Gene loci information

Transcript annotation

  • This transcript has been annotated as Probable cytochrome P450 6a13.

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 g50 g50.t1 TSS g50.t1 416790 416790
chr_3 g50 g50.t1 isoform g50.t1 416839 418477
chr_3 g50 g50.t1 exon g50.t1.exon1 416839 417185
chr_3 g50 g50.t1 cds g50.t1.CDS1 416839 417185
chr_3 g50 g50.t1 exon g50.t1.exon2 417241 417473
chr_3 g50 g50.t1 cds g50.t1.CDS2 417241 417473
chr_3 g50 g50.t1 exon g50.t1.exon3 417531 418229
chr_3 g50 g50.t1 cds g50.t1.CDS3 417531 418229
chr_3 g50 g50.t1 exon g50.t1.exon4 418290 418477
chr_3 g50 g50.t1 cds g50.t1.CDS4 418290 418477
chr_3 g50 g50.t1 TTS g50.t1 418611 418611

Sequences

>g50.t1 Gene=g50 Length=1467
ATGAGTTTAACTTTATATTTTGTTGTCGCTGTTATCACACTCTGTTATCTATGGATAAAA
AGACGTTATAGTTTTTGGAAAAATAGAGGATTTCTTCAAGCTGAAGCTTCATTTCCTTTT
GGCTCATTTAAAGGAATTGGTACAAAAGTCACATCATATGAAGCTCTTGATGTTTGCTAT
AAAGAATTTAAAGGAAAAGCTCCAGCAATTGGAATTTATTCATTCTTTTCACCAAATATC
ATGCCAATTGATCCTGAATTGATTAAAAATATTCTTGGTAAAGATTTTGCATCATTTCAA
AGTCGTGGAATGTATTACAATAAAAAAGATGATCCAATGAGTGCTAATATTCTCACTCTT
GATGGGCAAGAATGGAAAGATCGAAGACAAAAGTTTACATCAATGTTTAGTTCTAGTAAG
ATGAAAATGATGTTTGAAATTCTTGATAAAATTGGTGATAAATTAGTGAACACACTTGGA
AGAAAAATAACAGAATCATCAGAACAGGATATGAGAAATTGGGCTCAAAGATTTACAGCC
GATAATATTGGCACCACAGCTTTTGGGATTGATTGTTGTTGTATTGAAGATCCAAATTCA
GAATTTATGAAATATGGACGACGATTGTTTGATCTGACAACTTTTGAGCTCATAAAATTT
TTTTTCGCAGTTGATTATCCAAATTTGGCTAGAAAATTAGGAATAAGATTCAATCCAAAA
GAAGTTGCAGATTTTTTTTATGAAACTTTCATTCAAACTTTTGAATATCGTGAGAAAAAT
AAAATTCAAAGAAATGATTTTGTGTCGATGTTGCTTGAACTTAAAGAACAATTTACAAGA
GTTGAATTAGCAGCTGAAGCTATGTTAGTTTATGCTGCTGGCTATGAAACAAGTTCAACT
TTAATGACTTTCACACTCTATGCTTTAGCATTAAATCCAGAAATTCAACAAAGATTAAGA
AATGAAATTACAACAGAAATTGAAGAAAATGATGGAAAATTAACTTATGAAATGCTGTTT
GGTTTCAAATATCTTGACATGGTCATTAATGAAACTTTAAGAATGTTTCCACCTATAGCT
GATAATATGAGAACTTGCAATAAAGACTACACAATTCCCGGCACAAATTTAATTATTCCT
TCAGGAACGACAGTTGAAATCAATACTTATTCTTTACATCACGATCCTGAATATTTTCCA
GAACCTGAAAAGTTTATTCCGGAGAGATTTAGCGAGGAAAACATTAAGAATATTAAACCT
TCTACTTTTTTGCCATTTGGTTCTGGGCCAAGATTATGTTTAGGCATGAGATTTGGACTA
ATGCAATCAAAAATGGGAATTGCAAAATTAATTACAGAATTTTCATTTTCTGCTTGTGAT
AAAACTACAATTCCTATGAAATTTGTTCCTAGTGCACCATTTTTAACACCACAAAATGGA
ATGTGGCTGAAAGTTGAGAAAATTTGA

>g50.t1 Gene=g50 Length=488
MSLTLYFVVAVITLCYLWIKRRYSFWKNRGFLQAEASFPFGSFKGIGTKVTSYEALDVCY
KEFKGKAPAIGIYSFFSPNIMPIDPELIKNILGKDFASFQSRGMYYNKKDDPMSANILTL
DGQEWKDRRQKFTSMFSSSKMKMMFEILDKIGDKLVNTLGRKITESSEQDMRNWAQRFTA
DNIGTTAFGIDCCCIEDPNSEFMKYGRRLFDLTTFELIKFFFAVDYPNLARKLGIRFNPK
EVADFFYETFIQTFEYREKNKIQRNDFVSMLLELKEQFTRVELAAEAMLVYAAGYETSST
LMTFTLYALALNPEIQQRLRNEITTEIEENDGKLTYEMLFGFKYLDMVINETLRMFPPIA
DNMRTCNKDYTIPGTNLIIPSGTTVEINTYSLHHDPEYFPEPEKFIPERFSEENIKNIKP
STFLPFGSGPRLCLGMRFGLMQSKMGIAKLITEFSFSACDKTTIPMKFVPSAPFLTPQNG
MWLKVEKI

Protein features from InterProScan

Transcript Database ID Name Start End E.value
15 g50.t1 Gene3D G3DSA:1.10.630.10 Cytochrome p450 14 488 6.4E-132
2 g50.t1 PANTHER PTHR24292 CYTOCHROME P450 7 488 6.4E-166
3 g50.t1 PANTHER PTHR24292:SF95 CYP6A16, ISOFORM B-RELATED 7 488 6.4E-166
9 g50.t1 PRINTS PR00463 E-class P450 group I signature 282 299 2.4E-22
10 g50.t1 PRINTS PR00385 P450 superfamily signature 293 310 1.8E-12
5 g50.t1 PRINTS PR00463 E-class P450 group I signature 302 328 2.4E-22
4 g50.t1 PRINTS PR00463 E-class P450 group I signature 346 364 2.4E-22
13 g50.t1 PRINTS PR00385 P450 superfamily signature 347 358 1.8E-12
8 g50.t1 PRINTS PR00463 E-class P450 group I signature 388 412 2.4E-22
7 g50.t1 PRINTS PR00463 E-class P450 group I signature 423 433 2.4E-22
11 g50.t1 PRINTS PR00385 P450 superfamily signature 424 433 1.8E-12
6 g50.t1 PRINTS PR00463 E-class P450 group I signature 433 456 2.4E-22
12 g50.t1 PRINTS PR00385 P450 superfamily signature 433 444 1.8E-12
1 g50.t1 Pfam PF00067 Cytochrome P450 41 481 3.2E-97
17 g50.t1 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 5 -
18 g50.t1 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 6 23 -
16 g50.t1 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 24 488 -
20 g50.t1 ProSitePatterns PS00086 Cytochrome P450 cysteine heme-iron ligand signature. 426 435 -
14 g50.t1 SUPERFAMILY SSF48264 Cytochrome P450 60 486 2.49E-113
19 g50.t1 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 2 19 -

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g50/g50.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g50.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