Gene loci information

Transcript annotation

  • This transcript has been annotated as Cytochrome P450 4d1.

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_1 g12530 g12530.t2 TTS g12530.t2 24268524 24268524
chr_1 g12530 g12530.t2 isoform g12530.t2 24268592 24269517
chr_1 g12530 g12530.t2 exon g12530.t2.exon1 24268592 24269517
chr_1 g12530 g12530.t2 cds g12530.t2.CDS1 24268806 24269450
chr_1 g12530 g12530.t2 TSS g12530.t2 NA NA

Sequences

>g12530.t2 Gene=g12530 Length=926
AAGGATCATCACAATAAAATCATTTGATACAACAAAGCAAATTGAATTTCTGTATCGCTT
TACAGAAATGTATCGCAGAGAAAAGAAATTAATTGAAGAATTGCATGCGTTCACTGACAA
AATTATTCAATCGCGTAGAGAAGAATTACTGATGCACAATGAAGAAACGTCAGAGCAAAA
TGATGAGATCGGAACAAAAAAGAAGAAAGCTCTTTTGGATATTTTGTTGAGTTCAAGAGT
TGAAGGAGAGCCATTAAAAAATTCCGATATTCGAGAAGAAGTTGATACATTCATGTTTGC
CGGTCATGACACCTCTAAAAGTGGTATTTGTTTTGTATTTTATTGCATTGCTAAGTATCC
AGAAGTTCAACAAAAGGTTTATGAGGAAATAATTGAAGTGCTTGGTGATGAAGAGGAAAT
AAATTTACAAAAATTGAATGAACTGCACTATCTAGAATTGGTGATTCGTGAGTCATTAAG
ACTTTTTCCACCTGTACCTTATTATGGACGACAATTAGTAGAAGAGTTAATTACTGAAAA
ATATACTTTTCCAAAAGGAATGAATGTGTATGTGTCTCCTTATTTGATGGGAAGAGATGA
AAGGATTTTTCCTGAACCAAAAAAATTTGATCCGCACCGTTTTGAAGTAGAAATGGCTAA
TGATAAAATTAATCCCTTTTCGTATGTGCCTTTTTCAGCTGGTCCAAGGTAAAACTTTCT
TATTTCTTTCAAACTTTCAAGTTTTGAAATTTTCATTCAACAGAAATTGTATTGGCCAAA
AATTTGCACAATATGAAATGAGAATGATCGCTGCAAAAGTTTTAAGAAAATTTAAATTAT
CTATTGCTAGTGAAATCACTATCCTATCAGAATTAGTCTTGAGACCGGAAAATGGAGTAA
ACTTGAAAATCGAGAAGAGAAAATAA

>g12530.t2 Gene=g12530 Length=214
MYRREKKLIEELHAFTDKIIQSRREELLMHNEETSEQNDEIGTKKKKALLDILLSSRVEG
EPLKNSDIREEVDTFMFAGHDTSKSGICFVFYCIAKYPEVQQKVYEEIIEVLGDEEEINL
QKLNELHYLELVIRESLRLFPPVPYYGRQLVEELITEKYTFPKGMNVYVSPYLMGRDERI
FPEPKKFDPHRFEVEMANDKINPFSYVPFSAGPR

Protein features from InterProScan

Transcript Database ID Name Start End E.value
13 g12530.t2 Gene3D G3DSA:1.10.630.10 Cytochrome p450 1 214 0.0e+00
2 g12530.t2 PANTHER PTHR24291:SF143 CYTOCHROME P450 4D1-RELATED 2 214 0.0e+00
3 g12530.t2 PANTHER PTHR24291 CYTOCHROME P450 FAMILY 4 2 214 0.0e+00
5 g12530.t2 PRINTS PR00463 E-class P450 group I signature 67 84 0.0e+00
11 g12530.t2 PRINTS PR00385 P450 superfamily signature 78 95 3.6e-06
8 g12530.t2 PRINTS PR00463 E-class P450 group I signature 87 113 0.0e+00
6 g12530.t2 PRINTS PR00463 E-class P450 group I signature 130 148 0.0e+00
9 g12530.t2 PRINTS PR00385 P450 superfamily signature 131 142 3.6e-06
4 g12530.t2 PRINTS PR00463 E-class P450 group I signature 170 194 0.0e+00
7 g12530.t2 PRINTS PR00463 E-class P450 group I signature 206 214 0.0e+00
10 g12530.t2 PRINTS PR00385 P450 superfamily signature 207 214 3.6e-06
1 g12530.t2 Pfam PF00067 Cytochrome P450 1 214 0.0e+00
12 g12530.t2 SUPERFAMILY SSF48264 Cytochrome P450 2 214 0.0e+00

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

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