General information for g5946.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Luciferin 4-monooxygenase.
Parent gene
- The parent gene g5946 is located on chr_2: 12957465..12959337 (- 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 | g5946 | g5946.t1 | isoform | g5946.t1 | 12957465 | 12959337 |
| chr_2 | g5946 | g5946.t1 | exon | g5946.t1.exon1 | 12957465 | 12957613 |
| chr_2 | g5946 | g5946.t1 | cds | g5946.t1.CDS1 | 12957465 | 12957613 |
| chr_2 | g5946 | g5946.t1 | exon | g5946.t1.exon2 | 12957674 | 12958064 |
| chr_2 | g5946 | g5946.t1 | cds | g5946.t1.CDS2 | 12957674 | 12958064 |
| chr_2 | g5946 | g5946.t1 | exon | g5946.t1.exon3 | 12958134 | 12958228 |
| chr_2 | g5946 | g5946.t1 | cds | g5946.t1.CDS3 | 12958134 | 12958228 |
| chr_2 | g5946 | g5946.t1 | exon | g5946.t1.exon4 | 12958285 | 12958977 |
| chr_2 | g5946 | g5946.t1 | cds | g5946.t1.CDS4 | 12958285 | 12958977 |
| chr_2 | g5946 | g5946.t1 | exon | g5946.t1.exon5 | 12959040 | 12959337 |
| chr_2 | g5946 | g5946.t1 | cds | g5946.t1.CDS5 | 12959040 | 12959337 |
| chr_2 | g5946 | g5946.t1 | TSS | g5946.t1 | 12960040 | 12960040 |
| chr_2 | g5946 | g5946.t1 | TTS | g5946.t1 | NA | NA |
Sequences
>g5946.t1 Gene=g5946 Length=1626
ATGTTCTCATACGATAGAGAGAGCAAAATATTAAGCGGCATAGAGTTAGAACCTTTTTAT
CATCATAATGTTACAGCTGGACAATTATTGATTCATTATCTTCAAAGAGATCCTACAAAA
ATTATTCAATCATGCTATGACACTGGTGTTAATATAACTGCAGCAGAAATGGAACAGTTG
GGTCTGAGAGTAGCTAAGAATATTTTAAAAGAAAATCTTAAATTAGGTGATGTTATTGGC
CTTGTTGCAAAAAATACTACATATGTAGCTCCGTTAGTTCTTGGATGTCTTTTGACGGGC
AATCCTATTTCAACTTTAGATCCCACTTTTGATCCTAATGAAATTGCTAATATTTTTAGA
CAAACATTACCAAAACTTGTGTTTTGTGATCATGATAATTGGGAAAATGTAATTGAAGCA
TTAAAAATGTGTAAAAATGATGCAGAAGTTATAACAATTGATGAAAAAATGACAGGTGTT
CGATTTATTGGTGAATTTTTTGAATTATTACCTGGGGAAAGGCCATTCTTTCCACGTAGT
TTTGGTATTGAAGCTTTTAGATTGTGTGGAGTCATTTTGTGTAGTTCAGGAACAACAGCA
CTCTCAAAAGGAACAATGTTGTCACATTCTCAATGCATTCTCATGTCAAGAGCATTCCCT
ATACATTATCCTACTGGTATCTGCTTTAGCTCTCTATATTGGCTTTCAGGATTTACAGTT
TTGATGCAATCACTTTGTGGTAACATTAGAAGAATCATTACAAGACGACCTTTTAGTCCT
CTACTTATGATTCATTTAATTGAACAATATAAAGCATCAGTTTTGCTTACACCACCTTCA
CAAATTGCAATGCTTTTACAATCACCATTTCTTAAATTGGCGGATTTAAGTTCAGTGAGA
CTTCATGTTGTTGCTGGTGGATTTATTGATGAAAGTATGAGAAAATCTATGCAAGGACAT
CTTCTTTATGGAGCATTACTTGTTACTTATGGAATGACGGAAGTTGCCTCAATAATTTCT
ATTACAGCACCTTTACAAAAATTTTCAAATTCAAGTGGAAAAATCAACCCTAATTTCAAG
TTAAAAATTGTAGACGATGACGGAAATTCACTTGACCCAAATAATGTGGGAGAAATTTAT
TTAAAAGCACCGTATAGATTTTTGGGCTATGCTAATAATGTTGAGGACACAAAGAATGCA
TTTGATAGTGATGGTTGGCTAAAAACAGGTGATCTTGGTTATATAACTGAAGATGGGGAA
ATTTTCGTTGTTGATCGTAAAAAGGATATGATTAAGTATATGAATTATCAAGTTGCACCA
TCTGAAATTGAGGCATTTGTAAATGCAATGGATGGCGTGCAACAAGTGACAGTCGTCGGT
ATACCTGATATGCTAAGAGGAGATTTGGCAGTAGCAATTGTAGTGAAGGAAAAAGATGCA
GACTTAACTGAGCAAGATATTATTGACGAAGTAGCGAAAAATTTTCCATTATTTAAACGA
CTTCACGGAGGAGCATTTTTCGTAAATGAATTACCAATGACACCATCAGGAAAGATAAAG
AAACGTATTGTTCGGGAAATGGCAGCACGTATGTACAAGTCTCAAGAAATTAATGGAAAC
TATTAA
>g5946.t1 Gene=g5946 Length=541
MFSYDRESKILSGIELEPFYHHNVTAGQLLIHYLQRDPTKIIQSCYDTGVNITAAEMEQL
GLRVAKNILKENLKLGDVIGLVAKNTTYVAPLVLGCLLTGNPISTLDPTFDPNEIANIFR
QTLPKLVFCDHDNWENVIEALKMCKNDAEVITIDEKMTGVRFIGEFFELLPGERPFFPRS
FGIEAFRLCGVILCSSGTTALSKGTMLSHSQCILMSRAFPIHYPTGICFSSLYWLSGFTV
LMQSLCGNIRRIITRRPFSPLLMIHLIEQYKASVLLTPPSQIAMLLQSPFLKLADLSSVR
LHVVAGGFIDESMRKSMQGHLLYGALLVTYGMTEVASIISITAPLQKFSNSSGKINPNFK
LKIVDDDGNSLDPNNVGEIYLKAPYRFLGYANNVEDTKNAFDSDGWLKTGDLGYITEDGE
IFVVDRKKDMIKYMNYQVAPSEIEAFVNAMDGVQQVTVVGIPDMLRGDLAVAIVVKEKDA
DLTEQDIIDEVAKNFPLFKRLHGGAFFVNELPMTPSGKIKKRIVREMAARMYKSQEINGN
Y
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g5946.t1 | Gene3D | G3DSA:3.40.50.12780 | - | 8 | 429 | 4.7E-87 |
| 9 | g5946.t1 | Gene3D | G3DSA:3.30.300.30 | - | 430 | 533 | 3.5E-25 |
| 3 | g5946.t1 | PANTHER | PTHR24096:SF353 | GH16244P-RELATED | 3 | 534 | 3.1E-137 |
| 4 | g5946.t1 | PANTHER | PTHR24096 | LONG-CHAIN-FATTY-ACID–COA LIGASE | 3 | 534 | 3.1E-137 |
| 2 | g5946.t1 | Pfam | PF00501 | AMP-binding enzyme | 37 | 433 | 9.0E-63 |
| 1 | g5946.t1 | Pfam | PF13193 | AMP-binding enzyme C-terminal domain | 442 | 518 | 8.9E-14 |
| 12 | g5946.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 231 | - |
| 14 | g5946.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 232 | 253 | - |
| 10 | g5946.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 254 | 320 | - |
| 13 | g5946.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 321 | 345 | - |
| 11 | g5946.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 346 | 541 | - |
| 7 | g5946.t1 | SUPERFAMILY | SSF56801 | Acetyl-CoA synthetase-like | 23 | 531 | 6.41E-107 |
| 5 | g5946.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 223 | 245 | - |
| 6 | g5946.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 321 | 343 | - |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5946/g5946.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5946.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