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_2 g9086 g9086.t2 TTS g9086.t2 35200031 35200031
chr_2 g9086 g9086.t2 isoform g9086.t2 35200065 35201375
chr_2 g9086 g9086.t2 exon g9086.t2.exon1 35200065 35201375
chr_2 g9086 g9086.t2 cds g9086.t2.CDS1 35200065 35201375
chr_2 g9086 g9086.t2 TSS g9086.t2 35201429 35201429

Sequences

>g9086.t2 Gene=g9086 Length=1311
ATGACAAAATTACAATTGAGTGTGATCAGTGCTGGTGCTTCCGGATTGTGTGCTATAAAA
AATGCAATCAATTATAATTGTGAAGTAATAGCGTTTGAACAAACAAATAAAGTCGGTGGA
TTATGGAATTATACGGACGAAACGGAAAGAGATGAATATGGATTAGAAATTCATTCAAGC
ATGTATCAAAATTTAGTTACAAATTTGCCTATTGAAATCATGTGTTATCCAGACGAACCA
TTTCGCGATCAAAAAGAATCGTTTGTGACATCAAATGAAGTCTTAAATTATTATCAAAAA
TATGCTGAAAAATATGAGTTAAAAAAATATATAAAATTCAATCACCATGTAATCAGAGTG
AGGCCATTGGGTAATGTAATCATGAGTGAGGTATTGAATTCCGAAAAATGGGAGATAATG
GTCAAAAATTTGCGCGAAGATAAATTTGAAACATTTGTATTTGACGCTGTTTTGATTTGT
AGTGGACATTTTTCTCAGAGTTTCATACCAAAATTTAAAGGTCAAATGACATTCAAGGGT
AAACAAATGCACTCACATGTTTATCGATCATCTCATATTTTCAAAGATGAACGAGTTTTG
ATTATTGGAGGAAATAACAGTGCAGTAGATCTTATTATTGAAGCAACAAATAATTCTAAA
TATGCTACAATTTGGTCACATCATCTCAACAACAAACCAGATTTGACACAGTTCAATGGT
CGAGTAATTGAAAAACCTGATGTTTTAAAGATGACAGAAACTGGTGTCAGATTTACAGAT
GGCTCATTGGAAGAATGTTCCTTAATTGTGTATGCTACTGGTTATCTTTATTCGTATCCA
TATCTTTCAATCGATAGCGGTGTAACATGTAACGGCGACTATGTCCGACCTCTCTGGATG
CACTGTTTGAGTATTAATAAGCCAACTCTAGGATTTATTGGACTACCCAATCTTATTTGC
CCTAACCAAATGTTTCAATTACAAGTTGAATTTTGTTTAACGTTTATGACAAAAAGAAAG
AAATTACCATCAAAAGAACAAATGTTAGAAGAATATGAATTAGACATGCTTGAGCGTTGG
AAAAAAGGATTATCGAAAAGAAAAGGACATTTTCTCGGTCATAAAGCTGAAGCACAAAAG
AAATACTATGATGAACTTGCGAAAAAGGCAAATATTGAAGGAATTAAATCTTGTATTGTC
AAAATACATTCTCATGCACACCTCAATAGATCGAAACATTTTACAAATTACAGAAATGTC
AAATACACTATCATCGATGAGAACAATTTCATTGTTAGTCCATTACAATAA

>g9086.t2 Gene=g9086 Length=436
MTKLQLSVISAGASGLCAIKNAINYNCEVIAFEQTNKVGGLWNYTDETERDEYGLEIHSS
MYQNLVTNLPIEIMCYPDEPFRDQKESFVTSNEVLNYYQKYAEKYELKKYIKFNHHVIRV
RPLGNVIMSEVLNSEKWEIMVKNLREDKFETFVFDAVLICSGHFSQSFIPKFKGQMTFKG
KQMHSHVYRSSHIFKDERVLIIGGNNSAVDLIIEATNNSKYATIWSHHLNNKPDLTQFNG
RVIEKPDVLKMTETGVRFTDGSLEECSLIVYATGYLYSYPYLSIDSGVTCNGDYVRPLWM
HCLSINKPTLGFIGLPNLICPNQMFQLQVEFCLTFMTKRKKLPSKEQMLEEYELDMLERW
KKGLSKRKGHFLGHKAEAQKKYYDELAKKANIEGIKSCIVKIHSHAHLNRSKHFTNYRNV
KYTIIDENNFIVSPLQ

Protein features from InterProScan

Transcript Database ID Name Start End E.value
14 g9086.t2 Gene3D G3DSA:3.50.50.60 - 7 419 2.8E-117
13 g9086.t2 Gene3D G3DSA:3.50.50.60 - 171 272 2.8E-117
3 g9086.t2 PANTHER PTHR23023:SF208 FLAVIN-CONTAINING MONOOXYGENASE 3 430 5.0E-81
4 g9086.t2 PANTHER PTHR23023 DIMETHYLANILINE MONOOXYGENASE 3 430 5.0E-81
20 g9086.t2 PIRSF PIRSF000332 FMO 2 230 1.9E-58
21 g9086.t2 PIRSF PIRSF000332 FMO 226 422 6.0E-13
9 g9086.t2 PRINTS PR00370 Flavin-containing monooxygenase (FMO) signature 4 20 3.2E-19
6 g9086.t2 PRINTS PR00370 Flavin-containing monooxygenase (FMO) signature 28 52 3.2E-19
5 g9086.t2 PRINTS PR00370 Flavin-containing monooxygenase (FMO) signature 183 197 3.2E-19
7 g9086.t2 PRINTS PR00370 Flavin-containing monooxygenase (FMO) signature 210 225 3.2E-19
8 g9086.t2 PRINTS PR00370 Flavin-containing monooxygenase (FMO) signature 259 286 3.2E-19
10 g9086.t2 PRINTS PR00370 Flavin-containing monooxygenase (FMO) signature 307 324 3.2E-19
2 g9086.t2 Pfam PF00743 Flavin-binding monooxygenase-like 5 221 3.6E-48
1 g9086.t2 Pfam PF00743 Flavin-binding monooxygenase-like 238 366 3.3E-11
16 g9086.t2 Phobius SIGNAL_PEPTIDE Signal peptide region 1 17 -
17 g9086.t2 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 3 -
18 g9086.t2 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 4 12 -
19 g9086.t2 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 13 17 -
15 g9086.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 18 436 -
11 g9086.t2 SUPERFAMILY SSF51905 FAD/NAD(P)-binding domain 8 211 1.44E-39
12 g9086.t2 SUPERFAMILY SSF51905 FAD/NAD(P)-binding domain 252 429 1.94E-10

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