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 g54 g54.t1 TSS g54.t1 425560 425560
chr_3 g54 g54.t1 isoform g54.t1 426139 427243
chr_3 g54 g54.t1 exon g54.t1.exon1 426139 426655
chr_3 g54 g54.t1 cds g54.t1.CDS1 426139 426655
chr_3 g54 g54.t1 exon g54.t1.exon2 426716 426943
chr_3 g54 g54.t1 cds g54.t1.CDS2 426716 426943
chr_3 g54 g54.t1 exon g54.t1.exon3 427003 427025
chr_3 g54 g54.t1 cds g54.t1.CDS3 427003 427025
chr_3 g54 g54.t1 exon g54.t1.exon4 427079 427243
chr_3 g54 g54.t1 cds g54.t1.CDS4 427079 427243
chr_3 g54 g54.t1 TTS g54.t1 427348 427348

Sequences

>g54.t1 Gene=g54 Length=933
ATGTTGGTTGGACTTTCCATCAATGCAATCGATAATCCTGATACTGAATTTCGTCGAGTT
GGTGGAAAATTGTTTAACAAAGAAACAAAATTTATTTTAAGAATCGCCTTGCTTTCTAAT
TTCAAATGGATCGCAAGAAAACTTGGTTTAAAGTTGATTCCTTCGGATATTACTAAATTT
TTCATGGGTGTAGTTAAAGACACTGTAAATTATCGACTTGAGAATAATATCCAACGCAAT
GATGTTTTAGATACGCTTATGAAAATCAGAGATGAAACACAAGAAAATGAAGGAAAATTG
ACAATTGGAGAAATTGGTGCTCAATGTTTTGTCTTTTTTATTGGTGGCTTTGAAACATCT
TCAAGCACTGGAACTTTTGTGCTTTATAATCTTGTAAAATATCCAGAAGTACAGGAAAAA
TTACGTAATGAAATTAGAACTATTCTTGCTAGACATGATAATAAAATCACGTATGAAGCA
ATGCAGGAAATGAAATATTTGCAAATGGTTGTTGATGAAACACTTCGAATGTATCCACCA
GTTTTTCAAGCATTGAGACAAGCTGCAAGAGATTATAAAGTTGAAAAAGACAACTTCATT
ATTCCTAAAGACATTTTAGTTTCGATTCCGATTTATGCTATACATCATGACCCTGAATAT
TATCCAGAACCAGATAAATTCGATCCTGATAGATTCAACGATGAAAATAAAGCTCAACGA
CACCCAATGGCCTTTTTACCTTTTGGTCATGGACCAAGAAATTGCATAGGTTTTCGTTTT
GGATTAATGCAAACTAAAATCGCTTTGATACAACTTCTTTTGAATTTCCGAGTTTATGCA
TCAGAAAAGACTCCAGATCCAATTAAGTTTGATCCAGATGCAACTCCTTTGACATCGATA
ACTGACATGTGGTTGAAATTTGAAAAGTTGTGA

>g54.t1 Gene=g54 Length=310
MLVGLSINAIDNPDTEFRRVGGKLFNKETKFILRIALLSNFKWIARKLGLKLIPSDITKF
FMGVVKDTVNYRLENNIQRNDVLDTLMKIRDETQENEGKLTIGEIGAQCFVFFIGGFETS
SSTGTFVLYNLVKYPEVQEKLRNEIRTILARHDNKITYEAMQEMKYLQMVVDETLRMYPP
VFQALRQAARDYKVEKDNFIIPKDILVSIPIYAIHHDPEYYPEPDKFDPDRFNDENKAQR
HPMAFLPFGHGPRNCIGFRFGLMQTKIALIQLLLNFRVYASEKTPDPIKFDPDATPLTSI
TDMWLKFEKL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
15 g54.t1 Gene3D G3DSA:1.10.630.10 Cytochrome p450 1 310 3.0E-96
2 g54.t1 PANTHER PTHR24292 CYTOCHROME P450 3 310 1.8E-114
3 g54.t1 PANTHER PTHR24292:SF95 CYP6A16, ISOFORM B-RELATED 3 310 1.8E-114
8 g54.t1 PRINTS PR00463 E-class P450 group I signature 104 121 4.4E-20
9 g54.t1 PRINTS PR00385 P450 superfamily signature 115 132 9.9E-11
5 g54.t1 PRINTS PR00463 E-class P450 group I signature 124 150 4.4E-20
12 g54.t1 PRINTS PR00385 P450 superfamily signature 169 180 9.9E-11
4 g54.t1 PRINTS PR00463 E-class P450 group I signature 210 234 4.4E-20
6 g54.t1 PRINTS PR00463 E-class P450 group I signature 245 255 4.4E-20
11 g54.t1 PRINTS PR00385 P450 superfamily signature 246 255 9.9E-11
7 g54.t1 PRINTS PR00463 E-class P450 group I signature 255 278 4.4E-20
10 g54.t1 PRINTS PR00385 P450 superfamily signature 255 266 9.9E-11
1 g54.t1 Pfam PF00067 Cytochrome P450 13 291 7.9E-79
14 g54.t1 ProSitePatterns PS00086 Cytochrome P450 cysteine heme-iron ligand signature. 248 257 -
13 g54.t1 SUPERFAMILY SSF48264 Cytochrome P450 2 308 7.99E-86

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g54/g54.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g54.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. There were no conditions that were differentially expressed