General information for g10378.t3
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative 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.t3 | TTS | g10378.t3 | 9328610 | 9328610 |
| chr_1 | g10378 | g10378.t3 | isoform | g10378.t3 | 9328801 | 9329621 |
| chr_1 | g10378 | g10378.t3 | exon | g10378.t3.exon1 | 9328801 | 9329314 |
| chr_1 | g10378 | g10378.t3 | cds | g10378.t3.CDS1 | 9328801 | 9329217 |
| chr_1 | g10378 | g10378.t3 | exon | g10378.t3.exon2 | 9329384 | 9329532 |
| chr_1 | g10378 | g10378.t3 | exon | g10378.t3.exon3 | 9329597 | 9329621 |
| chr_1 | g10378 | g10378.t3 | TSS | g10378.t3 | 9329685 | 9329685 |
Sequences
>g10378.t3 Gene=g10378 Length=688
ATGTCTACTACAGTCGAGATTTCAGCCATAAGAGCAAAATATAGAGAACCACAAGATATT
TTTCATGAAAATTCAATGACGAAGAAAGATCCATTTCATTTATTTACGAAATGGTTTGAT
GAGGCTCTTGTCAGAGAAGACTTGGTTGAGCCAAATGCTATGTGCTTAGCAACCAGATGG
TTATCCTTCGGCTCGTTTTGTGTTGTTAAAGACATATGATGAGCGAGGTTTTACATTTTT
TACAAATTACGATAGTCGCAAGGCAAAAGATATGGAAGAAAATCCAAATGTCGCAGCTAC
AATTTATTGGTTACCATTAAAACGTTCTATAAGAATCGAGGGGAGCGTTACAAAAATTTC
AAAGGAGGAATCTGAAGTATATTTTCATTCACGTCCTCGGGCAAGTCAAATTGGTGCTTT
AGCTTCACCACAAAGTAAAGCAATTCCAAGTCGAGAGTATCTTGATGAGATAGAATCCGG
GATTAAAAAGGAGTTGGGTGATGGTCAAGTTCCTATTCCAAATTGGGGTGGTTATCTCAT
TACACCAAGAGCAATTGAGTTCTGGCAGGGACAAACTAACCGACTTCATGATAGAATTCG
TTTTCGCAAGAGTGATGAGAAGGCTGATGAAAAATTAGTTCATCAAGCAGATCTTGAAGG
TTGGGTTTATGAAAGACTTGCTCCTTAA
>g10378.t3 Gene=g10378 Length=138
MEENPNVAATIYWLPLKRSIRIEGSVTKISKEESEVYFHSRPRASQIGALASPQSKAIPS
REYLDEIESGIKKELGDGQVPIPNWGGYLITPRAIEFWQGQTNRLHDRIRFRKSDEKADE
KLVHQADLEGWVYERLAP
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g10378.t3 | Gene3D | G3DSA:2.30.110.10 | Electron Transport | 1 | 138 | 1.7E-43 |
| 2 | g10378.t3 | PANTHER | PTHR10851 | PYRIDOXINE-5-PHOSPHATE OXIDASE | 2 | 138 | 4.3E-47 |
| 3 | g10378.t3 | PANTHER | PTHR10851:SF0 | PYRIDOXINE-5’-PHOSPHATE OXIDASE | 2 | 138 | 4.3E-47 |
| 1 | g10378.t3 | Pfam | PF10590 | Pyridoxine 5’-phosphate oxidase C-terminal dimerisation region | 85 | 138 | 2.1E-20 |
| 5 | g10378.t3 | ProSitePatterns | PS01064 | Pyridoxamine 5’-phosphate oxidase signature. | 95 | 108 | - |
| 4 | g10378.t3 | SUPERFAMILY | SSF50475 | FMN-binding split barrel | 1 | 138 | 3.19E-33 |
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 gene did not have any KEGG ortholog annotations (KAAS, GHOSTZ).
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