Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Probable cytochrome P450 4d14.

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_3 g571 g571.t1 isoform g571.t1 4181401 4182162
chr_3 g571 g571.t1 exon g571.t1.exon1 4181401 4181410
chr_3 g571 g571.t1 cds g571.t1.CDS1 4181401 4181410
chr_3 g571 g571.t1 exon g571.t1.exon2 4181471 4181667
chr_3 g571 g571.t1 cds g571.t1.CDS2 4181471 4181667
chr_3 g571 g571.t1 exon g571.t1.exon3 4181723 4181928
chr_3 g571 g571.t1 cds g571.t1.CDS3 4181723 4181928
chr_3 g571 g571.t1 exon g571.t1.exon4 4181985 4182162
chr_3 g571 g571.t1 cds g571.t1.CDS4 4181985 4182162
chr_3 g571 g571.t1 TTS g571.t1 4182183 4182183
chr_3 g571 g571.t1 TSS g571.t1 NA NA

Sequences

>g571.t1 Gene=g571 Length=591
ATGTTTGAAGCTCATGACACGACTAGTTCTGCAATTGCTTTTACTCTTTTGAATTTAGCA
AAACATCAAGAAATTCAGAAAAAGGTTTATAATGAATGTTTCGAAATTTTCGGCAATGAT
TTGAGTCAACAACCGACAATGCAAGATTTGAATAAAATGAATTACTTAGACAAGGTTATT
AAAGAAAATCTTAGACTTTATCCTTCGGTTCCAAATTTTGGAAGAAAGTTCAATGATGAC
GAAGTAATTGGTGATTATATCTTTCCTAAAAATGTTGCAATACGAATTTCACCGTACTCA
ATGGGACGCGATCCAAAACTTTTCCCTGATCCTCTGAAGTTTGATCCATCAAGATTTGAA
ATTGAAAAAAATATAAAATTGTTCTCGTTTGTGCCTTTCTCAGCTGGTCCAAGGAATTGC
ATTGGCCAAAAATATGCAATGCTTGAATTGAAAAGTGTTCTTTCGAAAATTGTAAGAAAC
TTTGAAGTGTGCGTACGAAAAGAAAATGAAAACCCAATTTATGCTTCTGAACTTGTTCTA
CGACCAATGAATGGAATTTATTTGTATTTCAAAGATAGAAATCATTCATAA

>g571.t1 Gene=g571 Length=196
MFEAHDTTSSAIAFTLLNLAKHQEIQKKVYNECFEIFGNDLSQQPTMQDLNKMNYLDKVI
KENLRLYPSVPNFGRKFNDDEVIGDYIFPKNVAIRISPYSMGRDPKLFPDPLKFDPSRFE
IEKNIKLFSFVPFSAGPRNCIGQKYAMLELKSVLSKIVRNFEVCVRKENENPIYASELVL
RPMNGIYLYFKDRNHS

Protein features from InterProScan

Transcript Database ID Name Start End E.value
15 g571.t1 Gene3D G3DSA:1.10.630.10 Cytochrome p450 1 196 7.6E-68
2 g571.t1 PANTHER PTHR24291:SF143 CYTOCHROME P450 4D1-RELATED 1 193 6.2E-69
3 g571.t1 PANTHER PTHR24291 CYTOCHROME P450 FAMILY 4 1 193 6.2E-69
12 g571.t1 PRINTS PR00385 P450 superfamily signature 3 20 5.9E-13
8 g571.t1 PRINTS PR00463 E-class P450 group I signature 12 38 1.5E-19
7 g571.t1 PRINTS PR00463 E-class P450 group I signature 57 75 1.5E-19
11 g571.t1 PRINTS PR00385 P450 superfamily signature 58 69 5.9E-13
6 g571.t1 PRINTS PR00463 E-class P450 group I signature 97 121 1.5E-19
4 g571.t1 PRINTS PR00463 E-class P450 group I signature 130 140 1.5E-19
10 g571.t1 PRINTS PR00385 P450 superfamily signature 131 140 5.9E-13
5 g571.t1 PRINTS PR00463 E-class P450 group I signature 140 163 1.5E-19
9 g571.t1 PRINTS PR00385 P450 superfamily signature 140 151 5.9E-13
1 g571.t1 Pfam PF00067 Cytochrome P450 1 187 2.1E-64
14 g571.t1 ProSitePatterns PS00086 Cytochrome P450 cysteine heme-iron ligand signature. 133 142 -
13 g571.t1 SUPERFAMILY SSF48264 Cytochrome P450 1 193 6.68E-65

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g571/g571.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g571.t1.fa.iupred3.txt does not exist

GO terms from InterProScan

GOID TERM ONTOLOGY
GO:0020037 heme binding MF
GO:0016705 oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen MF
GO:0005506 iron ion binding MF
GO:0055114 NA NA

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.

Raw TPM values