General information for g5617.t7
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.t7 | isoform | g5617.t7 | 10648817 | 10649935 |
| chr_2 | g5617 | g5617.t7 | exon | g5617.t7.exon1 | 10648817 | 10649935 |
| chr_2 | g5617 | g5617.t7 | cds | g5617.t7.CDS1 | 10649018 | 10649935 |
| chr_2 | g5617 | g5617.t7 | TTS | g5617.t7 | 10649670 | 10649670 |
| chr_2 | g5617 | g5617.t7 | TSS | g5617.t7 | 10649982 | 10649982 |
Sequences
>g5617.t7 Gene=g5617 Length=1119
ATGAATAAATTTAATTTTTTCATTGATCGTGGAGGTACATTTACCGATTGCATTTGCATC
ACAGCAAATCAATCAGTTAAAACAATGAAACTTTTATCAGAAGACCCTGAAAATTACAAA
GATGCTCCAACTGAAATAATTAAAAGACTTTTAATTGAAGAACTTGGAAAAGATAAGGTC
ATTAATGAGAACGGTTTGATAAATACGTCTCATATTGGTTGTGTGCGGATGGGTACTACT
GTTGCGACAAATGCTTTATTAGAGAGAAAAGGAGAAAAAATTGTATTAGTCGTCAATAAA
GGATTGAAAGATATTTTGCAAATTGGTAATCAGGCACGTCCAAAAATTTTTGATCTCAAC
ATTAGAAAACCTTCGAATCTATACGAGAAAGTCATTGAAGTTGATTGCCGAATTGTTCCA
GAAAGAAATGATTGTGAACTTGGTGAGATTTCATCATCATGGAGAAAAGTTTCTGGAATA
TCCAATTCTACGTTTCTTGTTCAAAAAGAATTGAATGTTGATGAAGTTAGAGGTCAATTG
CAAAATGTCTTTGATTTAGGAATCACATCAGTTGCTGTTTGTTTAGCACACTCGTATGCA
TGTCCTGAACAAGAATTAATAATTGGAGACATCGCTAAAAGCGTTGGTTTTACTACAATT
ACGCTCAGTCATCAGGCAATGCCTATGATTCGACTTGTTAATAGATCATTTACTTCTTGT
GCTGAAGCCTATTTGGAGCCACATGTTCACCGTTATTTAAAATCATTTAAAGCTGGATTC
GAAAAAAATCTTGAAGGAGTGGAAGTTCTTTTTATGCAGAGTGATGGTGGTTTAACAAAT
ATTAATAGATTTAGAGGAGCAAAGGCTATTTTGTCAGGTCCCGCAGGTAATGTCACGCTC
TGTTTGCGAGTGGTTTAAAGCACAACCTTCCCTTAACAATATAATTTTTTTATTTTCCGT
TTTTGATATTTCTATGTTTCATTTAACAAGAATTTGAGTTCTTTTTAATTTTTTTTTAAT
ATCAAGTCACTTTAATTAGGCAAACTTCAAGTTAACATCCAATATGTAACTGATTTAAGA
CCATGAGGCCAATATCACAATTTTATCATGCAGCATTAA
>g5617.t7 Gene=g5617 Length=305
MNKFNFFIDRGGTFTDCICITANQSVKTMKLLSEDPENYKDAPTEIIKRLLIEELGKDKV
INENGLINTSHIGCVRMGTTVATNALLERKGEKIVLVVNKGLKDILQIGNQARPKIFDLN
IRKPSNLYEKVIEVDCRIVPERNDCELGEISSSWRKVSGISNSTFLVQKELNVDEVRGQL
QNVFDLGITSVAVCLAHSYACPEQELIIGDIAKSVGFTTITLSHQAMPMIRLVNRSFTSC
AEAYLEPHVHRYLKSFKAGFEKNLEGVEVLFMQSDGGLTNINRFRGAKAILSGPAGNVTL
CLRVV
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 3 | g5617.t7 | PANTHER | PTHR11365 | 5-OXOPROLINASE RELATED | 2 | 298 | 0 |
| 4 | g5617.t7 | PANTHER | PTHR11365:SF2 | 5-OXOPROLINASE | 2 | 298 | 0 |
| 1 | g5617.t7 | Pfam | PF05378 | Hydantoinase/oxoprolinase N-terminal region | 6 | 215 | 0 |
| 2 | g5617.t7 | Pfam | PF01968 | Hydantoinase/oxoprolinase | 236 | 302 | 0 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5617/g5617.t7; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5617.t7.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.
