General information for g15439.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Omega-amidase NIT2.
Parent gene
- The parent gene g15439 is located on chr_4: 5463299..5472209 (+ 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_4 | g15439 | g15439.t1 | TSS | g15439.t1 | 5463288 | 5463288 |
| chr_4 | g15439 | g15439.t1 | isoform | g15439.t1 | 5463299 | 5464245 |
| chr_4 | g15439 | g15439.t1 | exon | g15439.t1.exon1 | 5463299 | 5463476 |
| chr_4 | g15439 | g15439.t1 | cds | g15439.t1.CDS1 | 5463299 | 5463476 |
| chr_4 | g15439 | g15439.t1 | exon | g15439.t1.exon2 | 5463530 | 5464102 |
| chr_4 | g15439 | g15439.t1 | cds | g15439.t1.CDS2 | 5463530 | 5464102 |
| chr_4 | g15439 | g15439.t1 | exon | g15439.t1.exon3 | 5464157 | 5464245 |
| chr_4 | g15439 | g15439.t1 | cds | g15439.t1.CDS3 | 5464157 | 5464245 |
| chr_4 | g15439 | g15439.t1 | TTS | g15439.t1 | 5464390 | 5464390 |
Sequences
>g15439.t1 Gene=g15439 Length=840
ATGGATAAGCTGGCGAGAACACTTAGACTTGGTTGCATTCAACTCAAAGTTGGTGCAAAT
AAAAGTGAGAATGTAGCACGAGCAATAAACAAAATTCGTGATGCAAAAATGAAAGGAGCT
GAAGTTGTCAGCTTACCAGAATGTTTTAATAGCCCTTATGGAACTGCTTATTTTAATGAT
TATGCAGAAACAATTCCAGGTGAAACAACAAATCTTCTCTCACAAATTGCCAAAGAACTT
CAAATTATTCTCATTGGAGGAACAATTCCAGAACGTGATGGCGATAAGCTCTATAATACA
GCCACAATCTGGGGTAAATCGGGTGAACTTTTGGCCAAATACCGCAAAATGCATTTATTC
GACATTGATATTCCCAATGAAATTACATTTAAGGAATCTGACTCGCTTTCAGCTGGAAAT
GATTTGGCAATAATTAATGTAAAAGATTTTAAAATTGGCATTGGAATTTGCTATGACATA
AGATTTGAAGAATTGGCAAAAATATACAGGAAAAAAGGTTGCAATGTTTTGGTTTATCCA
GCTGCTTTTAATATGAAAACTGGACCATTACATTATGAATTGCTTGCACAATCAAGGTCA
AATGATAATCAACTTTATACGGCATTAATTTCACCTGCTAGAGATGTAAATGCGAGTTAT
GTTGCTTGGGGTCATTCATGTGTTGTTGATCCTTGGGCAGAAGTCATGTATACAAGTGAA
GCTGATGAGGACGTTTTTGTTGTTGACTTAGATTTGGATAAAGTTGATAAAGTTAGAGCA
AATATTCCTGTTTTCAATCAACGTCGTACTGATATTTATGAAACAATTGAAAAGAAATGA
>g15439.t1 Gene=g15439 Length=279
MDKLARTLRLGCIQLKVGANKSENVARAINKIRDAKMKGAEVVSLPECFNSPYGTAYFND
YAETIPGETTNLLSQIAKELQIILIGGTIPERDGDKLYNTATIWGKSGELLAKYRKMHLF
DIDIPNEITFKESDSLSAGNDLAIINVKDFKIGIGICYDIRFEELAKIYRKKGCNVLVYP
AAFNMKTGPLHYELLAQSRSNDNQLYTALISPARDVNASYVAWGHSCVVDPWAEVMYTSE
ADEDVFVVDLDLDKVDKVRANIPVFNQRRTDIYETIEKK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g15439.t1 | CDD | cd07572 | nit | 9 | 269 | 0.000 |
| 5 | g15439.t1 | Gene3D | G3DSA:3.60.110.10 | - | 5 | 279 | 0.000 |
| 2 | g15439.t1 | PANTHER | PTHR23088:SF30 | OMEGA-AMIDASE NIT2 | 8 | 276 | 0.000 |
| 3 | g15439.t1 | PANTHER | PTHR23088 | NITRILASE-RELATED | 8 | 276 | 0.000 |
| 1 | g15439.t1 | Pfam | PF00795 | Carbon-nitrogen hydrolase | 10 | 259 | 0.000 |
| 6 | g15439.t1 | ProSiteProfiles | PS50263 | Carbon-nitrogen hydrolase domain profile. | 8 | 252 | 58.842 |
| 4 | g15439.t1 | SUPERFAMILY | SSF56317 | Carbon-nitrogen hydrolase | 5 | 268 | 0.000 |
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:0006807 | nitrogen compound metabolic process | BP |
KEGG
Orthology
- This transcript has been annotated with K13566 (omega-amidase)
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.
