General information for g12558.t4
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Luciferin 4-monooxygenase.
Parent gene
- The parent gene g12558 is located on chr_1: 24382099..24383027 (- 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_1 | g12558 | g12558.t4 | TTS | g12558.t4 | 24380785 | 24380785 |
| chr_1 | g12558 | g12558.t4 | isoform | g12558.t4 | 24381576 | 24383027 |
| chr_1 | g12558 | g12558.t4 | exon | g12558.t4.exon1 | 24381576 | 24382316 |
| chr_1 | g12558 | g12558.t4 | cds | g12558.t4.CDS1 | 24381577 | 24382316 |
| chr_1 | g12558 | g12558.t4 | exon | g12558.t4.exon2 | 24382436 | 24383027 |
| chr_1 | g12558 | g12558.t4 | cds | g12558.t4.CDS2 | 24382436 | 24383027 |
| chr_1 | g12558 | g12558.t4 | TSS | g12558.t4 | 24383179 | 24383179 |
Sequences
>g12558.t4 Gene=g12558 Length=1333
ATGGCAAATAATAAAAATATACTTTATACACCCGAGATTACAAATGATTATCATGATGAA
CCTTCAATGGGACATTTGATTGAAAAAAGTTTACGTCAAGCTGGTGAAAAAGTATTGCTT
GTGTCAGGAATCACTGGTGAAGAGCTAACAGCAAAAGACCTCTTAGCTAAGGCAATTCAA
GTTGCACAATCGTTGTATGCTGCTGGAATAAGAAGTCAAGATAAAATTTCTCTTGTTTGT
GAAAATCGCTTTGAATTTGCTTATATACTTTTTGGAAGCCTTTTGCTGAATGTAACAGTG
GCTCCTATTAATCTTACATACTCTGAGCGTGAAATGATTCATGCTTTTAATCTATCAAAA
CCAAAAATTATCTTCATGAGTCCGTATGCATCTGAAAAAGTTTTTAATGTTGCAAAAACT
CTCAATTATGTTCAAAAAGTTATTTTATTTGATGAAGAAAATCCATTTGATAAAACTGTG
ACATTATTTGATGATTTTTTAAAACTGTCAATGAATGCTGGTCCTTACATTCCACAATCA
GTTAACAAAGAAAAATCTGTCTCATATATTCTTTGTTCCTCTGGAACCACAGGACTACCG
AAAGGCGTCATGCTATCCCAAGCAAACCTGCTTGTCGTAACTCGTTTTTGTAAAGATGTT
GTGTTAAATATGCCAAACATTCCAAAAAATGAAGAGAAAGTCTGTTTAGCATTGCTCCCC
TGGTTTCATGCGTTTGGTATAACAGTTTTGACAGGCGTCATTTCTGGAGCTTTGGCAAAA
ATTGTTTTGCTACCGAAATTTGAAGAAGCTCTCTTTCTTAGTTGCATTGAAAATAATCGA
TGCAATATTTGGTTTATGGTGCCACCACTTATGGTCTTTCTTGCAAAACATCCAATGGTT
GCCGATTATGATTTGAGCTGTGCACGCATAATTATTTGCGGTGCTGCACCTTTGTCAAAA
GAATCTGAGCAAGCAGTTTACGATCGATTAAAAATTCCAGAACTGAGAATTTTACAGGGC
TATGGTATGAGTGAACTTTCGCTTGCAGTTCTTTTGCAAAAAAATATATCAAAGCCAGGC
AGTGTTGGGGATCTTGTTGGTGGAAGTTATGCAAAAGTTATTGATGAACATGGAAATGCT
CTTGGACCTAATCAGAAAGGTGAATTGTGTTTTAAAGGCAATCAATTAATGATGGGATAC
ATTAATGACCAAGATGCAACAAGTAGTTGCATTGATAGCGAAGGATGGTTGCATACGGGT
GATGTTGGTTATTATGATGAAGATAAACAATTTTTCATTGTTGAGCGCATCAAAGAATTG
ATAAAATACAAAG
>g12558.t4 Gene=g12558 Length=444
MANNKNILYTPEITNDYHDEPSMGHLIEKSLRQAGEKVLLVSGITGEELTAKDLLAKAIQ
VAQSLYAAGIRSQDKISLVCENRFEFAYILFGSLLLNVTVAPINLTYSEREMIHAFNLSK
PKIIFMSPYASEKVFNVAKTLNYVQKVILFDEENPFDKTVTLFDDFLKLSMNAGPYIPQS
VNKEKSVSYILCSSGTTGLPKGVMLSQANLLVVTRFCKDVVLNMPNIPKNEEKVCLALLP
WFHAFGITVLTGVISGALAKIVLLPKFEEALFLSCIENNRCNIWFMVPPLMVFLAKHPMV
ADYDLSCARIIICGAAPLSKESEQAVYDRLKIPELRILQGYGMSELSLAVLLQKNISKPG
SVGDLVGGSYAKVIDEHGNALGPNQKGELCFKGNQLMMGYINDQDATSSCIDSEGWLHTG
DVGYYDEDKQFFIVERIKELIKYK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g12558.t4 | Gene3D | G3DSA:3.40.50.980 | - | 46 | 358 | 4.5E-112 |
| 7 | g12558.t4 | Gene3D | G3DSA:3.40.50.980 | - | 51 | 206 | 4.5E-112 |
| 9 | g12558.t4 | Gene3D | G3DSA:2.30.38.10 | Luciferase; Domain 3 | 359 | 436 | 4.5E-112 |
| 2 | g12558.t4 | PANTHER | PTHR24096:SF353 | GH16244P-RELATED | 4 | 444 | 5.2E-118 |
| 3 | g12558.t4 | PANTHER | PTHR24096 | LONG-CHAIN-FATTY-ACID–COA LIGASE | 4 | 444 | 5.2E-118 |
| 1 | g12558.t4 | Pfam | PF00501 | AMP-binding enzyme | 29 | 443 | 3.3E-84 |
| 11 | g12558.t4 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 240 | - |
| 12 | g12558.t4 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 241 | 263 | - |
| 10 | g12558.t4 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 264 | 444 | - |
| 6 | g12558.t4 | ProSitePatterns | PS00455 | Putative AMP-binding domain signature. | 190 | 201 | - |
| 5 | g12558.t4 | SUPERFAMILY | SSF56801 | Acetyl-CoA synthetase-like | 22 | 443 | 9.42E-92 |
| 4 | g12558.t4 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 86 | 108 | - |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
GO terms from InterProScan
There are no GO annotations for this transcript.
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.
