Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Phosphatidyl-N-methylethanolamine N-methyltransferase.

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_2 g5022 g5022.t2 isoform g5022.t2 6486711 6488337
chr_2 g5022 g5022.t2 exon g5022.t2.exon1 6486711 6486836
chr_2 g5022 g5022.t2 TSS g5022.t2 6486734 6486734
chr_2 g5022 g5022.t2 exon g5022.t2.exon2 6487290 6487810
chr_2 g5022 g5022.t2 cds g5022.t2.CDS1 6487290 6487810
chr_2 g5022 g5022.t2 exon g5022.t2.exon3 6487873 6487947
chr_2 g5022 g5022.t2 cds g5022.t2.CDS2 6487873 6487947
chr_2 g5022 g5022.t2 exon g5022.t2.exon4 6488277 6488337
chr_2 g5022 g5022.t2 cds g5022.t2.CDS3 6488277 6488337
chr_2 g5022 g5022.t2 TTS g5022.t2 NA NA

Sequences

>g5022.t2 Gene=g5022 Length=783
ATTCAGGACAGTACAAGGGAAGCATCAGTTTGAAATTAAAATTCGAGTGATCAACCTCGA
GTGGTGAAGGAGTTTAAAACTATCTGTGAAATTCTATTGTGATAATTTTTTTTAATCTAT
TGAAAAATGAACGTGTCACTTGATACAATTGTTGAAAATTTCGACTCGATCATCAACTAC
AAGCAACCAATTTTCTGGGCTGCAATTGTTCATGTGATTTTCAATCCAATTTTTTGGAAT
GTCACTGGCCGTTTGGAGAATAGAACACAAATTTTCACACGCATTTGCGGAAATTCAAAG
CATAGAGCATGCTATATTTTTGCATTTGTGACATTTACTCTTGGCCTTACTCGTGATTAT
CTCGTTGTCTCAGCTTTAGCCATGCAACCAAAAATTACTGATTTTCTTAGCTATTATATG
AATGTCAGTACACCAACTGATGTTATTCAAACACTTGGAACAATTGCTTTAATTTGGGGA
GGAATTCTTGTGCTTTCATCAATGTACAGATTGGGAATCACTGGCACATATCTTGGTGAT
TATTTTGGAATTTTCATGAATGAAAGAGTCACAGCTTTCCCTTATAATGTTTGTGAAAAT
CCAATGTATGTTGGTTCAACATTTTGCTTCTTTGGTCATGCTTTGAGAACTATGACAGCA
TCAGGACTTTTAATCGCAGCTATTGTATGGCTTGTTTATAGAATTGCTATTATGTTTGAA
GGACCATTCACTGCCAAAATTTTTGCTGAAAAAGCATTGAAAGAATCAACGAAAGTTGAG
TGA

>g5022.t2 Gene=g5022 Length=218
MNVSLDTIVENFDSIINYKQPIFWAAIVHVIFNPIFWNVTGRLENRTQIFTRICGNSKHR
ACYIFAFVTFTLGLTRDYLVVSALAMQPKITDFLSYYMNVSTPTDVIQTLGTIALIWGGI
LVLSSMYRLGITGTYLGDYFGIFMNERVTAFPYNVCENPMYVGSTFCFFGHALRTMTASG
LLIAAIVWLVYRIAIMFEGPFTAKIFAEKALKESTKVE

Protein features from InterProScan

Transcript Database ID Name Start End E.value
3 g5022.t2 Hamap MF_03216 Phosphatidyl-N-methylethanolamine N-methyltransferase [PEMT]. 19 208 25.915863
2 g5022.t2 PANTHER PTHR15458 PHOSPHATIDYLETHANOLAMINE N-METHYLTRANSFERASE 16 214 9.8E-53
18 g5022.t2 PIRSF PIRSF005444 PEMT_MPLS 1 218 1.1E-73
1 g5022.t2 Pfam PF04191 Phospholipid methyltransferase 109 209 1.7E-29
13 g5022.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 21 -
17 g5022.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 22 40 -
9 g5022.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 41 60 -
16 g5022.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 61 86 -
12 g5022.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 87 105 -
15 g5022.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 106 127 -
10 g5022.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 128 177 -
14 g5022.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 178 197 -
11 g5022.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 198 218 -
8 g5022.t2 ProSiteProfiles PS51599 Phospholipid methyltransferases (EC 2.1.1.17 and EC=2.1.1.71) family profile. 20 217 46.642
4 g5022.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 20 42 -
7 g5022.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 63 85 -
6 g5022.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 105 127 -
5 g5022.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 177 196 -

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g5022/g5022.t2; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5022.t2.fa.iupred3.txt does not exist

GO terms from InterProScan

GOID TERM ONTOLOGY
GO:0008757 S-adenosylmethionine-dependent methyltransferase activity MF
GO:0006656 phosphatidylcholine biosynthetic process BP

KEGG

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. There were no conditions that were differentially expressed