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.t6 TTS g12530.t6 24268524 24268524
chr_1 g12530 g12530.t6 isoform g12530.t6 24268592 24271106
chr_1 g12530 g12530.t6 exon g12530.t6.exon1 24268592 24268754
chr_1 g12530 g12530.t6 cds g12530.t6.CDS1 24268592 24268754
chr_1 g12530 g12530.t6 exon g12530.t6.exon2 24268810 24269523
chr_1 g12530 g12530.t6 cds g12530.t6.CDS2 24268810 24269523
chr_1 g12530 g12530.t6 exon g12530.t6.exon3 24270426 24271106
chr_1 g12530 g12530.t6 cds g12530.t6.CDS3 24270426 24270484
chr_1 g12530 g12530.t6 TSS g12530.t6 24271137 24271137

Sequences

>g12530.t6 Gene=g12530 Length=1558
ATGTTTCTCTTTACAATTTTGTCAATTTTAATTATTGCTTTAATATCATGGTATAAAAAG
CATTTTAGGCGGCGTGATTATTTATATTCAAAAATTCCTCATCCATATCATATACCGCTT
CTACATCATAGCCTTGAATTCATCGGCAAAACGCCTAAAGAGCTATTTGATTGGATGGAA
GACATGAGCAATGAACTTGGCAACGTATATTTCTTTTCTACGGGTATTTTTGGTAGTGGT
TTTGCAGTAATTTCTGATGTAAAAATTGTAGAAGCATTGCTGTCAAGTCAAGTACAATTG
GATAAGACAATCGATTATAATTATTTAATAGATTGGATTGGAACAGGCTTACTTATTTCA
AATTCAAAGAAATGGTTTACTAGAAGAAAACTTTTGACACCAGGATTTCATTTTAAAATT
TTAGAGAGATTTGTAGAAATTCAAAATAATCAAGCAAATGTTTTCGTGAATATACTTCAA
GAATATGATGGGAAAGAAGTTGATATTTTTCCACTTGCTAGTTTATATGCACTTGATACC
GTATGTGGCAAGTTTTGAAGTTATAATTTAAACTTTAAATGTGTAGGTAAATTTATATTT
TTTTATATTATCAGAAGCGGCAATGGGAATTAATATTCATGCGCAAACAAAACAATCGGA
TTATCTAAAAGCAGTACAAGAAATCACAAGGATCATCACAATAAAATCATTTGATACAAC
AAAGCAAATTGAATTTCTGTATCGCTTTACAGAAATGTATCGCAGAGAAAAGAAATTAAT
TGAAGAATTGCATGCGTTCACTGACAAAATTATTCAATCGCGTAGAGAAGAATTACTGAT
GCACAATGAAGAAACGTCAGAGCAAAATGATGAGATCGGAACAAAAAAGAAGAAAGCTCT
TTTGGATATTTTGTTGAGTTCAAGAGTTGAAGGAGAGCCATTAAAAAATTCCGATATTCG
AGAAGAAGTTGATACATTCATGTTTGCCGGTCATGACACCTCTAAAAGTGGTATTTGTTT
TGTATTTTATTGCATTGCTAAGTATCCAGAAGTTCAACAAAAGGTTTATGAGGAAATAAT
TGAAGTGCTTGGTGATGAAGAGGAAATAAATTTACAAAAATTGAATGAACTGCACTATCT
AGAATTGGTGATTCGTGAGTCATTAAGACTTTTTCCACCTGTACCTTATTATGGACGACA
ATTAGTAGAAGAGTTAATTACTGAAAAATATACTTTTCCAAAAGGAATGAATGTGTATGT
GTCTCCTTATTTGATGGGAAGAGATGAAAGGATTTTTCCTGAACCAAAAAAATTTGATCC
GCACCGTTTTGAAGTAGAAATGGCTAATGATAAAATTAATCCCTTTTCGTATGTGCCTTT
TTCAGCTGGTCCAAGAAATTGTATTGGCCAAAAATTTGCACAATATGAAATGAGAATGAT
CGCTGCAAAAGTTTTAAGAAAATTTAAATTATCTATTGCTAGTGAAATCACTATCCTATC
AGAATTAGTCTTGAGACCGGAAAATGGAGTAAACTTGAAAATCGAGAAGAGAAAATAA

>g12530.t6 Gene=g12530 Length=311
MGINIHAQTKQSDYLKAVQEITRIITIKSFDTTKQIEFLYRFTEMYRREKKLIEELHAFT
DKIIQSRREELLMHNEETSEQNDEIGTKKKKALLDILLSSRVEGEPLKNSDIREEVDTFM
FAGHDTSKSGICFVFYCIAKYPEVQQKVYEEIIEVLGDEEEINLQKLNELHYLELVIRES
LRLFPPVPYYGRQLVEELITEKYTFPKGMNVYVSPYLMGRDERIFPEPKKFDPHRFEVEM
ANDKINPFSYVPFSAGPRNCIGQKFAQYEMRMIAAKVLRKFKLSIASEITILSELVLRPE
NGVNLKIEKRK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
16 g12530.t6 Gene3D G3DSA:1.10.630.10 Cytochrome p450 1 311 9.5E-84
2 g12530.t6 PANTHER PTHR24291:SF143 CYTOCHROME P450 4D1-RELATED 1 310 2.1E-101
3 g12530.t6 PANTHER PTHR24291 CYTOCHROME P450 FAMILY 4 1 310 2.1E-101
8 g12530.t6 PRINTS PR00463 E-class P450 group I signature 111 128 1.2E-21
10 g12530.t6 PRINTS PR00385 P450 superfamily signature 122 139 3.3E-11
9 g12530.t6 PRINTS PR00463 E-class P450 group I signature 131 157 1.2E-21
4 g12530.t6 PRINTS PR00463 E-class P450 group I signature 174 192 1.2E-21
12 g12530.t6 PRINTS PR00385 P450 superfamily signature 175 186 3.3E-11
7 g12530.t6 PRINTS PR00463 E-class P450 group I signature 214 238 1.2E-21
5 g12530.t6 PRINTS PR00463 E-class P450 group I signature 250 260 1.2E-21
13 g12530.t6 PRINTS PR00385 P450 superfamily signature 251 260 3.3E-11
6 g12530.t6 PRINTS PR00463 E-class P450 group I signature 260 283 1.2E-21
11 g12530.t6 PRINTS PR00385 P450 superfamily signature 260 271 3.3E-11
1 g12530.t6 Pfam PF00067 Cytochrome P450 6 301 5.2E-82
15 g12530.t6 ProSitePatterns PS00086 Cytochrome P450 cysteine heme-iron ligand signature. 253 262 -
14 g12530.t6 SUPERFAMILY SSF48264 Cytochrome P450 10 310 4.19E-79

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