General information for g55.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Probable cytochrome P450 6a20.
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.t2 | TSS | g55.t2 | 427482 | 427482 |
| chr_3 | g55 | g55.t2 | isoform | g55.t2 | 427521 | 428582 |
| chr_3 | g55 | g55.t2 | exon | g55.t2.exon1 | 427521 | 428582 |
| chr_3 | g55 | g55.t2 | cds | g55.t2.CDS1 | 427521 | 428582 |
| chr_3 | g55 | g55.t2 | TTS | g55.t2 | NA | NA |
Sequences
>g55.t2 Gene=g55 Length=1062
ATGGCCATCACTATAATTATTTCGTTTTTATTAGCTGTGTTCACATTAGCTTATTTGTGG
ATACAACGACGTTATTCATTTTTTGCTCGTCTTGGAGTTCTTCATGATAAGCCAAAGTTT
CCATTAGGAAATATGCATGGAAAAACGCATCCAAGTGAAGTTTTCAAACAATTTTACGAT
AAATTTTGTCGTAAAGCATCGGCATTTGGCGTGTATTTGTTTATCAATCCACTTTTTGTC
ATCACCGACCTTGATCTTGCCAAAGATGTTTTAATTCGCGATTTTGAAGCATTTCATAAT
CGTGGAGCATTTTATAATAAAAAAGATGATCCACTTAGTGCTCATTTATTAACTATTGAA
GATCAAGAATGGAAAGATATGAGAAATAAGCTCACACCGACATTCACTTCAGGAAAAATG
AGGATGTATTTTAGCACACTTTTAGAAGTGTCAGATCGAATGATTGAGAAATTAAAAAGA
AATTGTGACAATATTATTGAAGTAAAAGAAATGTTAGCTCAGTACACAACTGATGTCATA
GGAAATGTTGGGTTTGGACTTTCCATCAATGCAATCGATAATCCTGATACTGAATTTCGT
CGAGTTGGTGGAAAATTGTTTAACAAAGAAACAAAATTTATTTTACGAGTTGCTTTGTTT
GCGACCTTTAAGAATATTGCAAGAAAACTTGGTTTAAAGTTGATTCCTTCGGATATTACT
AAATTTTTCATGGGTGTAGTTAAAGACACTGTAAATTATCGACTTGAAAATAATATCGAA
CGCAATGATGTTTTAGATACGCTTATGAAAATCAGAGACGAAACACAAGAAAATGAAGGA
AAATTGACAACAGAAGAAATAGCAGCTCAATGTTTTATCTTTTTTGTGGCTGGTTTTGAA
ACATCTTCAACGACTGGAACCTTAGTTCTTTATAATCTTGTAAAATATCCAGAAGTGCAG
GAAAAGTTACGTGATGAAATTAGAACTATTCTTGCTAGACATGATAATAAAATCACTTAT
GAAGCAATGCAGGAAATGAAATATTTGCAAATGGTTGTTGAT
>g55.t2 Gene=g55 Length=354
MAITIIISFLLAVFTLAYLWIQRRYSFFARLGVLHDKPKFPLGNMHGKTHPSEVFKQFYD
KFCRKASAFGVYLFINPLFVITDLDLAKDVLIRDFEAFHNRGAFYNKKDDPLSAHLLTIE
DQEWKDMRNKLTPTFTSGKMRMYFSTLLEVSDRMIEKLKRNCDNIIEVKEMLAQYTTDVI
GNVGFGLSINAIDNPDTEFRRVGGKLFNKETKFILRVALFATFKNIARKLGLKLIPSDIT
KFFMGVVKDTVNYRLENNIERNDVLDTLMKIRDETQENEGKLTTEEIAAQCFIFFVAGFE
TSSTTGTLVLYNLVKYPEVQEKLRDEIRTILARHDNKITYEAMQEMKYLQMVVD
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g55.t2 | Gene3D | G3DSA:1.10.630.10 | Cytochrome p450 | 16 | 354 | 9.6E-82 |
| 2 | g55.t2 | PANTHER | PTHR24292 | CYTOCHROME P450 | 5 | 353 | 7.9E-114 |
| 3 | g55.t2 | PANTHER | PTHR24292:SF95 | CYP6A16, ISOFORM B-RELATED | 5 | 353 | 7.9E-114 |
| 5 | g55.t2 | PRINTS | PR00464 | Group II E-class P450 signature | 121 | 141 | 5.8E-8 |
| 4 | g55.t2 | PRINTS | PR00464 | Group II E-class P450 signature | 174 | 192 | 5.8E-8 |
| 1 | g55.t2 | Pfam | PF00067 | Cytochrome P450 | 42 | 353 | 2.2E-53 |
| 10 | g55.t2 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 19 | - |
| 11 | g55.t2 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 2 | - |
| 12 | g55.t2 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 3 | 14 | - |
| 13 | g55.t2 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 15 | 19 | - |
| 9 | g55.t2 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 20 | 354 | - |
| 7 | g55.t2 | SUPERFAMILY | SSF48264 | Cytochrome P450 | 40 | 353 | 3.8E-64 |
| 6 | g55.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 g55/g55.t2; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g55.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:0004497 | monooxygenase activity | 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