General information for g10378.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Pyridoxine-5’-phosphate oxidase.
Parent gene
- The parent gene g10378 is located on chr_1: 9328801..9329621 (- strand)
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.t1 | TTS | g10378.t1 | 9328610 | 9328610 |
| chr_1 | g10378 | g10378.t1 | isoform | g10378.t1 | 9328801 | 9329621 |
| chr_1 | g10378 | g10378.t1 | exon | g10378.t1.exon1 | 9328801 | 9329314 |
| chr_1 | g10378 | g10378.t1 | cds | g10378.t1.CDS1 | 9328801 | 9329314 |
| chr_1 | g10378 | g10378.t1 | exon | g10378.t1.exon2 | 9329376 | 9329532 |
| chr_1 | g10378 | g10378.t1 | cds | g10378.t1.CDS2 | 9329376 | 9329532 |
| chr_1 | g10378 | g10378.t1 | exon | g10378.t1.exon3 | 9329597 | 9329621 |
| chr_1 | g10378 | g10378.t1 | cds | g10378.t1.CDS3 | 9329597 | 9329621 |
| chr_1 | g10378 | g10378.t1 | TSS | g10378.t1 | 9329685 | 9329685 |
Sequences
>g10378.t1 Gene=g10378 Length=696
ATGTCTACTACAGTCGAGATTTCAGCCATAAGAGCAAAATATAGAGAACCACAAGATATT
TTTCATGAAAATTCAATGACGAAGAAAGATCCATTTCATTTATTTACGAAATGGTTTGAT
GAGGCTCTTGTCAGAGAAGACTTGGTTGAGCCAAATGCTATGTGCTTAGCAACCGTGAAT
AAAGATGGTTATCCTTCGGCTCGTTTTGTGTTGTTAAAGACATATGATGAGCGAGGTTTT
ACATTTTTTACAAATTACGATAGTCGCAAGGCAAAAGATATGGAAGAAAATCCAAATGTC
GCAGCTACAATTTATTGGTTACCATTAAAACGTTCTATAAGAATCGAGGGGAGCGTTACA
AAAATTTCAAAGGAGGAATCTGAAGTATATTTTCATTCACGTCCTCGGGCAAGTCAAATT
GGTGCTTTAGCTTCACCACAAAGTAAAGCAATTCCAAGTCGAGAGTATCTTGATGAGATA
GAATCCGGGATTAAAAAGGAGTTGGGTGATGGTCAAGTTCCTATTCCAAATTGGGGTGGT
TATCTCATTACACCAAGAGCAATTGAGTTCTGGCAGGGACAAACTAACCGACTTCATGAT
AGAATTCGTTTTCGCAAGAGTGATGAGAAGGCTGATGAAAAATTAGTTCATCAAGCAGAT
CTTGAAGGTTGGGTTTATGAAAGACTTGCTCCTTAA
>g10378.t1 Gene=g10378 Length=231
MSTTVEISAIRAKYREPQDIFHENSMTKKDPFHLFTKWFDEALVREDLVEPNAMCLATVN
KDGYPSARFVLLKTYDERGFTFFTNYDSRKAKDMEENPNVAATIYWLPLKRSIRIEGSVT
KISKEESEVYFHSRPRASQIGALASPQSKAIPSREYLDEIESGIKKELGDGQVPIPNWGG
YLITPRAIEFWQGQTNRLHDRIRFRKSDEKADEKLVHQADLEGWVYERLAP
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g10378.t1 | Gene3D | G3DSA:2.30.110.10 | Electron Transport | 22 | 231 | 9.1E-77 |
| 5 | g10378.t1 | Hamap | MF_01629 | Pyridoxine/pyridoxamine 5’-phosphate oxidase [pdxH]. | 13 | 231 | 34.958458 |
| 3 | g10378.t1 | PANTHER | PTHR10851 | PYRIDOXINE-5-PHOSPHATE OXIDASE | 3 | 231 | 4.1E-84 |
| 4 | g10378.t1 | PANTHER | PTHR10851:SF0 | PYRIDOXINE-5’-PHOSPHATE OXIDASE | 3 | 231 | 4.1E-84 |
| 8 | g10378.t1 | PIRSF | PIRSF000190 | Pyd_amn-ph_oxd | 1 | 231 | 1.3E-79 |
| 1 | g10378.t1 | Pfam | PF01243 | Pyridoxamine 5’-phosphate oxidase | 43 | 126 | 1.2E-24 |
| 2 | g10378.t1 | Pfam | PF10590 | Pyridoxine 5’-phosphate oxidase C-terminal dimerisation region | 178 | 231 | 5.9E-20 |
| 9 | g10378.t1 | ProSitePatterns | PS01064 | Pyridoxamine 5’-phosphate oxidase signature. | 188 | 201 | - |
| 6 | g10378.t1 | SUPERFAMILY | SSF50475 | FMN-binding split barrel | 27 | 231 | 1.63E-58 |
| 10 | g10378.t1 | TIGRFAM | TIGR00558 | pdxH: pyridoxamine 5’-phosphate oxidase | 4 | 210 | 2.9E-74 |
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
- This transcript has been annotated with K00275 (pyridoxamine 5’-phosphate oxidase)
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.
