Gene loci information

Transcript annotation

  • This transcript has been annotated as Probable cytochrome P450 6a14.

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 g56 g56.t2 TSS g56.t2 432560 432560
chr_3 g56 g56.t2 isoform g56.t2 432590 434279
chr_3 g56 g56.t2 exon g56.t2.exon1 432590 433686
chr_3 g56 g56.t2 cds g56.t2.CDS1 432618 433686
chr_3 g56 g56.t2 exon g56.t2.exon2 433750 433992
chr_3 g56 g56.t2 cds g56.t2.CDS2 433750 433985
chr_3 g56 g56.t2 exon g56.t2.exon3 434112 434279
chr_3 g56 g56.t2 TTS g56.t2 NA NA

Sequences

>g56.t2 Gene=g56 Length=1508
ATTAGAAAATCTTGAGCTCTTCTTTGCAATGGCATGGTCTTCTATTTCAATAATTTTTGT
CACTCTAATCTTGCTACTTTATCGCTGGATTAAAAAACGATATTCTTTTTTCAAAATCAA
TAAATTTCCCTATGTTGAACCAACTTTTCCATTTGGCAATTTAAAAGGCGCTGGCAGTAA
GTATCATGCCAATGAACTTTTTCAAAAACTTTATATCGAATTAAAGCATCAGGGACCGGC
ATGTGGCGTTTATTTTTTTCTCACACCAAATGTTATGATAACCGATTTGGATGTAATCAG
AGATGTTTTAATAAAGAATTTTGATAATTTTCATAATCGTGGACTTTATTCAAATGAGCG
TGATGATCCATTAAGTTCAAATTTGTTTAGTCTTGAAGATAATGAATGGCAGCATACGAG
AATGAAGTTGACACCAGTTTTTACAAGTGCCAAAATGAAAATGATGTTCAATATAATTGT
TGACATTGCTAATGAAATGACCGATGAATTAAAGTCTAAAAAATCATTAGAAATGATAGA
AGCAAGAGACACATTAATAAAATTTACAATTGATGTTATAGGAATGGTAGCATTTGGCCT
TCATTGGTCTGCCATTAAAGATCCAAATTCAAAATTTCATGAAATGGCACTAAAAGTCTT
TAAACCTGACAAAAATTTCTTTATGAAATCTTTCTTCCTTACAACATTTAAAAGTCTCGG
TCGAGCGTTACGAATGAAGTTTTTCCCGGCAGATGTTTCTGAATTTTTCATGACAACAAT
TAAAGAGACTGTTGACTATCGTCTTAGAAATAATGTTGAAAGAAATGACTTTATGAGTCT
AATGTTGAAAATGTATACAGAGGAAAGTGATGAAAAATTAACGTTAAATCAACTGGCAGC
ACAATGCTTTTTGTTCACAGTTGCTGGCTTTGAAACAAGTTCCAGTACATCGTCATTTGT
GCTTTACAATCTTGCAGTTCATCAAGATATTCAAGATAAACTCCGTAATGATGTCATGAA
TATTATAGCTAAAAATAATAATAAAGTAACTTATGAAGCTGTTAATGAGATGAAATATCT
GCAGATGGTCATTGATGAAACTCTTAGGCTTTATGGGCCTGTAGCGACAATTGTTCGAGT
TTCATTCAAAGATTATAAAATTTTGAATTCAGATTTAATTATTCCCAAAGGAACTTTTAC
TGGAATTCCAACATTTGCCATTCATTATGACCCTGAATATTACCCAGAGCCAGAGAAATT
TGATCCTGAGAGATTTAATGATGAAAATAAAGCTAAAAGACATCCAATGGCTTTCTTGCC
TTTTGGTAAATAATTCATAAGGTGAACGTTTTGGTTTAATGCAAACAAAAATTGCTATCA
TACAGTTGATTTGTAATTTCAAGATTCTCCCAAATGAAAAAACACAAATTCCAATGAAAT
TCGATCCAACTGTGCCAACTTTATCACCACTCGGTGGAATGTGGTTGAAGTTCGAGAAAT
TGAAATAA

>g56.t2 Gene=g56 Length=434
MAWSSISIIFVTLILLLYRWIKKRYSFFKINKFPYVEPTFPFGNLKGAGSKYHANELFQK
LYIELKHQGPACGVYFFLTPNVMITDLDVIRDVLIKNFDNFHNRGLYSNERDDPLSSNLF
SLEDNEWQHTRMKLTPVFTSAKMKMMFNIIVDIANEMTDELKSKKSLEMIEARDTLIKFT
IDVIGMVAFGLHWSAIKDPNSKFHEMALKVFKPDKNFFMKSFFLTTFKSLGRALRMKFFP
ADVSEFFMTTIKETVDYRLRNNVERNDFMSLMLKMYTEESDEKLTLNQLAAQCFLFTVAG
FETSSSTSSFVLYNLAVHQDIQDKLRNDVMNIIAKNNNKVTYEAVNEMKYLQMVIDETLR
LYGPVATIVRVSFKDYKILNSDLIIPKGTFTGIPTFAIHYDPEYYPEPEKFDPERFNDEN
KAKRHPMAFLPFGK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
11 g56.t2 Gene3D G3DSA:1.10.630.10 Cytochrome p450 16 434 9.4E-111
2 g56.t2 PANTHER PTHR24292 CYTOCHROME P450 6 433 4.3E-153
3 g56.t2 PANTHER PTHR24292:SF95 CYP6A16, ISOFORM B-RELATED 6 433 4.3E-153
6 g56.t2 PRINTS PR00463 E-class P450 group I signature 89 110 1.9E-11
7 g56.t2 PRINTS PR00463 E-class P450 group I signature 288 305 1.9E-11
5 g56.t2 PRINTS PR00463 E-class P450 group I signature 308 334 1.9E-11
8 g56.t2 PRINTS PR00463 E-class P450 group I signature 394 418 1.9E-11
4 g56.t2 PRINTS PR00463 E-class P450 group I signature 429 434 1.9E-11
1 g56.t2 Pfam PF00067 Cytochrome P450 40 433 5.7E-80
14 g56.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 5 -
16 g56.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 6 21 -
12 g56.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 22 174 -
15 g56.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 175 196 -
13 g56.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 197 434 -
10 g56.t2 SUPERFAMILY SSF48264 Cytochrome P450 36 433 2.62E-94
9 g56.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 2 21 -

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g56/g56.t2; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g56.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

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