General information for g56.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 g56 is located on chr_3: 432590..434279 (+ 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 | g56 | g56.t1 | isoform | g56.t1 | 430366 | 434279 |
| chr_3 | g56 | g56.t1 | exon | g56.t1.exon1 | 430366 | 431308 |
| chr_3 | g56 | g56.t1 | cds | g56.t1.CDS1 | 430366 | 431308 |
| chr_3 | g56 | g56.t1 | exon | g56.t1.exon2 | 431368 | 431595 |
| chr_3 | g56 | g56.t1 | cds | g56.t1.CDS2 | 431368 | 431595 |
| chr_3 | g56 | g56.t1 | exon | g56.t1.exon3 | 431653 | 431675 |
| chr_3 | g56 | g56.t1 | cds | g56.t1.CDS3 | 431653 | 431675 |
| chr_3 | g56 | g56.t1 | exon | g56.t1.exon4 | 431732 | 431892 |
| chr_3 | g56 | g56.t1 | cds | g56.t1.CDS4 | 431732 | 431892 |
| chr_3 | g56 | g56.t1 | exon | g56.t1.exon5 | 432590 | 433686 |
| chr_3 | g56 | g56.t1 | cds | g56.t1.CDS5 | 432590 | 433686 |
| chr_3 | g56 | g56.t1 | exon | g56.t1.exon6 | 433750 | 433977 |
| chr_3 | g56 | g56.t1 | cds | g56.t1.CDS6 | 433750 | 433977 |
| chr_3 | g56 | g56.t1 | exon | g56.t1.exon7 | 434035 | 434057 |
| chr_3 | g56 | g56.t1 | cds | g56.t1.CDS7 | 434035 | 434057 |
| chr_3 | g56 | g56.t1 | exon | g56.t1.exon8 | 434112 | 434279 |
| chr_3 | g56 | g56.t1 | cds | g56.t1.CDS8 | 434112 | 434279 |
| chr_3 | g56 | g56.t1 | TSS | g56.t1 | NA | NA |
| chr_3 | g56 | g56.t1 | TTS | g56.t1 | NA | NA |
Sequences
>g56.t1 Gene=g56 Length=2871
ATGTATGGAAATATTTTAGATAAAAATCATTTAGTAGACGTAATTGATTCATTTTATAAT
GAATATAAAAAACAAGCACCTGCTTTTGGATTGTACTTTTTCTTAAGTCCAGCTGTTGTT
ATTACAGATTTAAATGTTATAAGAGATATTTTAATAAAAGATTTCGATGTTTTTACTAAT
CGTGGTGCATATCATAATAAAGAAAGTGATCCATTGAGTGCACAATTATTAAGTTTAGAA
GATTCTGAATGGAAAGTTTTAAGGCATAAATTAACTCCATTTTTTAGTAATTATAAAATG
AAAATGATTTTTAGAACACTTTTAAATGTGTCAGTTCAAACAATTGAGAATTTAAAACTT
GAAAATGATTTACAAATGATCGATGCTAAAGATATGTTTTTAAAATATACAACAGATGTG
ATGGCCAATATTGTTTACGGAATTGATATGGACAGTAAAAATGAACTTAGCTATAAATTT
AGAAATATGGGATCGATTTTGTTTGAATATAAAACTTATACAATTTTTAAAGCATTATGC
ATGCTATATTTAGAAAAAGTCTCTAAGAAATTTGGCTTAAAGTTGATTCCATCAGATATA
TCGGAATTCTTTCTTGGTATTGTTAAAACGACTGTAAAATATCGCTTACAGAATAAAATA
GAAAGAAAAGATGTCATTGATATTTTACTTAAAATTGAGCTAGAAAATAAAGATGGTGTG
AAGCTTTCAATTGAAGAAATTGCTGCTCAATGTTTCGTTTTTTATCTTTATGGATTTGAA
ACTGTCGCATGTACTGGAAGTTTTCTTCTTTACAATCTTGCAATGCATTTAGAAATTCAA
AATAAATTGCGAGATGAAATCAAAATGGTTTTATGGCGACATGAAAATAAATTCACATAT
GAAGCAGTACAGGAAATGAATTATTTGCAAATGGTCATTGATGAAACATTACGACTTTAT
CCTCCAATATTTGATATTGTCAGAAAATCATCGAGAAAATATGAAATTGCCAATAGTGAT
TTGATTATTCCAAGCAATACTTATGTGTTAATACCAATTTACTCTATTCATCGTGATCCA
GATTATTATTTTGAACCAGAAAAATTTAATCCTGATAGGTTTATTGATAGAACAAAAGCA
AATCTACATTCAATGGCTTTTATACCTTTTGGTTCGGGAAATAGAAATTGCATTGGTTCA
CAATTTGGACTTTTAAAACTGAAAATTGCTCTCATCCAACTTCTAACAAATTTTAAAATT
CTTCCAAATGAAAAAACTCCAAATCCTCTTGTTTTTGATCCAAGAAAATCTATTTTGACA
TCATCAACTGATATGTGGCTTACATTTGAAAGACTATTAGAAAATCTTGAGCTCTTCTTT
GCAATGGCATGGTCTTCTATTTCAATAATTTTTGTCACTCTAATCTTGCTACTTTATCGC
TGGATTAAAAAACGATATTCTTTTTTCAAAATCAATAAATTTCCCTATGTTGAACCAACT
TTTCCATTTGGCAATTTAAAAGGCGCTGGCAGTAAGTATCATGCCAATGAACTTTTTCAA
AAACTTTATATCGAATTAAAGCATCAGGGACCGGCATGTGGCGTTTATTTTTTTCTCACA
CCAAATGTTATGATAACCGATTTGGATGTAATCAGAGATGTTTTAATAAAGAATTTTGAT
AATTTTCATAATCGTGGACTTTATTCAAATGAGCGTGATGATCCATTAAGTTCAAATTTG
TTTAGTCTTGAAGATAATGAATGGCAGCATACGAGAATGAAGTTGACACCAGTTTTTACA
AGTGCCAAAATGAAAATGATGTTCAATATAATTGTTGACATTGCTAATGAAATGACCGAT
GAATTAAAGTCTAAAAAATCATTAGAAATGATAGAAGCAAGAGACACATTAATAAAATTT
ACAATTGATGTTATAGGAATGGTAGCATTTGGCCTTCATTGGTCTGCCATTAAAGATCCA
AATTCAAAATTTCATGAAATGGCACTAAAAGTCTTTAAACCTGACAAAAATTTCTTTATG
AAATCTTTCTTCCTTACAACATTTAAAAGTCTCGGTCGAGCGTTACGAATGAAGTTTTTC
CCGGCAGATGTTTCTGAATTTTTCATGACAACAATTAAAGAGACTGTTGACTATCGTCTT
AGAAATAATGTTGAAAGAAATGACTTTATGAGTCTAATGTTGAAAATGTATACAGAGGAA
AGTGATGAAAAATTAACGTTAAATCAACTGGCAGCACAATGCTTTTTGTTCACAGTTGCT
GGCTTTGAAACAAGTTCCAGTACATCGTCATTTGTGCTTTACAATCTTGCAGTTCATCAA
GATATTCAAGATAAACTCCGTAATGATGTCATGAATATTATAGCTAAAAATAATAATAAA
GTAACTTATGAAGCTGTTAATGAGATGAAATATCTGCAGATGGTCATTGATGAAACTCTT
AGGCTTTATGGGCCTGTAGCGACAATTGTTCGAGTTTCATTCAAAGATTATAAAATTTTG
AATTCAGATTTAATTATTCCCAAAGGAACTTTTACTGGAATTCCAACATTTGCCATTCAT
TATGACCCTGAATATTACCCAGAGCCAGAGAAATTTGATCCTGAGAGATTTAATGATGAA
AATAAAGCTAAAAGACATCCAATGGCTTTCTTGCCTTTTGGTGCAGGAAGAAGAAATTGT
ATCGGTGAACGTTTTGGTTTAATGCAAACAAAAATTGCTATCATACAGTTGATTTGTAAT
TTCAAGATTCTCCCAAATGAAAAAACACAAATTCCAATGAAATTCGATCCAACTGTGCCA
ACTTTATCACCACTCGGTGGAATGTGGTTGAAGTTCGAGAAATTGAAATAA
>g56.t1 Gene=g56 Length=956
MYGNILDKNHLVDVIDSFYNEYKKQAPAFGLYFFLSPAVVITDLNVIRDILIKDFDVFTN
RGAYHNKESDPLSAQLLSLEDSEWKVLRHKLTPFFSNYKMKMIFRTLLNVSVQTIENLKL
ENDLQMIDAKDMFLKYTTDVMANIVYGIDMDSKNELSYKFRNMGSILFEYKTYTIFKALC
MLYLEKVSKKFGLKLIPSDISEFFLGIVKTTVKYRLQNKIERKDVIDILLKIELENKDGV
KLSIEEIAAQCFVFYLYGFETVACTGSFLLYNLAMHLEIQNKLRDEIKMVLWRHENKFTY
EAVQEMNYLQMVIDETLRLYPPIFDIVRKSSRKYEIANSDLIIPSNTYVLIPIYSIHRDP
DYYFEPEKFNPDRFIDRTKANLHSMAFIPFGSGNRNCIGSQFGLLKLKIALIQLLTNFKI
LPNEKTPNPLVFDPRKSILTSSTDMWLTFERLLENLELFFAMAWSSISIIFVTLILLLYR
WIKKRYSFFKINKFPYVEPTFPFGNLKGAGSKYHANELFQKLYIELKHQGPACGVYFFLT
PNVMITDLDVIRDVLIKNFDNFHNRGLYSNERDDPLSSNLFSLEDNEWQHTRMKLTPVFT
SAKMKMMFNIIVDIANEMTDELKSKKSLEMIEARDTLIKFTIDVIGMVAFGLHWSAIKDP
NSKFHEMALKVFKPDKNFFMKSFFLTTFKSLGRALRMKFFPADVSEFFMTTIKETVDYRL
RNNVERNDFMSLMLKMYTEESDEKLTLNQLAAQCFLFTVAGFETSSSTSSFVLYNLAVHQ
DIQDKLRNDVMNIIAKNNNKVTYEAVNEMKYLQMVIDETLRLYGPVATIVRVSFKDYKIL
NSDLIIPKGTFTGIPTFAIHYDPEYYPEPEKFDPERFNDENKAKRHPMAFLPFGAGRRNC
IGERFGLMQTKIAIIQLICNFKILPNEKTQIPMKFDPTVPTLSPLGGMWLKFEKLK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 20 | g56.t1 | Gene3D | G3DSA:1.10.630.10 | Cytochrome p450 | 1 | 456 | 1.2E-112 |
| 21 | g56.t1 | Gene3D | G3DSA:1.10.630.10 | Cytochrome p450 | 477 | 956 | 5.7E-131 |
| 3 | g56.t1 | PANTHER | PTHR24292 | CYTOCHROME P450 | 5 | 452 | 0.0 |
| 5 | g56.t1 | PANTHER | PTHR24292:SF95 | CYP6A16, ISOFORM B-RELATED | 5 | 452 | 0.0 |
| 4 | g56.t1 | PANTHER | PTHR24292 | CYTOCHROME P450 | 466 | 955 | 0.0 |
| 6 | g56.t1 | PANTHER | PTHR24292:SF95 | CYP6A16, ISOFORM B-RELATED | 466 | 955 | 0.0 |
| 8 | g56.t1 | PRINTS | PR00463 | E-class P450 group I signature | 22 | 41 | 1.6E-20 |
| 13 | g56.t1 | PRINTS | PR00463 | E-class P450 group I signature | 46 | 67 | 1.6E-20 |
| 11 | g56.t1 | PRINTS | PR00463 | E-class P450 group I signature | 136 | 154 | 1.6E-20 |
| 10 | g56.t1 | PRINTS | PR00463 | E-class P450 group I signature | 266 | 292 | 1.6E-20 |
| 12 | g56.t1 | PRINTS | PR00463 | E-class P450 group I signature | 352 | 376 | 1.6E-20 |
| 7 | g56.t1 | PRINTS | PR00463 | E-class P450 group I signature | 387 | 397 | 1.6E-20 |
| 9 | g56.t1 | PRINTS | PR00463 | E-class P450 group I signature | 397 | 420 | 1.6E-20 |
| 17 | g56.t1 | PRINTS | PR00385 | P450 superfamily signature | 760 | 777 | 1.5E-10 |
| 16 | g56.t1 | PRINTS | PR00385 | P450 superfamily signature | 814 | 825 | 1.5E-10 |
| 15 | g56.t1 | PRINTS | PR00385 | P450 superfamily signature | 891 | 900 | 1.5E-10 |
| 14 | g56.t1 | PRINTS | PR00385 | P450 superfamily signature | 900 | 911 | 1.5E-10 |
| 2 | g56.t1 | Pfam | PF00067 | Cytochrome P450 | 2 | 440 | 1.1E-82 |
| 1 | g56.t1 | Pfam | PF00067 | Cytochrome P450 | 501 | 939 | 4.2E-97 |
| 24 | g56.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 457 | - |
| 25 | g56.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 458 | 479 | - |
| 22 | g56.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 480 | 635 | - |
| 26 | g56.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 636 | 657 | - |
| 23 | g56.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 658 | 956 | - |
| 30 | g56.t1 | ProSitePatterns | PS00086 | Cytochrome P450 cysteine heme-iron ligand signature. | 390 | 399 | - |
| 29 | g56.t1 | ProSitePatterns | PS00086 | Cytochrome P450 cysteine heme-iron ligand signature. | 893 | 902 | - |
| 19 | g56.t1 | SUPERFAMILY | SSF48264 | Cytochrome P450 | 10 | 450 | 2.36E-99 |
| 18 | g56.t1 | SUPERFAMILY | SSF48264 | Cytochrome P450 | 498 | 953 | 1.31E-113 |
| 27 | g56.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 460 | 482 | - |
| 28 | g56.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 640 | 657 | - |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g56/g56.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g56.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 K14999 (cytochrome P450 family 6 [EC:1.14.-.-])
Pathway
This gene does not belong to any 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