Gene loci information

Transcript annotation

  • This transcript has been annotated as Pyridoxine-5’-phosphate oxidase.

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 g10378 g10378.t5 TTS g10378.t5 9328610 9328610
chr_1 g10378 g10378.t5 isoform g10378.t5 9328801 9329621
chr_1 g10378 g10378.t5 exon g10378.t5.exon1 9328801 9329314
chr_1 g10378 g10378.t5 cds g10378.t5.CDS1 9328801 9329314
chr_1 g10378 g10378.t5 exon g10378.t5.exon2 9329376 9329621
chr_1 g10378 g10378.t5 cds g10378.t5.CDS2 9329376 9329548
chr_1 g10378 g10378.t5 TSS g10378.t5 9329685 9329685

Sequences

>g10378.t5 Gene=g10378 Length=760
ATGTCTACTACAGTCGAGATTTCAGGTAAATATTTAGATAATATAAAATATATTGTGGTA
TCATTAAATATTTATGACCGTTCATATAGCCATAAGAGCAAAATATAGAGAACCACAAGA
TATTTTTCATGAAAATTCAATGACGAAGAAAGATCCATTTCATTTATTTACGAAATGGTT
TGATGAGGCTCTTGTCAGAGAAGACTTGGTTGAGCCAAATGCTATGTGCTTAGCAACCGT
GAATAAAGATGGTTATCCTTCGGCTCGTTTTGTGTTGTTAAAGACATATGATGAGCGAGG
TTTTACATTTTTTACAAATTACGATAGTCGCAAGGCAAAAGATATGGAAGAAAATCCAAA
TGTCGCAGCTACAATTTATTGGTTACCATTAAAACGTTCTATAAGAATCGAGGGGAGCGT
TACAAAAATTTCAAAGGAGGAATCTGAAGTATATTTTCATTCACGTCCTCGGGCAAGTCA
AATTGGTGCTTTAGCTTCACCACAAAGTAAAGCAATTCCAAGTCGAGAGTATCTTGATGA
GATAGAATCCGGGATTAAAAAGGAGTTGGGTGATGGTCAAGTTCCTATTCCAAATTGGGG
TGGTTATCTCATTACACCAAGAGCAATTGAGTTCTGGCAGGGACAAACTAACCGACTTCA
TGATAGAATTCGTTTTCGCAAGAGTGATGAGAAGGCTGATGAAAAATTAGTTCATCAAGC
AGATCTTGAAGGTTGGGTTTATGAAAGACTTGCTCCTTAA

>g10378.t5 Gene=g10378 Length=228
MTVHIAIRAKYREPQDIFHENSMTKKDPFHLFTKWFDEALVREDLVEPNAMCLATVNKDG
YPSARFVLLKTYDERGFTFFTNYDSRKAKDMEENPNVAATIYWLPLKRSIRIEGSVTKIS
KEESEVYFHSRPRASQIGALASPQSKAIPSREYLDEIESGIKKELGDGQVPIPNWGGYLI
TPRAIEFWQGQTNRLHDRIRFRKSDEKADEKLVHQADLEGWVYERLAP

Protein features from InterProScan

Transcript Database ID Name Start End E.value
7 g10378.t5 Gene3D G3DSA:2.30.110.10 Electron Transport 19 228 8.7E-77
5 g10378.t5 Hamap MF_01629 Pyridoxine/pyridoxamine 5’-phosphate oxidase [pdxH]. 10 228 34.958458
3 g10378.t5 PANTHER PTHR10851 PYRIDOXINE-5-PHOSPHATE OXIDASE 4 228 5.3E-83
4 g10378.t5 PANTHER PTHR10851:SF0 PYRIDOXINE-5’-PHOSPHATE OXIDASE 4 228 5.3E-83
8 g10378.t5 PIRSF PIRSF000190 Pyd_amn-ph_oxd 2 228 2.5E-79
1 g10378.t5 Pfam PF01243 Pyridoxamine 5’-phosphate oxidase 40 123 1.2E-24
2 g10378.t5 Pfam PF10590 Pyridoxine 5’-phosphate oxidase C-terminal dimerisation region 175 228 5.8E-20
9 g10378.t5 ProSitePatterns PS01064 Pyridoxamine 5’-phosphate oxidase signature. 185 198 -
6 g10378.t5 SUPERFAMILY SSF50475 FMN-binding split barrel 24 228 1.55E-58
10 g10378.t5 TIGRFAM TIGR00558 pdxH: pyridoxamine 5’-phosphate oxidase 7 207 3.9E-73

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:0004733 pyridoxamine-phosphate oxidase activity MF
GO:0008615 pyridoxine biosynthetic process BP
GO:0016638 oxidoreductase activity, acting on the CH-NH2 group of donors MF
GO:0010181 FMN binding 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