Gene loci information

Transcript annotation

  • This transcript has been annotated as Probable cytochrome P450 6a20.

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 g51 g51.t4 TSS g51.t4 419263 419263
chr_3 g51 g51.t4 isoform g51.t4 419293 420813
chr_3 g51 g51.t4 exon g51.t4.exon1 419293 419665
chr_3 g51 g51.t4 cds g51.t4.CDS1 419293 419665
chr_3 g51 g51.t4 exon g51.t4.exon2 419735 420287
chr_3 g51 g51.t4 cds g51.t4.CDS2 419735 420287
chr_3 g51 g51.t4 exon g51.t4.exon3 420345 420514
chr_3 g51 g51.t4 cds g51.t4.CDS3 420345 420514
chr_3 g51 g51.t4 exon g51.t4.exon4 420586 420813
chr_3 g51 g51.t4 cds g51.t4.CDS4 420586 420812
chr_3 g51 g51.t4 TTS g51.t4 421411 421411

Sequences

>g51.t4 Gene=g51 Length=1324
ATGTCATCGTTAGAAGTATTTTTAGCGTTATTTTTAGTAGCTTTAGGGCTATGCGTGTTT
TTTATCAAGAAAAAATTTTCTTATTGGAAAGAACGCGGTTTCGATTACATCGAGCCTGAA
TTTCCATTTGGTAATTTAAAGGGCGTTGGCTACAAAATTCACTTTTCAGAATTATCTCGT
GAATATTATGAGCGTTATAAAAATAAAACGTCGGCAATCGGCCTTTATTTTTTCACACAA
CCGGTTGTATTTTTAACGAATTTGGACGCCGTAAAAAATATTCTGGTAAAAGACTTTTAT
AATTTTCATGATCGCGGTCTTTATGTCAACACAAAGTCAGATCCACTTTCAGCACATTTG
TTTGCTATTGAGGGAGCAGAATGGAAACGTATGCGAACCAAATTATCACCAACTTTTACG
AGCATGAGAATGAAAACGATGTTTGGAACGGTACTGAATATTTCTGAGGAAATGATAAAT
TATTTGAGTGAAAATAATGGCATAAGAGAAATAGAAATGAAAGACATATTAGCGCGTTTT
ACCACGGATGTCATTGGCAGCGTGGCGTTTGGGATCCAAATTTCATCAATGCGCGACCCA
AAATCAATATTTAGAAAAATGGGAAGCAGAGTCTTCAATCCACCCAGATCACAAACATTA
AAAATCATTTTTCTTACAACATTTAGAAAATGGGCACGAAAATTTAGTTTCAGAGTTATT
GAGAAAGAAGTTGCTGACTTTTTTCTTTCAACGATTGAAGAAAACATCAATTATCGAGAG
AAAAACAATATTCAGAGAAATGATTTCTTTAATTTATTACTTGAATTAAAGAATCTTGGA
AAATTAAAAGACGACATAAGTGAAGCAGGAGAAAAATTGACATTTAATGAAATTGCAGCT
CAAAGTTTTCTATTCTATCTTGCTGGATTTGAGACGAGTTCAACGACAATGACATTTGCT
CTCTATGAGTTGTCATTAAATATAAATGTTCAAGAAAAGCTACGAAATGAAATCAAGTCT
GTGTTAGAAAAACATGAGAACAAAATTACTTATGATGCCATGATGGAGATGAAATACTTG
CAAATGGTCATTGATGAAACATTGAGAATGTATCCACCAGTTGACAACTTGATAAGAATA
GCTAAAGATGATTATCAAATTCCTGATACTAAATTGAAAATTGAGAAAGATACTTTACTC
TTTATACCAGTACTTGCTATTCAACATGATTCTAACATTTATGAGAATCCTGAGAAATTT
GATCCTGAGAGATTCAATGATGAAATGAAAGCTGAAAGACATCCAATGGCCTTTTTACCT
TTTG

>g51.t4 Gene=g51 Length=441
MSSLEVFLALFLVALGLCVFFIKKKFSYWKERGFDYIEPEFPFGNLKGVGYKIHFSELSR
EYYERYKNKTSAIGLYFFTQPVVFLTNLDAVKNILVKDFYNFHDRGLYVNTKSDPLSAHL
FAIEGAEWKRMRTKLSPTFTSMRMKTMFGTVLNISEEMINYLSENNGIREIEMKDILARF
TTDVIGSVAFGIQISSMRDPKSIFRKMGSRVFNPPRSQTLKIIFLTTFRKWARKFSFRVI
EKEVADFFLSTIEENINYREKNNIQRNDFFNLLLELKNLGKLKDDISEAGEKLTFNEIAA
QSFLFYLAGFETSSTTMTFALYELSLNINVQEKLRNEIKSVLEKHENKITYDAMMEMKYL
QMVIDETLRMYPPVDNLIRIAKDDYQIPDTKLKIEKDTLLFIPVLAIQHDSNIYENPEKF
DPERFNDEMKAERHPMAFLPF

Protein features from InterProScan

Transcript Database ID Name Start End E.value
15 g51.t4 Coils Coil Coil 328 348 -
14 g51.t4 Gene3D G3DSA:1.10.630.10 Cytochrome p450 18 441 2.5E-111
2 g51.t4 PANTHER PTHR24292 CYTOCHROME P450 7 441 6.3E-164
3 g51.t4 PANTHER PTHR24292:SF95 CYP6A16, ISOFORM B-RELATED 7 441 6.3E-164
8 g51.t4 PRINTS PR00463 E-class P450 group I signature 90 111 2.2E-14
6 g51.t4 PRINTS PR00463 E-class P450 group I signature 180 198 2.2E-14
5 g51.t4 PRINTS PR00463 E-class P450 group I signature 297 314 2.2E-14
12 g51.t4 PRINTS PR00385 P450 superfamily signature 308 325 3.6E-6
10 g51.t4 PRINTS PR00463 E-class P450 group I signature 317 343 2.2E-14
9 g51.t4 PRINTS PR00463 E-class P450 group I signature 361 379 2.2E-14
11 g51.t4 PRINTS PR00385 P450 superfamily signature 362 373 3.6E-6
7 g51.t4 PRINTS PR00463 E-class P450 group I signature 403 427 2.2E-14
4 g51.t4 PRINTS PR00463 E-class P450 group I signature 438 441 2.2E-14
1 g51.t4 Pfam PF00067 Cytochrome P450 43 441 1.1E-82
17 g51.t4 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 5 -
18 g51.t4 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 6 22 -
16 g51.t4 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 23 441 -
13 g51.t4 SUPERFAMILY SSF48264 Cytochrome P450 44 441 1.7E-92
19 g51.t4 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 4 22 -
20 g51.t4 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 72 91 -

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g51/g51.t4; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g51.t4.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. There were no conditions that were differentially expressed