTTGGAGTTTAGCTTATATTGGAATTTAT
GGTTTCACACGTGAAGAATTGAAACTTAGACCTTTGAGTGGTTGGAGAAGGAAACTGAGG
ACATTCGTTGGATGGGTCTTTAGATGGATGTTTTTTGTTGGCTCAGCTCATTTTGTGAAA
GTAAAAGGCAAATTAGCTTCACCGAAAGAGGCTAAAATTTTATTAGGTGCACCACATACT
AGCTTTTTTGATGCTCTTTCCGTGATTTTATCTGGACCTTCTGCAGTAGTAGCGAAGCAT
GAGGCAAATGACATTCCTTTTTACGGAAAAATCATTGATATGGCCCAACCTTTATATGTC
AAACGTGAAGATCACAGTTCTCGTACGACAACAATTCAAGATATTCTCACACGTGTGAAA
TCAAAAGAAGATTGGCCGAGTCTTATAATATTTCCAGAAGGAACTTGCACAAATAGGACG
AGTCTCATTAAATTTAAGCTTGGTGCATTCTATCCTGGACAACCCGTTCAACCAATTTTA
ATTCGATATCCGAACAAAATTGACACATTTACTTGGACTTGGAAAGGGCCTCATGTTATG
TTATTGATATGGAGAACTTTGGCTCAATTTCACACATTTGTGGAAATTGAATATTTACCC
GTTTATACCCCGAGTGAAGAAGAGAAACAAAATCCAAAACTGTTTGCTCAAAATGTACAA
AATTTAATGTCGAAAGCATTAAATATTCCTATATCGGACTATACATTCGACGATTGTAAG
CTAATGGAATACGCTCAAAAATGCAAATTACAGTTTGCTGAAAAAGTCTCTGATATGTTG
AGACTTCGTGAGAAAATTGGACTTGCACAATCTCAAATTGAGGAGTACATTGTAAAGGAA
AATTTCAAAGGAAATGAAGATTATTATTTTGAATTCAGTGAATTTGTACATCGTTTAAAA
ATTCCAGCAGACAACATTTCATTTACATTGTTTAAGCTATTTATTAGTGAAAGTGATATT
GCTGATGTGATTGACTTCAAGGAGTATTTATTGCACGCTATATTTTTGATCAAAAACTCT
GAGCCTAAAATTGAGTTGCTAAGAATGATGTTTATGTTATATGGTGAAGATGGTCGAGTG
AATCGAGAGCCATTTATAAAAATTATGCAGCACTTTTCATCAGTGAGTCTAAAAGAGCTC
ACAAAATTATTTTATTCATTGGATACAAGGAATTTAGGATCAATAGCTTTCTATCAATTT
GTTGAAGCAACTCAAAATAATTCAAAATTTACCCAATTATATACACCAAATCGCAACTTC
CGTCAGAAAAATAAGGATCCTCGTTAA

>g14139.t1 Gene=g14139 Length=508
MSFDEEKREINESPSCTKKKFKEIPIKNAFIRDKNYWDKDNELFDKIKTAILTVFLVPIR
VICIIVLLLFAWSLAYIGIYGFTREELKLRPLSGWRRKLRTFVGWVFRWMFFVGSAHFVK
VKGKLASPKEAKILLGAPHTSFFDALSVILSGPSAVVAKHEANDIPFYGKIIDMAQPLYV
KREDHSSRTTTIQDILTRVKSKEDWPSLIIFPEGTCTNRTSLIKFKLGAFYPGQPVQPIL
IRYPNKIDTFTWTWKGPHVMLLIWRTLAQFHTFVEIEYLPVYTPSEEEKQNPKLFAQNVQ
NLMSKALNIPISDYTFDDCKLMEYAQKCKLQFAEKVSDMLRLREKIGLAQSQIEEYIVKE
NFKGNEDYYFEFSEFVHRLKIPADNISFTLFKLFISESDIADVIDFKEYLLHAIFLIKNS
EPKIELLRMMFMLYGEDGRVNREPFIKIMQHFSSVSLKELTKLFYSLDTRNLGSIAFYQF
VEATQNNSKFTQLYTPNRNFRQKNKDPR

Protein features from InterProScan

Transcript Database ID Name Start End E.value
12 g14139.t1 CDD cd07991 LPLAT_LPCAT1-like 107 320 5.00734E-79
6 g14139.t1 Gene3D G3DSA:1.10.238.10 - 328 495 8.2E-6
2 g14139.t1 PANTHER PTHR23063 PHOSPHOLIPID ACYLTRANSFERASE 19 499 8.2E-115
3 g14139.t1 PANTHER PTHR23063:SF21 LYSOPHOSPHATIDYLCHOLINE ACYLTRANSFERASE 2 19 499 8.2E-115
1 g14139.t1 Pfam PF01553 Acyltransferase 119 232 1.1E-11
7 g14139.t1 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 48 -
10 g14139.t1 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 49 82 -
9 g14139.t1 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 83 101 -
11 g14139.t1 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 102 119 -
8 g14139.t1 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 120 508 -
14 g14139.t1 SMART SM00563 plsc_2 133 244 1.5E-18
4 g14139.t1 SUPERFAMILY SSF69593 Glycerol-3-phosphate (1)-acyltransferase 26 308 1.44E-22
5 g14139.t1 SUPERFAMILY SSF47473 EF-hand 362 485 6.46E-8
13 g14139.t1 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

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