General information for g12434.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Hydroxyacid oxidase 1.
Parent gene
- The parent gene g12434 is located on chr_1: 23606019..23607441 (+ 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 | g12434 | g12434.t1 | TSS | g12434.t1 | 23605971 | 23605971 |
| chr_1 | g12434 | g12434.t1 | isoform | g12434.t1 | 23606019 | 23607441 |
| chr_1 | g12434 | g12434.t1 | exon | g12434.t1.exon1 | 23606019 | 23606304 |
| chr_1 | g12434 | g12434.t1 | cds | g12434.t1.CDS1 | 23606019 | 23606304 |
| chr_1 | g12434 | g12434.t1 | exon | g12434.t1.exon2 | 23606386 | 23606679 |
| chr_1 | g12434 | g12434.t1 | cds | g12434.t1.CDS2 | 23606386 | 23606679 |
| chr_1 | g12434 | g12434.t1 | exon | g12434.t1.exon3 | 23606742 | 23606817 |
| chr_1 | g12434 | g12434.t1 | cds | g12434.t1.CDS3 | 23606742 | 23606817 |
| chr_1 | g12434 | g12434.t1 | exon | g12434.t1.exon4 | 23606871 | 23607148 |
| chr_1 | g12434 | g12434.t1 | cds | g12434.t1.CDS4 | 23606871 | 23607148 |
| chr_1 | g12434 | g12434.t1 | exon | g12434.t1.exon5 | 23607209 | 23607223 |
| chr_1 | g12434 | g12434.t1 | cds | g12434.t1.CDS5 | 23607209 | 23607223 |
| chr_1 | g12434 | g12434.t1 | exon | g12434.t1.exon6 | 23607305 | 23607441 |
| chr_1 | g12434 | g12434.t1 | cds | g12434.t1.CDS6 | 23607305 | 23607441 |
| chr_1 | g12434 | g12434.t1 | TTS | g12434.t1 | 23607700 | 23607700 |
Sequences
>g12434.t1 Gene=g12434 Length=1086
ATGAGTAAACTGATTTCCCTCGATGAATATGAGAAGCGTGCTTTGGAAATTCTACCTGAA
AATGCCAGAGACTATTATCAAAGTGGTGCTGGCAACGAAAAATCACTAGCCTGGAATCGT
GCAGATTTTAGCAATTTTCGTATTCGTCCAAAAGTGCTAAGAGATGTTTCGAAACGTGAC
ACATCAGTGAATATTTTTAATACGAAAATAGAATTTCCAATAGGAATTTCACCTACAGCA
ATGCAAAAAATGGCTCACACTGATGGTGAAACAGCAACTGCAAAAGCTGCTGCCAACGAA
AATGTTATTGCTATTTTCAGTACAATTGCAACAACTTCAATTGAAGATATTGCAGCTGCA
GCTCCAAATTCTATAAAATGGTTTCAATTATACATTTATAGAGATAGAAAACTGACTGAA
AATCTTGTTAGACGTGCAGAAGCAGCTGGTTTTAAAGCACTTGTGTTAACGGTCGATGCA
CCTTTGTTTGGATTAAGGAGAAGAGACCTAAAGAATAAATTTTCTATGCCACCGCATTTA
AAATTGGCCAATTTTCAGGATGTTGTTTTAAGCATGGATGGTTCTGGTATTAATGAATAC
GTTGCAAGACAATTTGACCAAAGTATTTCTTGGGATGATGTAAAATGGCTAATGAATTTC
ACAAATCTGCCAATAATACTAAAAGGTATCATGACGAAAGAAGATGCTCGACTTGCATGT
AAATTAGGAGTTTCAGGTATAATGGTTTCAAATCATGGCGCACGTCAAATTGACAACACT
GCGTCATCGATTGAAGCTTTGGCAGAGGTAGCGGCTGAAGTTAAGGATGAAATTCCAATA
TTTTTCGATGGTGGTATACGTGAAGCTACAGATATTTTGATTGCATTGGCATTGGGTGCC
AAAATGTGTTTCATAGGAAGACCAGTAGTATATGGTTTGGCATGTGCAGGTCAAGAAGGA
GTTGAAGATGTCATAAGAATTCTCAAAAGAGAGTTCGATTTAGCTATGTGCCTGGCAGGC
GTGAAAAATGTTTCAGAGATTAATCGTGACATGGTGGTTCATAAAAATTATTACGCTCGG
TTGTAA
>g12434.t1 Gene=g12434 Length=361
MSKLISLDEYEKRALEILPENARDYYQSGAGNEKSLAWNRADFSNFRIRPKVLRDVSKRD
TSVNIFNTKIEFPIGISPTAMQKMAHTDGETATAKAAANENVIAIFSTIATTSIEDIAAA
APNSIKWFQLYIYRDRKLTENLVRRAEAAGFKALVLTVDAPLFGLRRRDLKNKFSMPPHL
KLANFQDVVLSMDGSGINEYVARQFDQSISWDDVKWLMNFTNLPIILKGIMTKEDARLAC
KLGVSGIMVSNHGARQIDNTASSIEALAEVAAEVKDEIPIFFDGGIREATDILIALALGA
KMCFIGRPVVYGLACAGQEGVEDVIRILKREFDLAMCLAGVKNVSEINRDMVVHKNYYAR
L
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g12434.t1 | CDD | cd02809 | alpha_hydroxyacid_oxid_FMN | 8 | 349 | 3.37012E-156 |
| 5 | g12434.t1 | Gene3D | G3DSA:3.20.20.70 | Aldolase class I | 2 | 360 | 6.6E-148 |
| 2 | g12434.t1 | PANTHER | PTHR10578:SF127 | HYDROXYACID OXIDASE 1 | 2 | 351 | 2.8E-146 |
| 3 | g12434.t1 | PANTHER | PTHR10578 | S -2-HYDROXY-ACID OXIDASE-RELATED | 2 | 351 | 2.8E-146 |
| 6 | g12434.t1 | PIRSF | PIRSF000138 | Al-hdrx_acd_dh | 1 | 357 | 5.1E-133 |
| 1 | g12434.t1 | Pfam | PF01070 | FMN-dependent dehydrogenase | 16 | 352 | 3.2E-130 |
| 8 | g12434.t1 | ProSitePatterns | PS00557 | FMN-dependent alpha-hydroxy acid dehydrogenases active site. | 250 | 256 | - |
| 9 | g12434.t1 | ProSiteProfiles | PS51349 | FMN-dependent alpha-hydroxy acid dehydrogenase domain profile. | 1 | 357 | 107.492 |
| 4 | g12434.t1 | SUPERFAMILY | SSF51395 | FMN-linked oxidoreductases | 4 | 353 | 1.04E-99 |
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:0010181 | FMN binding | MF |
| GO:0003824 | catalytic activity | MF |
| GO:0055114 | NA | NA |
| GO:0016491 | oxidoreductase activity | MF |
KEGG
Orthology
- This transcript has been annotated with K11517 ((S)-2-hydroxy-acid 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. There were no conditions that were differentially expressed