General information for g14390.t13
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.t13 | TTS | g14390.t13 | 245077 | 245077 |
| chr_4 | g14390 | g14390.t13 | isoform | g14390.t13 | 245152 | 247021 |
| chr_4 | g14390 | g14390.t13 | exon | g14390.t13.exon1 | 245152 | 245316 |
| chr_4 | g14390 | g14390.t13 | cds | g14390.t13.CDS1 | 245287 | 245316 |
| chr_4 | g14390 | g14390.t13 | exon | g14390.t13.exon2 | 245391 | 245888 |
| chr_4 | g14390 | g14390.t13 | cds | g14390.t13.CDS2 | 245391 | 245888 |
| chr_4 | g14390 | g14390.t13 | exon | g14390.t13.exon3 | 246336 | 246464 |
| chr_4 | g14390 | g14390.t13 | cds | g14390.t13.CDS3 | 246336 | 246464 |
| chr_4 | g14390 | g14390.t13 | exon | g14390.t13.exon4 | 246998 | 247021 |
| chr_4 | g14390 | g14390.t13 | cds | g14390.t13.CDS4 | 246998 | 247021 |
| chr_4 | g14390 | g14390.t13 | TSS | g14390.t13 | 247105 | 247105 |
Sequences
>g14390.t13 Gene=g14390 Length=816
ATGACATCAAAATTACTTGAAAAATTTAATCAAGATGGTTTTCTTGTTCTTGAAGACTTT
TATACTCCTGCCGAAATCAATGAACTATTAAAAGCGGGACGTGCATTGCCATCACAAGCA
CCTAAAGAAGAACGATGTGCTTTTCAAAGTCAACAACGAGATAAGAAATATTTTCTAGAA
TCGGGCAATAAGATTTGTTACTTTTTTGAAGCTACTGCATTAGGACCGAACAATGAATTA
ATTGTTCCTGAAGAATTTTCACTTAATAAAGTCGGCCATGCATTAGGCGTTCAACATCCT
GTTTTTCGAAAGTATACATTTGATAATAGAATAAGAGAACTTTGTTGGCAACTTGGTTTT
CAAAAACCTGCTTTAACTCAAAGCATGTACATGTTTAAAAATCCCGGAATCGGTGCAGAA
GTTACTGCACATCAAGATGCAACTTATATGTATACTGAACCATTATCAGTCGTTGGATTC
TGGATTGCATTAGATGATGCAACTTTTGAGAATGGTTGCCTCAAATTTATCAGAGGATCT
CATAAAAATGGAGTACACCGTCGATATATGAGGAATAATGATCCTAATTCAGAAGATGTT
TTAGTTTTTGATAAGCCAGCTCCTATTTATCAACAATCAAGTTTCACTGCAGCACACTTG
TTGTTATTCACGGCAATGTAGTTCATCGAAGTGATCCAAATAGATCTCAGAAATCTCGTC
ATGCCTATACATTTCATGTCATTGAAACAAAAGACACCAAATATAGTCCTGATAATTGGC
TTCAACCAAATGAACCTTTTCCTATTTTGTATGAAC
>g14390.t13 Gene=g14390 Length=226
MTSKLLEKFNQDGFLVLEDFYTPAEINELLKAGRALPSQAPKEERCAFQSQQRDKKYFLE
SGNKICYFFEATALGPNNELIVPEEFSLNKVGHALGVQHPVFRKYTFDNRIRELCWQLGF
QKPALTQSMYMFKNPGIGAEVTAHQDATYMYTEPLSVVGFWIALDDATFENGCLKFIRGS
HKNGVHRRYMRNNDPNSEDVLVFDKPAPIYQQSSFTAAHLLLFTAM
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g14390.t13 | Gene3D | G3DSA:2.60.120.620 | q2cbj1_9rhob like domain | 1 | 224 | 0 |
| 2 | g14390.t13 | PANTHER | PTHR20883 | PHYTANOYL-COA DIOXYGENASE DOMAIN CONTAINING 1 | 2 | 217 | 0 |
| 3 | g14390.t13 | PANTHER | PTHR20883:SF15 | PHYTANOYL-COA DIOXYGENASE DOMAIN-CONTAINING PROTEIN 1 | 2 | 217 | 0 |
| 1 | g14390.t13 | Pfam | PF05721 | Phytanoyl-CoA dioxygenase (PhyH) | 9 | 218 | 0 |
| 4 | g14390.t13 | SUPERFAMILY | SSF51197 | Clavaminate synthase-like | 2 | 198 | 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. There were no conditions that were differentially expressed