General information for g15439.t4
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative 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.t4 | TSS | g15439.t4 | 5463288 | 5463288 |
| chr_4 | g15439 | g15439.t4 | isoform | g15439.t4 | 5463299 | 5464245 |
| chr_4 | g15439 | g15439.t4 | exon | g15439.t4.exon1 | 5463299 | 5464102 |
| chr_4 | g15439 | g15439.t4 | cds | g15439.t4.CDS1 | 5463700 | 5464102 |
| chr_4 | g15439 | g15439.t4 | exon | g15439.t4.exon2 | 5464157 | 5464245 |
| chr_4 | g15439 | g15439.t4 | cds | g15439.t4.CDS2 | 5464157 | 5464245 |
| chr_4 | g15439 | g15439.t4 | TTS | g15439.t4 | 5464390 | 5464390 |
Sequences
>g15439.t4 Gene=g15439 Length=893
ATGGATAAGCTGGCGAGAACACTTAGACTTGGTTGCATTCAACTCAAAGTTGGTGCAAAT
AAAAGTGAGAATGTAGCACGAGCAATAAACAAAATTCGTGATGCAAAAATGAAAGGAGCT
GAAGTTGTCAGCTTACCAGAATGTTTTAATAGCCCTTATGGAACTGCTTATTTTAATGGT
AAAAATTTTTTTTTTATCAAAATCTTTAAATTAATTCTTAAAAATTTTCAGATTATGCAG
AAACAATTCCAGGTGAAACAACAAATCTTCTCTCACAAATTGCCAAAGAACTTCAAATTA
TTCTCATTGGAGGAACAATTCCAGAACGTGATGGCGATAAGCTCTATAATACAGCCACAA
TCTGGGGTAAATCGGGTGAACTTTTGGCCAAATACCGCAAAATGCATTTATTCGACATTG
ATATTCCCAATGAAATTACATTTAAGGAATCTGACTCGCTTTCAGCTGGAAATGATTTGG
CAATAATTAATGTAAAAGATTTTAAAATTGGCATTGGAATTTGCTATGACATAAGATTTG
AAGAATTGGCAAAAATATACAGGAAAAAAGGTTGCAATGTTTTGGTTTATCCAGCTGCTT
TTAATATGAAAACTGGACCATTACATTATGAATTGCTTGCACAATCAAGGTCAAATGATA
ATCAACTTTATACGGCATTAATTTCACCTGCTAGAGATGTAAATGCGAGTTATGTTGCTT
GGGGTCATTCATGTGTTGTTGATCCTTGGGCAGAAGTCATGTATACAAGTGAAGCTGATG
AGGACGTTTTTGTTGTTGACTTAGATTTGGATAAAGTTGATAAAGTTAGAGCAAATATTC
CTGTTTTCAATCAACGTCGTACTGATATTTATGAAACAATTGAAAAGAAATGA
>g15439.t4 Gene=g15439 Length=163
MHLFDIDIPNEITFKESDSLSAGNDLAIINVKDFKIGIGICYDIRFEELAKIYRKKGCNV
LVYPAAFNMKTGPLHYELLAQSRSNDNQLYTALISPARDVNASYVAWGHSCVVDPWAEVM
YTSEADEDVFVVDLDLDKVDKVRANIPVFNQRRTDIYETIEKK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g15439.t4 | Gene3D | G3DSA:3.60.110.10 | - | 1 | 163 | 0.000 |
| 2 | g15439.t4 | PANTHER | PTHR23088:SF30 | OMEGA-AMIDASE NIT2 | 1 | 160 | 0.000 |
| 3 | g15439.t4 | PANTHER | PTHR23088 | NITRILASE-RELATED | 1 | 160 | 0.000 |
| 1 | g15439.t4 | Pfam | PF00795 | Carbon-nitrogen hydrolase | 1 | 143 | 0.000 |
| 6 | g15439.t4 | ProSiteProfiles | PS50263 | Carbon-nitrogen hydrolase domain profile. | 1 | 136 | 31.955 |
| 4 | g15439.t4 | SUPERFAMILY | SSF56317 | Carbon-nitrogen hydrolase | 1 | 153 | 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 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