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.t3 TTS g12530.t3 24268524 24268524
chr_1 g12530 g12530.t3 isoform g12530.t3 24268592 24269517
chr_1 g12530 g12530.t3 exon g12530.t3.exon1 24268592 24268754
chr_1 g12530 g12530.t3 cds g12530.t3.CDS1 24268592 24268754
chr_1 g12530 g12530.t3 exon g12530.t3.exon2 24268810 24269517
chr_1 g12530 g12530.t3 cds g12530.t3.CDS2 24268810 24269450
chr_1 g12530 g12530.t3 TSS g12530.t3 NA NA

Sequences

>g12530.t3 Gene=g12530 Length=871
AAGGATCATCACAATAAAATCATTTGATACAACAAAGCAAATTGAATTTCTGTATCGCTT
TACAGAAATGTATCGCAGAGAAAAGAAATTAATTGAAGAATTGCATGCGTTCACTGACAA
AATTATTCAATCGCGTAGAGAAGAATTACTGATGCACAATGAAGAAACGTCAGAGCAAAA
TGATGAGATCGGAACAAAAAAGAAGAAAGCTCTTTTGGATATTTTGTTGAGTTCAAGAGT
TGAAGGAGAGCCATTAAAAAATTCCGATATTCGAGAAGAAGTTGATACATTCATGTTTGC
CGGTCATGACACCTCTAAAAGTGGTATTTGTTTTGTATTTTATTGCATTGCTAAGTATCC
AGAAGTTCAACAAAAGGTTTATGAGGAAATAATTGAAGTGCTTGGTGATGAAGAGGAAAT
AAATTTACAAAAATTGAATGAACTGCACTATCTAGAATTGGTGATTCGTGAGTCATTAAG
ACTTTTTCCACCTGTACCTTATTATGGACGACAATTAGTAGAAGAGTTAATTACTGAAAA
ATATACTTTTCCAAAAGGAATGAATGTGTATGTGTCTCCTTATTTGATGGGAAGAGATGA
AAGGATTTTTCCTGAACCAAAAAAATTTGATCCGCACCGTTTTGAAGTAGAAATGGCTAA
TGATAAAATTAATCCCTTTTCGTATGTGCCTTTTTCAGCTGGTCCAAGAAATTGTATTGG
CCAAAAATTTGCACAATATGAAATGAGAATGATCGCTGCAAAAGTTTTAAGAAAATTTAA
ATTATCTATTGCTAGTGAAATCACTATCCTATCAGAATTAGTCTTGAGACCGGAAAATGG
AGTAAACTTGAAAATCGAGAAGAGAAAATAA

>g12530.t3 Gene=g12530 Length=267
MYRREKKLIEELHAFTDKIIQSRREELLMHNEETSEQNDEIGTKKKKALLDILLSSRVEG
EPLKNSDIREEVDTFMFAGHDTSKSGICFVFYCIAKYPEVQQKVYEEIIEVLGDEEEINL
QKLNELHYLELVIRESLRLFPPVPYYGRQLVEELITEKYTFPKGMNVYVSPYLMGRDERI
FPEPKKFDPHRFEVEMANDKINPFSYVPFSAGPRNCIGQKFAQYEMRMIAAKVLRKFKLS
IASEITILSELVLRPENGVNLKIEKRK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
16 g12530.t3 Gene3D G3DSA:1.10.630.10 Cytochrome p450 1 267 1.0E-81
2 g12530.t3 PANTHER PTHR24291:SF143 CYTOCHROME P450 4D1-RELATED 2 266 1.6E-90
3 g12530.t3 PANTHER PTHR24291 CYTOCHROME P450 FAMILY 4 2 266 1.6E-90
6 g12530.t3 PRINTS PR00463 E-class P450 group I signature 67 84 5.7E-22
13 g12530.t3 PRINTS PR00385 P450 superfamily signature 78 95 2.0E-11
8 g12530.t3 PRINTS PR00463 E-class P450 group I signature 87 113 5.7E-22
7 g12530.t3 PRINTS PR00463 E-class P450 group I signature 130 148 5.7E-22
10 g12530.t3 PRINTS PR00385 P450 superfamily signature 131 142 2.0E-11
5 g12530.t3 PRINTS PR00463 E-class P450 group I signature 170 194 5.7E-22
9 g12530.t3 PRINTS PR00463 E-class P450 group I signature 206 216 5.7E-22
12 g12530.t3 PRINTS PR00385 P450 superfamily signature 207 216 2.0E-11
4 g12530.t3 PRINTS PR00463 E-class P450 group I signature 216 239 5.7E-22
11 g12530.t3 PRINTS PR00385 P450 superfamily signature 216 227 2.0E-11
1 g12530.t3 Pfam PF00067 Cytochrome P450 1 257 2.1E-77
15 g12530.t3 ProSitePatterns PS00086 Cytochrome P450 cysteine heme-iron ligand signature. 209 218 -
14 g12530.t3 SUPERFAMILY SSF48264 Cytochrome P450 2 266 2.1E-76

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