General information for g5617.t3
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as 5-oxoprolinase.
Parent gene
- The parent gene g5617 is located on chr_2: 10648817..10649935 (- 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 | g5617 | g5617.t3 | isoform | g5617.t3 | 10647440 | 10648167 |
| chr_2 | g5617 | g5617.t3 | exon | g5617.t3.exon1 | 10647440 | 10648167 |
| chr_2 | g5617 | g5617.t3 | cds | g5617.t3.CDS1 | 10647441 | 10648100 |
| chr_2 | g5617 | g5617.t3 | TSS | g5617.t3 | NA | NA |
| chr_2 | g5617 | g5617.t3 | TTS | g5617.t3 | NA | NA |
Sequences
>g5617.t3 Gene=g5617 Length=728
TTCTGAAATTACCAAACTCATCAATGATTATAACAAAACTGAAGAGCTTTCAATTCAAGA
TGTAGCAATGGGATTTATTCGTGTTGCTAATGAGTCCATGTGTCGTCCAATAAGAGCTTT
GACTCAGTCACGTGGTTTTGACACATCGAAGCATGCACTTGCTGTGTTTGGTGGAGCTGG
AGGACAACATGCTTGTTCAATTGCAAAAGAACTTGGCATGAAAACAGTTTTAATTCATAA
ATATGCTGGAATATTATCAGCTTACGGTATGGCTTATGCTGATGTTGTTTATGAAAGTCA
AGAGCCTTATGGATTTGCTTTTGAAACTAAAAATATTGAAGCGATAAAAAATCTATTGGA
TAAATTATCATCTCAATGCATTACACAATTAAAAAATCAGGGATTTTCAGAGGAAAATAT
TCAATGTGAACCATATTTACATTTACGATACAATTCTACAGATTGCGCTCTTATGATTTC
ACCAGACAAGGTTTCAAAACATGAACTGAGTGTTCCAAATTATGGTGATTTTATATCAGC
TTTTCTCACACGCTATCAAAAAGAATTTGGATTTATTTTAGAAAATCGTTCAATTATTGT
AGATGACGTAAGAGTTAGAGGACTAGGGAAAACTAAAATTCCTGATGAACCATTAGTTGA
GAAAGCAAAAAGTAAAAAGCCCAATCCAGAAAAAATGATCAAAGTGTTTTTCGATAATAA
ATGGATGG
>g5617.t3 Gene=g5617 Length=220
MGFIRVANESMCRPIRALTQSRGFDTSKHALAVFGGAGGQHACSIAKELGMKTVLIHKYA
GILSAYGMAYADVVYESQEPYGFAFETKNIEAIKNLLDKLSSQCITQLKNQGFSEENIQC
EPYLHLRYNSTDCALMISPDKVSKHELSVPNYGDFISAFLTRYQKEFGFILENRSIIVDD
VRVRGLGKTKIPDEPLVEKAKSKKPNPEKMIKVFFDNKWM
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 2 | g5617.t3 | PANTHER | PTHR11365 | 5-OXOPROLINASE RELATED | 1 | 219 | 0 |
| 3 | g5617.t3 | PANTHER | PTHR11365:SF2 | 5-OXOPROLINASE | 1 | 219 | 0 |
| 1 | g5617.t3 | Pfam | PF01968 | Hydantoinase/oxoprolinase | 2 | 76 | 0 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5617/g5617.t3; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5617.t3.fa.iupred3.txt does not exist
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0016787 | hydrolase activity | MF |
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.
