General information for g14390.t12
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Phytanoyl-CoA dioxygenase.
Parent gene
- The parent gene g14390 is located on chr_4: 245391..247021 (- 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_4 | g14390 | g14390.t12 | TTS | g14390.t12 | 245077 | 245077 |
| chr_4 | g14390 | g14390.t12 | isoform | g14390.t12 | 245152 | 247021 |
| chr_4 | g14390 | g14390.t12 | exon | g14390.t12.exon1 | 245152 | 245316 |
| chr_4 | g14390 | g14390.t12 | cds | g14390.t12.CDS1 | 245153 | 245316 |
| chr_4 | g14390 | g14390.t12 | exon | g14390.t12.exon2 | 245375 | 245888 |
| chr_4 | g14390 | g14390.t12 | cds | g14390.t12.CDS2 | 245375 | 245657 |
| chr_4 | g14390 | g14390.t12 | exon | g14390.t12.exon3 | 246336 | 246433 |
| chr_4 | g14390 | g14390.t12 | exon | g14390.t12.exon4 | 246998 | 247021 |
| chr_4 | g14390 | g14390.t12 | TSS | g14390.t12 | 247105 | 247105 |
Sequences
>g14390.t12 Gene=g14390 Length=801
ATGACATCAAAATTACTTGAAAAAACTTTTATACTCCTGCCGAAATCAATGAACTATTAA
AAGCGGGACGTGCATTGCCATCACAAGCACCTAAAGAAGAACGATGTGCTTTTCAAAGTC
AACAACGAGATAAGAAATATTTTCTAGAATCGGGCAATAAGATTTGTTACTTTTTTGAAG
CTACTGCATTAGGACCGAACAATGAATTAATTGTTCCTGAAGAATTTTCACTTAATAAAG
TCGGCCATGCATTAGGCGTTCAACATCCTGTTTTTCGAAAGTATACATTTGATAATAGAA
TAAGAGAACTTTGTTGGCAACTTGGTTTTCAAAAACCTGCTTTAACTCAAAGCATGTACA
TGTTTAAAAATCCCGGAATCGGTGCAGAAGTTACTGCACATCAAGATGCAACTTATATGT
ATACTGAACCATTATCAGTCGTTGGATTCTGGATTGCATTAGATGATGCAACTTTTGAGA
ATGGTTGCCTCAAATTTATCAGAGGATCTCATAAAAATGGAGTACACCGTCGATATATGA
GGAATAATGATCCTAATTCAGAAGATGTTTTAGTTTTTGATAAGCCAGCTCCTATTTATC
AACAATCAAGTTTCACTGCAGTGCCTGTTAAAAGCGGCACACTTGTTGTTATTCACGGCA
ATGTAGTTCATCGAAGTGATCCAAATAGATCTCAGAAATCTCGTCATGCCTATACATTTC
ATGTCATTGAAACAAAAGACACCAAATATAGTCCTGATAATTGGCTTCAACCAAATGAAC
CTTTTCCTATTTTGTATGAAC
>g14390.t12 Gene=g14390 Length=149
MYMFKNPGIGAEVTAHQDATYMYTEPLSVVGFWIALDDATFENGCLKFIRGSHKNGVHRR
YMRNNDPNSEDVLVFDKPAPIYQQSSFTAVPVKSGTLVVIHGNVVHRSDPNRSQKSRHAY
TFHVIETKDTKYSPDNWLQPNEPFPILYE
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g14390.t12 | Gene3D | G3DSA:2.60.120.620 | q2cbj1_9rhob like domain | 1 | 149 | 0 |
| 2 | g14390.t12 | PANTHER | PTHR20883 | PHYTANOYL-COA DIOXYGENASE DOMAIN CONTAINING 1 | 1 | 148 | 0 |
| 3 | g14390.t12 | PANTHER | PTHR20883:SF15 | PHYTANOYL-COA DIOXYGENASE DOMAIN-CONTAINING PROTEIN 1 | 1 | 148 | 0 |
| 1 | g14390.t12 | Pfam | PF05721 | Phytanoyl-CoA dioxygenase (PhyH) | 1 | 119 | 0 |
| 4 | g14390.t12 | SUPERFAMILY | SSF51197 | Clavaminate synthase-like | 1 | 145 | 0 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
GO terms from InterProScan
There are no GO annotations for this transcript.
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.
