General information for g17447.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Phytanoyl-CoA dioxygenase domain-containing protein 1.
Parent gene
- The parent gene g17447 is located on chr_4: 13555720..13556800 (+ 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 | g17447 | g17447.t1 | TSS | g17447.t1 | 13554692 | 13554692 |
| chr_4 | g17447 | g17447.t1 | isoform | g17447.t1 | 13554770 | 13556604 |
| chr_4 | g17447 | g17447.t1 | exon | g17447.t1.exon1 | 13554770 | 13554793 |
| chr_4 | g17447 | g17447.t1 | cds | g17447.t1.CDS1 | 13554770 | 13554793 |
| chr_4 | g17447 | g17447.t1 | exon | g17447.t1.exon2 | 13555721 | 13556360 |
| chr_4 | g17447 | g17447.t1 | cds | g17447.t1.CDS2 | 13555721 | 13556360 |
| chr_4 | g17447 | g17447.t1 | exon | g17447.t1.exon3 | 13556435 | 13556604 |
| chr_4 | g17447 | g17447.t1 | cds | g17447.t1.CDS3 | 13556435 | 13556604 |
| chr_4 | g17447 | g17447.t1 | TTS | g17447.t1 | 13556777 | 13556777 |
Sequences
>g17447.t1 Gene=g17447 Length=834
ATGGCAACTGAATTATATGACAGGTTTGATCGCGATGGCTATCTAATTGTCGATGATTTC
TTCAGTTCATCTGAAGTCAGTGAACTCCTTAAAGCTGGTCGAACTCTACCTAAGCAGGCA
CCAAAAGAAGATCGAAGTGCCTTTCAAAATCAAAATCGTGACAAATATTTCATTGAATCA
GGCGATAAAATTCGTTTCTTTTTTGAAGCTGATGCTCTTGGACCAAATAATGAATTGCTT
GTGCCTGAAGAATATTCTTTAAATAAAGTTGGCCATTCATTGCATGTCGATCATCCTGTT
TTTAGAAAATACACATTTGATAATAGAGTAAGAGAATTATGCTGGCAATTGGGTTTTCAA
CGTCCTGCAGTTGCTCAAAGCATGTACATGTTTAAAAATCCAAATGTTGGTGGTGAAGTG
ACTTCACATCAAGATGCAACTTATTTGTATACTGAACCATCATCAGTTGTTGGATTTTGG
ATTGCATTAGAAGATGCAACACTCGAAAATGGCTGCTTAAAATTCATTCGTGGTTCACAT
AAAAATGGAATTCATCGTCGCTTTGTGAGAAATAGCGATCCAAGTTCGAAAGAAATTTTG
ATTTATGATAAACCTGAATGTGTTTATCAAATGTCAAATTTCACTGCTATGCCAGTCAAA
GCTGGAACTCTTGTAGTCATCCATGGATCAGTTGTTCATCGCAGTGAGCCAAATAGATCG
AAAAATTCAAGACACGCCTACACTTTTCATGTTATTGAAACAAAAGGAACAAGATGGTCA
GCTGACAATTGGCTTCAACCCAATGAACCTTTCCCTATTTTGTATGAGCGATAG
>g17447.t1 Gene=g17447 Length=277
MATELYDRFDRDGYLIVDDFFSSSEVSELLKAGRTLPKQAPKEDRSAFQNQNRDKYFIES
GDKIRFFFEADALGPNNELLVPEEYSLNKVGHSLHVDHPVFRKYTFDNRVRELCWQLGFQ
RPAVAQSMYMFKNPNVGGEVTSHQDATYLYTEPSSVVGFWIALEDATLENGCLKFIRGSH
KNGIHRRFVRNSDPSSKEILIYDKPECVYQMSNFTAMPVKAGTLVVIHGSVVHRSEPNRS
KNSRHAYTFHVIETKGTRWSADNWLQPNEPFPILYER
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g17447.t1 | Gene3D | G3DSA:2.60.120.620 | q2cbj1_9rhob like domain | 1 | 276 | 0 |
| 2 | g17447.t1 | PANTHER | PTHR20883 | PHYTANOYL-COA DIOXYGENASE DOMAIN CONTAINING 1 | 5 | 275 | 0 |
| 3 | g17447.t1 | PANTHER | PTHR20883:SF15 | PHYTANOYL-COA DIOXYGENASE DOMAIN-CONTAINING PROTEIN 1 | 5 | 275 | 0 |
| 1 | g17447.t1 | Pfam | PF05721 | Phytanoyl-CoA dioxygenase (PhyH) | 9 | 246 | 0 |
| 4 | g17447.t1 | SUPERFAMILY | SSF51197 | Clavaminate synthase-like | 4 | 274 | 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.
