Gene loci information

Transcript annotation

  • This transcript has been annotated as 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 g573 g573.t2 isoform g573.t2 4185745 4187603
chr_3 g573 g573.t2 exon g573.t2.exon1 4185745 4186285
chr_3 g573 g573.t2 exon g573.t2.exon2 4186352 4186421
chr_3 g573 g573.t2 exon g573.t2.exon3 4186478 4186789
chr_3 g573 g573.t2 cds g573.t2.CDS1 4186682 4186789
chr_3 g573 g573.t2 exon g573.t2.exon4 4186849 4187043
chr_3 g573 g573.t2 cds g573.t2.CDS2 4186849 4187043
chr_3 g573 g573.t2 exon g573.t2.exon5 4187170 4187375
chr_3 g573 g573.t2 cds g573.t2.CDS3 4187170 4187375
chr_3 g573 g573.t2 exon g573.t2.exon6 4187432 4187603
chr_3 g573 g573.t2 cds g573.t2.CDS4 4187432 4187603
chr_3 g573 g573.t2 TTS g573.t2 4187682 4187682
chr_3 g573 g573.t2 TSS g573.t2 NA NA

Sequences

>g573.t2 Gene=g573 Length=1496
ATGAATGTATTGGCATTATTTTTAATTTTCATCGTTGGTGTTTATTTTTGGTATCAAAAA
AAGTATAAACGATATAATGAACTTATGAACAAAATTCCTTGTGCTAAAACATATCCAATT
TTCAATCACTTAATGTACTTTATCAACAAGAAACCAGCTGAGATTTTTACAGTTCTTAAA
GAAATGGCAAAAGATCATGGACCAGTTTGGAAAGTTTTAGTTCCATTCGGTGATCAAATT
TTCGTTCATGACCCAAAAATCGTTGAAGAAATTTTATCAAGTCAAAAAATTATTGACAAG
TCTATGGAATATGATTTTATAATCGATTGGCTTGGTACAGGACTTTTGATATCAACTGGC
AGTAAATGGCATAAAAGACGAAAGATCATAACACCAGCATTTCATTTTAAAATTCTTGAT
CAGTTTGTTGACATCATGAACAAAAACGGAGATGTTTTTGTCGAAAAATTGAAGCATTTT
GAAGGTCGCGAGATTAACATATATCCATTGATATCACTTTATGCGCTTGATGTTGTTTGT
GAATCTGCTATGGGATATCAACTTAATGCCCAAACTGATGAAGACTCTGAATATGTCAAA
GCGGTCAAAGAAATTATCGAAATAATTGTTATTCGTTTATTTGACTCAACAAAAAAATTA
AATTTTTATAGCAATTTTCATCAATGTATAAACGTGAAAAAGAATTGATAAAATTTTTAC
ATAACTTTACAGATTCAGTTATTTTTTCACGACGGGAATATTGGAAAAGTCAAGGCATTA
ATGCTAGTAATGCTGAAAATGTTGATGAAATTGGAATGAAAAAGAAAACTGCATTTTTGG
ATTTACTTTTACAAGTTCAAGTTAACGGTCAGCCACTTGATAATGAAGGAATTCGTGAAG
AAGTTGATACTTTTATGTTCGAAGCTCATGACACGACTAGTTCTGCAATTGCTTTTACGC
TTTTGAATCTAGCAAAATTCAAAGACATTCAGAAGCAAGTTCTTGAAGAATGTGAAGAAA
TTCTTGGTGATTTGAGTCAACAACCGACAATGCTAGATCTGAATAAAATGAATTATTTGG
AGAAAGTTATTAAGGAAACTTTAAGATTGTATCCATCAGTTCCATTATTTTCTAGATCGC
TCAAATCCGAGTTTATCTCAAATGGCTACTCCTTTCCTGAGAATTCGACTGTTGTTTTAT
CACCTTATTTTATGGGTCGAGATGAAAAACTTTTCCCTGATCCTCTGAAATTTGATCCAT
CAAGATTTGATGATGAGAAAAATATAAGATTGTTTTCGTTTGTGCCTTTCTCAGCTGGTC
CAAGGAATTGCATTGGCCAAAAATATGCAATGCTTGAAATGAAAAGCATCATTTCAAAAC
TTGTAAGAAATTTCGAAATTGCAATCAGAAAGGAAAATAAAGAGCCACAAATTTATGCAC
AATTAACTTTGCAATCAACAAATGGAATAAATTTGTCATTGAAACCCAGAAAATAA

>g573.t2 Gene=g573 Length=226
MKKKTAFLDLLLQVQVNGQPLDNEGIREEVDTFMFEAHDTTSSAIAFTLLNLAKFKDIQK
QVLEECEEILGDLSQQPTMLDLNKMNYLEKVIKETLRLYPSVPLFSRSLKSEFISNGYSF
PENSTVVLSPYFMGRDEKLFPDPLKFDPSRFDDEKNIRLFSFVPFSAGPRNCIGQKYAML
EMKSIISKLVRNFEIAIRKENKEPQIYAQLTLQSTNGINLSLKPRK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
15 g573.t2 Gene3D G3DSA:1.10.630.10 Cytochrome p450 1 226 3.2E-75
2 g573.t2 PANTHER PTHR24291:SF143 CYTOCHROME P450 4D1-RELATED 2 225 1.5E-82
3 g573.t2 PANTHER PTHR24291 CYTOCHROME P450 FAMILY 4 2 225 1.5E-82
10 g573.t2 PRINTS PR00385 P450 superfamily signature 36 53 1.5E-13
6 g573.t2 PRINTS PR00463 E-class P450 group I signature 45 71 7.2E-21
8 g573.t2 PRINTS PR00463 E-class P450 group I signature 89 107 7.2E-21
12 g573.t2 PRINTS PR00385 P450 superfamily signature 90 101 1.5E-13
4 g573.t2 PRINTS PR00463 E-class P450 group I signature 129 153 7.2E-21
7 g573.t2 PRINTS PR00463 E-class P450 group I signature 162 172 7.2E-21
11 g573.t2 PRINTS PR00385 P450 superfamily signature 163 172 1.5E-13
5 g573.t2 PRINTS PR00463 E-class P450 group I signature 172 195 7.2E-21
9 g573.t2 PRINTS PR00385 P450 superfamily signature 172 183 1.5E-13
1 g573.t2 Pfam PF00067 Cytochrome P450 2 214 6.5E-70
17 g573.t2 Phobius SIGNAL_PEPTIDE Signal peptide region 1 18 -
18 g573.t2 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 5 -
19 g573.t2 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 6 14 -
20 g573.t2 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 15 18 -
16 g573.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 19 226 -
14 g573.t2 ProSitePatterns PS00086 Cytochrome P450 cysteine heme-iron ligand signature. 165 174 -
13 g573.t2 SUPERFAMILY SSF48264 Cytochrome P450 5 225 1.83E-69

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g573/g573.t2; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g573.t2.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

Pathway

  • This transcript belongs to the following pathways

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