General information for g5209.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Luciferin 4-monooxygenase.
Parent gene
- The parent gene g5209 is located on chr_2: 7695265..7700466 (- 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_2 | g5209 | g5209.t1 | isoform | g5209.t1 | 7695265 | 7700466 |
| chr_2 | g5209 | g5209.t1 | exon | g5209.t1.exon1 | 7695265 | 7695783 |
| chr_2 | g5209 | g5209.t1 | cds | g5209.t1.CDS1 | 7695265 | 7695783 |
| chr_2 | g5209 | g5209.t1 | exon | g5209.t1.exon2 | 7696366 | 7697273 |
| chr_2 | g5209 | g5209.t1 | cds | g5209.t1.CDS2 | 7696366 | 7697273 |
| chr_2 | g5209 | g5209.t1 | exon | g5209.t1.exon3 | 7700457 | 7700466 |
| chr_2 | g5209 | g5209.t1 | cds | g5209.t1.CDS3 | 7700457 | 7700466 |
| chr_2 | g5209 | g5209.t1 | TSS | g5209.t1 | NA | NA |
| chr_2 | g5209 | g5209.t1 | TTS | g5209.t1 | NA | NA |
Sequences
>g5209.t1 Gene=g5209 Length=1437
ATGCCGAAAGTGCAACCAGTCTTCAATCCTGATCAAAACCTCGGTCAATTAATTGTGAAA
GTTCTCGAACAAACTCCCGATGCTATTACACAAATATCAGATGATACAAATGTTTCAGTG
ACTTGTGGTGAGATGCGAGATAGAATTTTGAAATTTGCAGTTCATTTGAATAGTCTTAGA
CTTAAACAAAGTGATGTTGTTGGAGTTATAGCTGGAAATACTGAAAATATTGCACCAGTC
GTTTTTGCTTGTTTTTTACTTGGACTTCCTATCAATCCTTTGGCACCAATCATGATTGAA
AGTGACATTATTCAAGTTTATTCAAAAACTAAGCCAAAATTGATCTTTTGTGATGTCAAT
AACTTAAAAATTGTGCAAAATGCTGTAGACAGGATGAAAAGTGAAGCAAAAATTTACACC
GTGATGGAAAAAATTGATGGATATGAATGTGTAACTGATATACTCAAAAAGATTTTTAAT
TTTGAAGATCTAATCTATCCAGAACTTGACCCAAATTCAGTAATTTTTATTCCATGCTCA
TCTGGCTCAACAGGTCCACAAAAAGGAATTTGCAAGACTTATAAAGAATTGCTTTCACTT
TTCGTTCCTCCAACAATTGACTCACATATTTTATATCAATCAACAGGACTTTTTTGGTTT
TCTGGAATTTATTTTCTTCTTTATGGTGCACTTTTTAAATGTTTAAGAATCACAACAGCT
CAATCAACAACAGCTGAACTCTTTTTTAATATTATTAAAAAATATGAAGTCACTAGAGTT
TCAACTGCTCCTTATCTCATTATCAACTTATTACAACTAGATAATTTGGAGCCTCTTGAG
TCAATAAAAATGTGGATGATTGTGGCTGCAAGAGCAACTGAAGATCTTTGTTTAAAGCTA
AAAAAATTGTGCCAAATGATAGTTGATGACAATGGAAATGCACTTGATAATAATCAGCAA
GGTGAAATTTATGTCAAAAAAGATTATAAATTAACTGGATATTACAATGATATGGAAAAA
TTTAAACAAGTTTATGATGGTGAATGGTTTAAGACAGGAGATATTGGTTATATTGATGAT
GAAGGTTTCCTTTATGTTATTGACCGAAAAAAAGAAGTTTTAAAATACAATAATATGCAA
ATTACTCCTGTAGAACTAGAAGAAATTATAAATCAAATCGAAGGAGTTGTCAGCAGTTGT
GCTGTTGGAGTTTTAGAAGAGAAAACTGGAAATGACATAATTCATGCTTTTGTAATTGTC
GATAATATGAAAAATATAACAGAAGATCAAATTCAAAATTATGTCAATGAAAGAGTCATC
GATAATAAAAAGCTTCGAGGTGGTATTCATTTTTTGGAAAAATTTCCTACTGCAATCACT
GGAAAAATTGACAAGAAAAAACTCAGAAGTTTAGCAATTGAAAATTTCACAAACTAA
>g5209.t1 Gene=g5209 Length=478
MPKVQPVFNPDQNLGQLIVKVLEQTPDAITQISDDTNVSVTCGEMRDRILKFAVHLNSLR
LKQSDVVGVIAGNTENIAPVVFACFLLGLPINPLAPIMIESDIIQVYSKTKPKLIFCDVN
NLKIVQNAVDRMKSEAKIYTVMEKIDGYECVTDILKKIFNFEDLIYPELDPNSVIFIPCS
SGSTGPQKGICKTYKELLSLFVPPTIDSHILYQSTGLFWFSGIYFLLYGALFKCLRITTA
QSTTAELFFNIIKKYEVTRVSTAPYLIINLLQLDNLEPLESIKMWMIVAARATEDLCLKL
KKLCQMIVDDNGNALDNNQQGEIYVKKDYKLTGYYNDMEKFKQVYDGEWFKTGDIGYIDD
EGFLYVIDRKKEVLKYNNMQITPVELEEIINQIEGVVSSCAVGVLEEKTGNDIIHAFVIV
DNMKNITEDQIQNYVNERVIDNKKLRGGIHFLEKFPTAITGKIDKKKLRSLAIENFTN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 11 | g5209.t1 | Gene3D | G3DSA:3.40.50.12780 | - | 3 | 305 | 1.3E-43 |
| 10 | g5209.t1 | Gene3D | G3DSA:3.40.50.12780 | - | 306 | 372 | 2.0E-17 |
| 12 | g5209.t1 | Gene3D | G3DSA:3.30.300.30 | - | 373 | 476 | 1.1E-17 |
| 5 | g5209.t1 | PANTHER | PTHR24096:SF353 | GH16244P-RELATED | 3 | 304 | 1.6E-102 |
| 7 | g5209.t1 | PANTHER | PTHR24096 | LONG-CHAIN-FATTY-ACID–COA LIGASE | 3 | 304 | 1.6E-102 |
| 4 | g5209.t1 | PANTHER | PTHR24096:SF353 | GH16244P-RELATED | 307 | 474 | 1.6E-102 |
| 6 | g5209.t1 | PANTHER | PTHR24096 | LONG-CHAIN-FATTY-ACID–COA LIGASE | 307 | 474 | 1.6E-102 |
| 3 | g5209.t1 | Pfam | PF00501 | AMP-binding enzyme | 22 | 303 | 5.2E-27 |
| 2 | g5209.t1 | Pfam | PF00501 | AMP-binding enzyme | 306 | 376 | 1.6E-18 |
| 1 | g5209.t1 | Pfam | PF13193 | AMP-binding enzyme C-terminal domain | 385 | 462 | 7.4E-6 |
| 14 | g5209.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 209 | - |
| 15 | g5209.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 210 | 231 | - |
| 13 | g5209.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 232 | 478 | - |
| 9 | g5209.t1 | SUPERFAMILY | SSF56801 | Acetyl-CoA synthetase-like | 4 | 473 | 1.96E-78 |
| 8 | g5209.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 210 | 232 | - |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5209/g5209.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5209.t1.fa.iupred3.txt does not exist
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. There were no conditions that were differentially expressed