General information for g55.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Probable cytochrome P450 6a14.
Parent gene
- The parent gene g55 is located on chr_3: 428547..429633 (+ strand)
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 | g55 | g55.t1 | TSS | g55.t1 | 427482 | 427482 |
| chr_3 | g55 | g55.t1 | isoform | g55.t1 | 427521 | 429258 |
| chr_3 | g55 | g55.t1 | exon | g55.t1.exon1 | 427521 | 428583 |
| chr_3 | g55 | g55.t1 | cds | g55.t1.CDS1 | 427521 | 428583 |
| chr_3 | g55 | g55.t1 | exon | g55.t1.exon2 | 428644 | 428871 |
| chr_3 | g55 | g55.t1 | cds | g55.t1.CDS2 | 428644 | 428871 |
| chr_3 | g55 | g55.t1 | exon | g55.t1.exon3 | 428934 | 428956 |
| chr_3 | g55 | g55.t1 | cds | g55.t1.CDS3 | 428934 | 428956 |
| chr_3 | g55 | g55.t1 | exon | g55.t1.exon4 | 429094 | 429258 |
| chr_3 | g55 | g55.t1 | cds | g55.t1.CDS4 | 429094 | 429258 |
| chr_3 | g55 | g55.t1 | TTS | g55.t1 | 429627 | 429627 |
Sequences
>g55.t1 Gene=g55 Length=1479
ATGGCCATCACTATAATTATTTCGTTTTTATTAGCTGTGTTCACATTAGCTTATTTGTGG
ATACAACGACGTTATTCATTTTTTGCTCGTCTTGGAGTTCTTCATGATAAGCCAAAGTTT
CCATTAGGAAATATGCATGGAAAAACGCATCCAAGTGAAGTTTTCAAACAATTTTACGAT
AAATTTTGTCGTAAAGCATCGGCATTTGGCGTGTATTTGTTTATCAATCCACTTTTTGTC
ATCACCGACCTTGATCTTGCCAAAGATGTTTTAATTCGCGATTTTGAAGCATTTCATAAT
CGTGGAGCATTTTATAATAAAAAAGATGATCCACTTAGTGCTCATTTATTAACTATTGAA
GATCAAGAATGGAAAGATATGAGAAATAAGCTCACACCGACATTCACTTCAGGAAAAATG
AGGATGTATTTTAGCACACTTTTAGAAGTGTCAGATCGAATGATTGAGAAATTAAAAAGA
AATTGTGACAATATTATTGAAGTAAAAGAAATGTTAGCTCAGTACACAACTGATGTCATA
GGAAATGTTGGGTTTGGACTTTCCATCAATGCAATCGATAATCCTGATACTGAATTTCGT
CGAGTTGGTGGAAAATTGTTTAACAAAGAAACAAAATTTATTTTACGAGTTGCTTTGTTT
GCGACCTTTAAGAATATTGCAAGAAAACTTGGTTTAAAGTTGATTCCTTCGGATATTACT
AAATTTTTCATGGGTGTAGTTAAAGACACTGTAAATTATCGACTTGAAAATAATATCGAA
CGCAATGATGTTTTAGATACGCTTATGAAAATCAGAGACGAAACACAAGAAAATGAAGGA
AAATTGACAACAGAAGAAATAGCAGCTCAATGTTTTATCTTTTTTGTGGCTGGTTTTGAA
ACATCTTCAACGACTGGAACCTTAGTTCTTTATAATCTTGTAAAATATCCAGAAGTGCAG
GAAAAGTTACGTGATGAAATTAGAACTATTCTTGCTAGACATGATAATAAAATCACTTAT
GAAGCAATGCAGGAAATGAAATATTTGCAAATGGTTGTTGATGAATCACTTCGAATTTAT
CCACCAATTTTTCAAGTTTTACGACAGGCTGCAAGAGACTACAAAATTGAAAAAGACAAC
TTCGTCATTCCTAAAGGCAGTTTAGTAGGAGTTCCTGTTTATGCCATTCATCATGACCCT
GAATATTATCCAGAACCACATAAATTTGATCCTGAGAGATTCAACGATGAAAATAAGGCA
AACAGACATCCAATGGCTTTCTTACCTTTTGGTCAAGGTCCAAGAAATTGCATAGGTTTT
CGTTTTGGATTAATGCAAACTAAAGTTGCTTTGATACAACTTCTTTTGAATTTTCGAGTT
CATTCATCAGAAAAGACACCAGATCCAATTAAGTTTGATCCTGATACAGCTACATTGTCA
TCAGAAAACGATATGTGGTTGAAATTTGAAAAGTTATAA
>g55.t1 Gene=g55 Length=492
MAITIIISFLLAVFTLAYLWIQRRYSFFARLGVLHDKPKFPLGNMHGKTHPSEVFKQFYD
KFCRKASAFGVYLFINPLFVITDLDLAKDVLIRDFEAFHNRGAFYNKKDDPLSAHLLTIE
DQEWKDMRNKLTPTFTSGKMRMYFSTLLEVSDRMIEKLKRNCDNIIEVKEMLAQYTTDVI
GNVGFGLSINAIDNPDTEFRRVGGKLFNKETKFILRVALFATFKNIARKLGLKLIPSDIT
KFFMGVVKDTVNYRLENNIERNDVLDTLMKIRDETQENEGKLTTEEIAAQCFIFFVAGFE
TSSTTGTLVLYNLVKYPEVQEKLRDEIRTILARHDNKITYEAMQEMKYLQMVVDESLRIY
PPIFQVLRQAARDYKIEKDNFVIPKGSLVGVPVYAIHHDPEYYPEPHKFDPERFNDENKA
NRHPMAFLPFGQGPRNCIGFRFGLMQTKVALIQLLLNFRVHSSEKTPDPIKFDPDTATLS
SENDMWLKFEKL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 15 | g55.t1 | Gene3D | G3DSA:1.10.630.10 | Cytochrome p450 | 16 | 492 | 1.8E-140 |
| 2 | g55.t1 | PANTHER | PTHR24292 | CYTOCHROME P450 | 5 | 492 | 4.5E-178 |
| 3 | g55.t1 | PANTHER | PTHR24292:SF95 | CYP6A16, ISOFORM B-RELATED | 5 | 492 | 4.5E-178 |
| 7 | g55.t1 | PRINTS | PR00463 | E-class P450 group I signature | 86 | 107 | 1.5E-22 |
| 6 | g55.t1 | PRINTS | PR00463 | E-class P450 group I signature | 286 | 303 | 1.5E-22 |
| 10 | g55.t1 | PRINTS | PR00385 | P450 superfamily signature | 297 | 314 | 1.2E-9 |
| 8 | g55.t1 | PRINTS | PR00463 | E-class P450 group I signature | 306 | 332 | 1.5E-22 |
| 13 | g55.t1 | PRINTS | PR00385 | P450 superfamily signature | 351 | 362 | 1.2E-9 |
| 5 | g55.t1 | PRINTS | PR00463 | E-class P450 group I signature | 392 | 416 | 1.5E-22 |
| 4 | g55.t1 | PRINTS | PR00463 | E-class P450 group I signature | 427 | 437 | 1.5E-22 |
| 11 | g55.t1 | PRINTS | PR00385 | P450 superfamily signature | 428 | 437 | 1.2E-9 |
| 9 | g55.t1 | PRINTS | PR00463 | E-class P450 group I signature | 437 | 460 | 1.5E-22 |
| 12 | g55.t1 | PRINTS | PR00385 | P450 superfamily signature | 437 | 448 | 1.2E-9 |
| 1 | g55.t1 | Pfam | PF00067 | Cytochrome P450 | 42 | 479 | 4.2E-105 |
| 17 | g55.t1 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 19 | - |
| 18 | g55.t1 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 2 | - |
| 19 | g55.t1 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 3 | 14 | - |
| 20 | g55.t1 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 15 | 19 | - |
| 16 | g55.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 20 | 492 | - |
| 22 | g55.t1 | ProSitePatterns | PS00086 | Cytochrome P450 cysteine heme-iron ligand signature. | 430 | 439 | - |
| 14 | g55.t1 | SUPERFAMILY | SSF48264 | Cytochrome P450 | 40 | 490 | 4.58E-118 |
| 21 | g55.t1 | 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 g55/g55.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g55.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 transcript has been annotated with K07424 (cytochrome P450 family 3 subfamily A)
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