General information for g14390.t23
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Phytanoyl-CoA dioxygenase domain-containing protein 1-like protein.
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.t23 | TTS | g14390.t23 | 245077 | 245077 |
| chr_4 | g14390 | g14390.t23 | isoform | g14390.t23 | 245152 | 247021 |
| chr_4 | g14390 | g14390.t23 | exon | g14390.t23.exon1 | 245152 | 245316 |
| chr_4 | g14390 | g14390.t23 | cds | g14390.t23.CDS1 | 245153 | 245316 |
| chr_4 | g14390 | g14390.t23 | exon | g14390.t23.exon2 | 245375 | 245888 |
| chr_4 | g14390 | g14390.t23 | cds | g14390.t23.CDS2 | 245375 | 245888 |
| chr_4 | g14390 | g14390.t23 | exon | g14390.t23.exon3 | 246336 | 246464 |
| chr_4 | g14390 | g14390.t23 | cds | g14390.t23.CDS3 | 246336 | 246464 |
| chr_4 | g14390 | g14390.t23 | exon | g14390.t23.exon4 | 247016 | 247021 |
| chr_4 | g14390 | g14390.t23 | cds | g14390.t23.CDS4 | 247016 | 247021 |
| chr_4 | g14390 | g14390.t23 | TSS | g14390.t23 | 247105 | 247105 |
Sequences
>g14390.t23 Gene=g14390 Length=814
ATGACATTTAATCAAGATGGTTTTCTTGTTCTTGAAGACTTTTATACTCCTGCCGAAATC
AATGAACTATTAAAAGCGGGACGTGCATTGCCATCACAAGCACCTAAAGAAGAACGATGT
GCTTTTCAAAGTCAACAACGAGATAAGAAATATTTTCTAGAATCGGGCAATAAGATTTGT
TACTTTTTTGAAGCTACTGCATTAGGACCGAACAATGAATTAATTGTTCCTGAAGAATTT
TCACTTAATAAAGTCGGCCATGCATTAGGCGTTCAACATCCTGTTTTTCGAAAGTATACA
TTTGATAATAGAATAAGAGAACTTTGTTGGCAACTTGGTTTTCAAAAACCTGCTTTAACT
CAAAGCATGTACATGTTTAAAAATCCCGGAATCGGTGCAGAAGTTACTGCACATCAAGAT
GCAACTTATATGTATACTGAACCATTATCAGTCGTTGGATTCTGGATTGCATTAGATGAT
GCAACTTTTGAGAATGGTTGCCTCAAATTTATCAGAGGATCTCATAAAAATGGAGTACAC
CGTCGATATATGAGGAATAATGATCCTAATTCAGAAGATGTTTTAGTTTTTGATAAGCCA
GCTCCTATTTATCAACAATCAAGTTTCACTGCAGTGCCTGTTAAAAGCGGCACACTTGTT
GTTATTCACGGCAATGTAGTTCATCGAAGTGATCCAAATAGATCTCAGAAATCTCGTCAT
GCCTATACATTTCATGTCATTGAAACAAAAGACACCAAATATAGTCCTGATAATTGGCTT
CAACCAAATGAACCTTTTCCTATTTTGTATGAAC
>g14390.t23 Gene=g14390 Length=271
MTFNQDGFLVLEDFYTPAEINELLKAGRALPSQAPKEERCAFQSQQRDKKYFLESGNKIC
YFFEATALGPNNELIVPEEFSLNKVGHALGVQHPVFRKYTFDNRIRELCWQLGFQKPALT
QSMYMFKNPGIGAEVTAHQDATYMYTEPLSVVGFWIALDDATFENGCLKFIRGSHKNGVH
RRYMRNNDPNSEDVLVFDKPAPIYQQSSFTAVPVKSGTLVVIHGNVVHRSDPNRSQKSRH
AYTFHVIETKDTKYSPDNWLQPNEPFPILYE
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g14390.t23 | Gene3D | G3DSA:2.60.120.620 | q2cbj1_9rhob like domain | 1 | 271 | 0 |
| 2 | g14390.t23 | PANTHER | PTHR20883 | PHYTANOYL-COA DIOXYGENASE DOMAIN CONTAINING 1 | 2 | 270 | 0 |
| 3 | g14390.t23 | PANTHER | PTHR20883:SF15 | PHYTANOYL-COA DIOXYGENASE DOMAIN-CONTAINING PROTEIN 1 | 2 | 270 | 0 |
| 1 | g14390.t23 | Pfam | PF05721 | Phytanoyl-CoA dioxygenase (PhyH) | 3 | 241 | 0 |
| 4 | g14390.t23 | SUPERFAMILY | SSF51197 | Clavaminate synthase-like | 3 | 266 | 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.
