General information for g13990.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Kynurenine formamidase.
Parent gene
- The parent gene g13990 is located on chr_1: 33859070..33860493 (+ 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 | g13990 | g13990.t1 | isoform | g13990.t1 | 33859070 | 33860493 |
| chr_1 | g13990 | g13990.t1 | exon | g13990.t1.exon1 | 33859070 | 33859184 |
| chr_1 | g13990 | g13990.t1 | cds | g13990.t1.CDS1 | 33859070 | 33859184 |
| chr_1 | g13990 | g13990.t1 | exon | g13990.t1.exon2 | 33859730 | 33860493 |
| chr_1 | g13990 | g13990.t1 | cds | g13990.t1.CDS2 | 33859730 | 33860493 |
| chr_1 | g13990 | g13990.t1 | TSS | g13990.t1 | NA | NA |
| chr_1 | g13990 | g13990.t1 | TTS | g13990.t1 | NA | NA |
Sequences
>g13990.t1 Gene=g13990 Length=879
ATGAGCTCTGTTGAAAAACTTGAACTCGAAATACAATACACGCCTTCACTTTCATCTAAA
AGATTTTCTTCTCGAGATGAATTATTGAAAAACAACATAACTGTCTGTAAAAACGAATCC
GAAAAAAATCGATTAAATTATGATTGTCATTTAAATATCGCATATGGACGAAGTAAACGT
GAAAAATTCGATATTTATGGCGATGATCTTCCGAAATCTGCTCCGCTTTTTGTTTTTATA
CATGGCGGCTATTGGCAGCTTTGTGACAAAGAAATGTCTGCATTTATGGTTAAACCACTA
TATGAAAATGGAATACGAGTCATAACGATCGACTACGAATTGTGCCCAAATGTGACTCTT
GAAGAAATTGTTGAGCAGGTTAAAAAATGTTTTAAATGGATTGCTCAGTACATAAAACAA
AACGAGATAAGAAAAGTTGCCCTATCGGGTCACTCAGCTGGAGCACATTTACTTTGTTAT
GGAATTAATGAAGAATTTATGAAAACAATATCTTCTTCTGTTGAACTTCATGCGTTTTTC
ATTTCCGGAGTGTACTATCTTGAAGAATTGAGATATTTAAAAGCTGCTAATGAAAATAAC
ATCTTGCATATTACTGATGAAAACTGTCGTCGTCTTTCACCACAATACATGGATTTCAAC
TATTTGAAAAAATTCAATTTTCATGCTCACGTGTTTGCTGGTGAATTTGAATCAGAAAAA
TTTCGTGAGCATTCAAAAGAATTTGCAGAAGGTCCAATGAAAGACTTTTTAAAAACTTTT
AAAATTTTTGAAAAACTTGATCATTTTGATATAGTTGAAAAAATGTGTGATAGTAATTAT
GAACTCATACTTTTGATCATTGAAAATCTTAAAAATTAA
>g13990.t1 Gene=g13990 Length=292
MSSVEKLELEIQYTPSLSSKRFSSRDELLKNNITVCKNESEKNRLNYDCHLNIAYGRSKR
EKFDIYGDDLPKSAPLFVFIHGGYWQLCDKEMSAFMVKPLYENGIRVITIDYELCPNVTL
EEIVEQVKKCFKWIAQYIKQNEIRKVALSGHSAGAHLLCYGINEEFMKTISSSVELHAFF
ISGVYYLEELRYLKAANENNILHITDENCRRLSPQYMDFNYLKKFNFHAHVFAGEFESEK
FREHSKEFAEGPMKDFLKTFKIFEKLDHFDIVEKMCDSNYELILLIIENLKN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g13990.t1 | Gene3D | G3DSA:3.40.50.1820 | - | 33 | 288 | 0 |
| 2 | g13990.t1 | PANTHER | PTHR23024 | ARYLACETAMIDE DEACETYLASE | 45 | 269 | 0 |
| 3 | g13990.t1 | PANTHER | PTHR23024:SF554 | KYNURENINE FORMAMIDASE | 45 | 269 | 0 |
| 1 | g13990.t1 | Pfam | PF07859 | alpha/beta hydrolase fold | 78 | 159 | 0 |
| 4 | g13990.t1 | SUPERFAMILY | SSF53474 | alpha/beta-Hydrolases | 44 | 277 | 0 |
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:0016787 | hydrolase activity | MF |
KEGG
Orthology
- This transcript has been annotated with K01432 (arylformamidase)
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.
