Gene loci information

Transcript annotation

  • This transcript has been annotated as Phytanoyl-CoA dioxygenase domain-containing protein 1-like protein.

Parent gene

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.t25 TTS g14390.t25 245077 245077
chr_4 g14390 g14390.t25 isoform g14390.t25 245152 247021
chr_4 g14390 g14390.t25 exon g14390.t25.exon1 245152 245316
chr_4 g14390 g14390.t25 cds g14390.t25.CDS1 245153 245316
chr_4 g14390 g14390.t25 exon g14390.t25.exon2 245375 245888
chr_4 g14390 g14390.t25 cds g14390.t25.CDS2 245375 245888
chr_4 g14390 g14390.t25 exon g14390.t25.exon3 246336 246464
chr_4 g14390 g14390.t25 cds g14390.t25.CDS3 246336 246464
chr_4 g14390 g14390.t25 exon g14390.t25.exon4 246779 246825
chr_4 g14390 g14390.t25 cds g14390.t25.CDS4 246779 246825
chr_4 g14390 g14390.t25 exon g14390.t25.exon5 246993 247021
chr_4 g14390 g14390.t25 cds g14390.t25.CDS5 246993 246993
chr_4 g14390 g14390.t25 TSS g14390.t25 247105 247105

Sequences

>g14390.t25 Gene=g14390 Length=884
ATGACATCAAAATTACTTGAAAAAGTATATGATTCAGTATTTAAATTTAGACATTTTTGC
TAGACATTTACGGTTATTTAATCAAGATGGTTTTCTTGTTCTTGAAGACTTTTATACTCC
TGCCGAAATCAATGAACTATTAAAAGCGGGACGTGCATTGCCATCACAAGCACCTAAAGA
AGAACGATGTGCTTTTCAAAGTCAACAACGAGATAAGAAATATTTTCTAGAATCGGGCAA
TAAGATTTGTTACTTTTTTGAAGCTACTGCATTAGGACCGAACAATGAATTAATTGTTCC
TGAAGAATTTTCACTTAATAAAGTCGGCCATGCATTAGGCGTTCAACATCCTGTTTTTCG
AAAGTATACATTTGATAATAGAATAAGAGAACTTTGTTGGCAACTTGGTTTTCAAAAACC
TGCTTTAACTCAAAGCATGTACATGTTTAAAAATCCCGGAATCGGTGCAGAAGTTACTGC
ACATCAAGATGCAACTTATATGTATACTGAACCATTATCAGTCGTTGGATTCTGGATTGC
ATTAGATGATGCAACTTTTGAGAATGGTTGCCTCAAATTTATCAGAGGATCTCATAAAAA
TGGAGTACACCGTCGATATATGAGGAATAATGATCCTAATTCAGAAGATGTTTTAGTTTT
TGATAAGCCAGCTCCTATTTATCAACAATCAAGTTTCACTGCAGTGCCTGTTAAAAGCGG
CACACTTGTTGTTATTCACGGCAATGTAGTTCATCGAAGTGATCCAAATAGATCTCAGAA
ATCTCGTCATGCCTATACATTTCATGTCATTGAAACAAAAGACACCAAATATAGTCCTGA
TAATTGGCTTCAACCAAATGAACCTTTTCCTATTTTGTATGAAC

>g14390.t25 Gene=g14390 Length=285
MIQYLNLDIFARHLRLFNQDGFLVLEDFYTPAEINELLKAGRALPSQAPKEERCAFQSQQ
RDKKYFLESGNKICYFFEATALGPNNELIVPEEFSLNKVGHALGVQHPVFRKYTFDNRIR
ELCWQLGFQKPALTQSMYMFKNPGIGAEVTAHQDATYMYTEPLSVVGFWIALDDATFENG
CLKFIRGSHKNGVHRRYMRNNDPNSEDVLVFDKPAPIYQQSSFTAVPVKSGTLVVIHGNV
VHRSDPNRSQKSRHAYTFHVIETKDTKYSPDNWLQPNEPFPILYE

Protein features from InterProScan

Transcript Database ID Name Start End E.value
5 g14390.t25 Gene3D G3DSA:2.60.120.620 q2cbj1_9rhob like domain 10 285 0
2 g14390.t25 PANTHER PTHR20883 PHYTANOYL-COA DIOXYGENASE DOMAIN CONTAINING 1 13 284 0
3 g14390.t25 PANTHER PTHR20883:SF15 PHYTANOYL-COA DIOXYGENASE DOMAIN-CONTAINING PROTEIN 1 13 284 0
1 g14390.t25 Pfam PF05721 Phytanoyl-CoA dioxygenase (PhyH) 17 255 0
4 g14390.t25 SUPERFAMILY SSF51197 Clavaminate synthase-like 14 280 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