Gene loci information

Transcript annotation

  • This transcript has been annotated as Senecionine N-oxygenase.

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 g9765 g9765.t1 isoform g9765.t1 5095112 5096365
chr_1 g9765 g9765.t1 exon g9765.t1.exon1 5095112 5096365
chr_1 g9765 g9765.t1 cds g9765.t1.CDS1 5095112 5096365
chr_1 g9765 g9765.t1 TTS g9765.t1 5096913 5096913
chr_1 g9765 g9765.t1 TSS g9765.t1 NA NA

Sequences

>g9765.t1 Gene=g9765 Length=1254
ATGCGAATTTGTGTGATCGGAGCAGGTGTTGCCGGTCTTTGTTCAATAAAGCGAGCCATT
GAATATCATTGTGAAGTAATGGCATTTGAACAGAGTGCAGAAATTGGTGGCACGTGGGTT
TTGCGAGAAGAAATAGGAAAGGACAAATTTGGTTTAAATGTTCACTCAAGCATGTACAAG
GGTTTGCGTACGGACATTCCAAAGGAAGTGATGAGCTACCCTGACTTTCCTTATCCAACC
AAGACCACATCCTACATACCATCATCTGACGTTCTTGATTATTTGAATGCATATGCAAAC
AAATTCGATTTGCTTGACAAAATAAAATTTCAACATAATGTCATCAGAGTTTGTCCTTTA
GCTGACAACAGTTGGGAAGTCATTGTGAGAAATTTACCCAAAAATTCATACGAAATTTTC
ATATTTGATGCAGTTTTTGTTTGTACTGGAAATTTTCACACTCCAAACAGTCCAATCATC
AAGGGAAATGAAATTTTTAAAGGCAAGCAGATTCATTCACATGATTATTGTGATGCAGAG
CAATTTCGGAATGAAAAAGTTTGTATAATTGGTTCTGGTCCAACAGGAATTGATGTTGTC
CAAGCAATTTCAAAAACAGCTCATAGCGTTATTTGGTCAACGCATCTCAAACAGCAATTA
AACATAACTCTGGCTGATAATGTCATCATGAAACCGGATATTGCTGAGTTATGTTCCAAT
AGAGCAATTTTTGTTGACGGTTCATATGAGAATTTTACAATTTTACTGCAATGCACTGGA
TACAAGCATTCATTTCCATTTTTATCTGTCGATTGTGATGTTGTGGTTGAAGAAAATTTT
GTATCGCCACTTTACAAGCATTGTTTAAACATTAATCGACCTACTTTGACATTTATTGGT
TTACCAACTGTCGGATGTAATAACCAACTTTTTGATTATCAAGTGAGATTCTGTTTAAAG
TTTATGACTCAACAGTTAAAGCTGCCAACGAAAGAAGAAATGTTACGTGACTATAAGAAA
AATATGGAAGAACAATGGAAGCGTGGACTTTCTAAAAGACGAGCACATTTGTTGGGCTTT
GATGTGCAAGAAAAATATTTCGAAGAACTTTCCACAATAGCGCAATTAGAGCCAGTGAAA
CCCGTGATTCTAAAAATATTCAACAAAAGCATTCTTAATTTGTTTTCAAATCTCGACAAT
TATAGAGAGAAAAATTTCAAGGTCATTAATGATGAAGAATTTAAAGAATTTTAA

>g9765.t1 Gene=g9765 Length=417
MRICVIGAGVAGLCSIKRAIEYHCEVMAFEQSAEIGGTWVLREEIGKDKFGLNVHSSMYK
GLRTDIPKEVMSYPDFPYPTKTTSYIPSSDVLDYLNAYANKFDLLDKIKFQHNVIRVCPL
ADNSWEVIVRNLPKNSYEIFIFDAVFVCTGNFHTPNSPIIKGNEIFKGKQIHSHDYCDAE
QFRNEKVCIIGSGPTGIDVVQAISKTAHSVIWSTHLKQQLNITLADNVIMKPDIAELCSN
RAIFVDGSYENFTILLQCTGYKHSFPFLSVDCDVVVEENFVSPLYKHCLNINRPTLTFIG
LPTVGCNNQLFDYQVRFCLKFMTQQLKLPTKEEMLRDYKKNMEEQWKRGLSKRRAHLLGF
DVQEKYFEELSTIAQLEPVKPVILKIFNKSILNLFSNLDNYREKNFKVINDEEFKEF

Protein features from InterProScan

Transcript Database ID Name Start End E.value
14 g9765.t1 Gene3D G3DSA:3.50.50.60 - 2 404 1.7E-122
13 g9765.t1 Gene3D G3DSA:3.50.50.60 - 159 258 1.7E-122
3 g9765.t1 PANTHER PTHR23023:SF208 FLAVIN-CONTAINING MONOOXYGENASE 1 414 8.1E-79
4 g9765.t1 PANTHER PTHR23023 DIMETHYLANILINE MONOOXYGENASE 1 414 8.1E-79
20 g9765.t1 PIRSF PIRSF000332 FMO 1 220 5.1E-53
21 g9765.t1 PIRSF PIRSF000332 FMO 215 394 2.5E-16
10 g9765.t1 PRINTS PR00370 Flavin-containing monooxygenase (FMO) signature 1 17 4.8E-21
9 g9765.t1 PRINTS PR00370 Flavin-containing monooxygenase (FMO) signature 25 49 4.8E-21
7 g9765.t1 PRINTS PR00370 Flavin-containing monooxygenase (FMO) signature 124 140 4.8E-21
8 g9765.t1 PRINTS PR00370 Flavin-containing monooxygenase (FMO) signature 171 185 4.8E-21
5 g9765.t1 PRINTS PR00370 Flavin-containing monooxygenase (FMO) signature 198 213 4.8E-21
6 g9765.t1 PRINTS PR00370 Flavin-containing monooxygenase (FMO) signature 245 272 4.8E-21
1 g9765.t1 Pfam PF00743 Flavin-binding monooxygenase-like 2 215 2.1E-47
2 g9765.t1 Pfam PF00743 Flavin-binding monooxygenase-like 223 387 3.1E-17
16 g9765.t1 Phobius SIGNAL_PEPTIDE Signal peptide region 1 19 -
17 g9765.t1 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 2 -
18 g9765.t1 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 3 14 -
19 g9765.t1 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 15 19 -
15 g9765.t1 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 20 417 -
11 g9765.t1 SUPERFAMILY SSF51905 FAD/NAD(P)-binding domain 1 218 5.18E-48
12 g9765.t1 SUPERFAMILY SSF51905 FAD/NAD(P)-binding domain 244 388 4.27E-8

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:0050661 NADP binding MF
GO:0050660 flavin adenine dinucleotide binding MF
GO:0004499 N,N-dimethylaniline monooxygenase activity MF
GO:0055114 NA NA

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