General information for g4003.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Cytochrome P450 18a1.
Parent gene
- The parent gene g4003 is located on chr_3: 29463946..29466368 (+ 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 | g4003 | g4003.t1 | TSS | g4003.t1 | 29462923 | 29462923 |
| chr_3 | g4003 | g4003.t1 | isoform | g4003.t1 | 29463159 | 29466368 |
| chr_3 | g4003 | g4003.t1 | exon | g4003.t1.exon1 | 29463159 | 29463522 |
| chr_3 | g4003 | g4003.t1 | cds | g4003.t1.CDS1 | 29463159 | 29463522 |
| chr_3 | g4003 | g4003.t1 | exon | g4003.t1.exon2 | 29463627 | 29463641 |
| chr_3 | g4003 | g4003.t1 | cds | g4003.t1.CDS2 | 29463627 | 29463641 |
| chr_3 | g4003 | g4003.t1 | exon | g4003.t1.exon3 | 29463946 | 29464067 |
| chr_3 | g4003 | g4003.t1 | cds | g4003.t1.CDS3 | 29463946 | 29464067 |
| chr_3 | g4003 | g4003.t1 | exon | g4003.t1.exon4 | 29464219 | 29464913 |
| chr_3 | g4003 | g4003.t1 | cds | g4003.t1.CDS4 | 29464219 | 29464913 |
| chr_3 | g4003 | g4003.t1 | exon | g4003.t1.exon5 | 29465898 | 29465960 |
| chr_3 | g4003 | g4003.t1 | cds | g4003.t1.CDS5 | 29465898 | 29465960 |
| chr_3 | g4003 | g4003.t1 | exon | g4003.t1.exon6 | 29466023 | 29466368 |
| chr_3 | g4003 | g4003.t1 | cds | g4003.t1.CDS6 | 29466023 | 29466368 |
| chr_3 | g4003 | g4003.t1 | TTS | g4003.t1 | 29467339 | 29467339 |
Sequences
>g4003.t1 Gene=g4003 Length=1605
ATGTTACTGGATTCATATGTTTTTAACTTTCTTAAAAGAGAATTGGAGCATGATATTCAA
AAATCGTTGTTAGTGTTTTGCTGTGTACTTTTTGTGGTTTTTATCGTTCAATCTATCATA
AAGAATCTTATCGAAATTGCAAAATTACCTCCTGGTCCAATTGGTGTTTGGCCATTTGGA
ATTTTAAAATTTATTGGTCATGAGAAGCATAAATCGTTAATGAAATTGGCATCGACTTAT
GGACCATTATTCAGTTGTAAATTAGGACAGCAGTTGTACGTTGTGATAAGTGATTATAAA
ATGATTCGTGAAATTTTCAAAAAAGAGTCCATGACGGGACGACCAAAGACTCCACTTTAT
GGAGTGTTGAATGGAGCAGGTGTGATAAATGCAGAAGGTGCACTTTGGAAGTCAGAAAGG
CGCTTCTTGCATGAGAAACTTAGACGTTTTGGAATGACGCATTTAAATAGTAAAAACAAC
AAATTGCACGACATCATAAATAATGAAATCAATGAGCTTCTAACGACGTTAAGGCACGAA
ACGAAGAAGCCAATCGACTTGGAACCGCACTTTGCCGTCTCAATTAGCAACGTCGTGTGC
AATTTATTAATGTCTGTTCGTTTTACACGAAATGATCCAAAATTCATCAGATTTAATAGC
ATGATTGAGGAGGGCATGAAATTATTTGGAAAAATCACTTCAGTCGATTACATTCCAATT
ACTCAGTATTTTCCATCATTCCAAACAGCAAAGAGTCAAATCGCTAGCAATCGCGAAGAA
ATGTTTGAATTTTATCGCGAAGTGATTGAAGACCATCGAAAGACATTTGATCGTAATAAC
ATTCGCGATTTAGTGGACTTTTATCTATTAGAAATTGAACTTGCAAAGGAAAATGGAACT
GAACATGAGCTTTTTAATGGTCGAAATCATGATGAACAAATAATGCAAGTGATGGGAGAT
TTATTCAGTGCTGGTATGGAAACCATCAAGACGACATTGCTTTGGTTGATCGTCTTTATG
TTGCGTAATCCTGTCGCAAAAAAGCAAGTTCAAGATGAATTAGATACTGTCATTGGACGT
GAGAAAATGCCTAAATTTCAGGACTTACAATATCTGCCAAATACCGAGAGTACAATTTAC
GAAGTGCTTCGAATAAGCTCGATAGTGCCACTAGCCACAACACACTCACCGATGATTGAT
GAAGAATTGAATGGTTTTAAAATACCCGCGGGCTCACATGTCGTACCGCTTATTAACAGT
GTGCATATGGATCCAAATCTTTGGGATTCACCGAATGACTTCCGACCAAGTCGATTTATT
AATGCAGAAGGCAAAGTTCATAAGCCCGAATATTTCATTCCATTCGGTACAGGCAGAAGA
ATGTGTCTAGGCGATGTTTTGGCGCGCATGGAATTATTTTTGTTCTTTGCATCGATCATG
CATACTTTTGATGTATGTTTACCAAATGGCGCTCAAGAGCCAAGTCTAAATGGAAATCCT
GGCGTAACAATTCATCCAGATAATTTTCTAGTATATTTAAAAGAGCGACCGCTTGATGTG
CCAATAGATGATCAAACGCCATTAAGAAATTTTGGCTCATATTGA
>g4003.t1 Gene=g4003 Length=534
MLLDSYVFNFLKRELEHDIQKSLLVFCCVLFVVFIVQSIIKNLIEIAKLPPGPIGVWPFG
ILKFIGHEKHKSLMKLASTYGPLFSCKLGQQLYVVISDYKMIREIFKKESMTGRPKTPLY
GVLNGAGVINAEGALWKSERRFLHEKLRRFGMTHLNSKNNKLHDIINNEINELLTTLRHE
TKKPIDLEPHFAVSISNVVCNLLMSVRFTRNDPKFIRFNSMIEEGMKLFGKITSVDYIPI
TQYFPSFQTAKSQIASNREEMFEFYREVIEDHRKTFDRNNIRDLVDFYLLEIELAKENGT
EHELFNGRNHDEQIMQVMGDLFSAGMETIKTTLLWLIVFMLRNPVAKKQVQDELDTVIGR
EKMPKFQDLQYLPNTESTIYEVLRISSIVPLATTHSPMIDEELNGFKIPAGSHVVPLINS
VHMDPNLWDSPNDFRPSRFINAEGKVHKPEYFIPFGTGRRMCLGDVLARMELFLFFASIM
HTFDVCLPNGAQEPSLNGNPGVTIHPDNFLVYLKERPLDVPIDDQTPLRNFGSY
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 17 | g4003.t1 | Gene3D | G3DSA:1.10.630.10 | Cytochrome p450 | 42 | 518 | 3.1E-127 |
| 2 | g4003.t1 | PANTHER | PTHR24300 | CYTOCHROME P450 508A4-RELATED | 29 | 509 | 9.4E-131 |
| 3 | g4003.t1 | PANTHER | PTHR24300:SF334 | CYTOCHROME P450 18A1 | 29 | 509 | 9.4E-131 |
| 8 | g4003.t1 | PRINTS | PR00463 | E-class P450 group I signature | 77 | 96 | 1.1E-52 |
| 11 | g4003.t1 | PRINTS | PR00463 | E-class P450 group I signature | 194 | 212 | 1.1E-52 |
| 10 | g4003.t1 | PRINTS | PR00463 | E-class P450 group I signature | 313 | 330 | 1.1E-52 |
| 14 | g4003.t1 | PRINTS | PR00385 | P450 superfamily signature | 324 | 341 | 2.1E-12 |
| 7 | g4003.t1 | PRINTS | PR00463 | E-class P450 group I signature | 333 | 359 | 1.1E-52 |
| 5 | g4003.t1 | PRINTS | PR00463 | E-class P450 group I signature | 376 | 394 | 1.1E-52 |
| 13 | g4003.t1 | PRINTS | PR00385 | P450 superfamily signature | 377 | 388 | 2.1E-12 |
| 9 | g4003.t1 | PRINTS | PR00463 | E-class P450 group I signature | 417 | 441 | 1.1E-52 |
| 6 | g4003.t1 | PRINTS | PR00463 | E-class P450 group I signature | 452 | 462 | 1.1E-52 |
| 15 | g4003.t1 | PRINTS | PR00385 | P450 superfamily signature | 453 | 462 | 2.1E-12 |
| 4 | g4003.t1 | PRINTS | PR00463 | E-class P450 group I signature | 462 | 485 | 1.1E-52 |
| 12 | g4003.t1 | PRINTS | PR00385 | P450 superfamily signature | 462 | 473 | 2.1E-12 |
| 1 | g4003.t1 | Pfam | PF00067 | Cytochrome P450 | 50 | 511 | 2.4E-104 |
| 18 | g4003.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 20 | - |
| 20 | g4003.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 21 | 40 | - |
| 19 | g4003.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 41 | 534 | - |
| 22 | g4003.t1 | ProSitePatterns | PS00086 | Cytochrome P450 cysteine heme-iron ligand signature. | 455 | 464 | - |
| 16 | g4003.t1 | SUPERFAMILY | SSF48264 | Cytochrome P450 | 50 | 516 | 1.96E-106 |
| 21 | g4003.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 21 | 40 | - |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
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 K14985 (26-hydroxylase [EC:1.14.-.-])
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.
