General information for g53.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Probable cytochrome P450 6a20.
Parent gene
- The parent gene g53 is located on chr_3: 425599..426099 (+ 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 | g53 | g53.t1 | TSS | g53.t1 | 425560 | 425560 |
| chr_3 | g53 | g53.t1 | isoform | g53.t1 | 425599 | 426099 |
| chr_3 | g53 | g53.t1 | exon | g53.t1.exon1 | 425599 | 426099 |
| chr_3 | g53 | g53.t1 | cds | g53.t1.CDS1 | 425599 | 426099 |
| chr_3 | g53 | g53.t1 | TTS | g53.t1 | NA | NA |
Sequences
>g53.t1 Gene=g53 Length=501
ATGGCATTTAAAATAATTTCAATTTTGTTAGCTGTGTTCACACTAACTTATTTGTGGATA
CAACGACGTTATTCATTTTTTGCTCGTCTTGGAGTTCTTCATGATAAGCCAAAGTTTCCA
TTAGGAAATGTACGTGGGAAAGTTCATCCAGCTGAAATTTTTAAAGGCTTTTATGACAAA
TTTTGTCGTAAAGCAACAGCTTTTGGCTTCTACACATTTATCAATCCAATTTTTGTCATC
ACTGACCTTGACCTTATAAAAGATGTTTTAATTCGCGATTTTGAAGCATTTCATAATCGT
GGAGCATTTTATAATAAAAAAGATGATCCACTTAGTGCTCATTTATTAACTATTGAAGAT
CAAGAATGGAAAGATATGAGAAAAAAGCTCACACCGACATTCACTTCAGGAAAAATGAGG
ATGTATTTTAGCACACTTTTAGAAGTGTCAGATCGAATGATTGAGAAATTAAAGAAAATT
GTGACAATATTATTGAAGTAA
>g53.t1 Gene=g53 Length=166
MAFKIISILLAVFTLTYLWIQRRYSFFARLGVLHDKPKFPLGNVRGKVHPAEIFKGFYDK
FCRKATAFGFYTFINPIFVITDLDLIKDVLIRDFEAFHNRGAFYNKKDDPLSAHLLTIED
QEWKDMRKKLTPTFTSGKMRMYFSTLLEVSDRMIEKLKKIVTILLK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g53.t1 | Gene3D | G3DSA:1.10.630.10 | Cytochrome p450 | 15 | 163 | 1.9E-25 |
| 2 | g53.t1 | PANTHER | PTHR24292 | CYTOCHROME P450 | 3 | 159 | 3.7E-43 |
| 3 | g53.t1 | PANTHER | PTHR24292:SF95 | CYP6A16, ISOFORM B-RELATED | 3 | 159 | 3.7E-43 |
| 1 | g53.t1 | Pfam | PF00067 | Cytochrome P450 | 53 | 159 | 1.1E-11 |
| 8 | g53.t1 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 18 | - |
| 9 | g53.t1 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 4 | - |
| 10 | g53.t1 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 5 | 13 | - |
| 11 | g53.t1 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 14 | 18 | - |
| 7 | g53.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 19 | 166 | - |
| 5 | g53.t1 | SUPERFAMILY | SSF48264 | Cytochrome P450 | 48 | 159 | 6.02E-19 |
| 4 | g53.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 g53/g53.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g53.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