General information for g5609.t4
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Phosphoribosylformylglycinamidine synthase.
Parent gene
- The parent gene g5609 is located on chr_2: 10597946..10598677 (+ 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 | g5609 | g5609.t4 | isoform | g5609.t4 | 10597946 | 10598677 |
| chr_2 | g5609 | g5609.t4 | exon | g5609.t4.exon1 | 10597946 | 10598677 |
| chr_2 | g5609 | g5609.t4 | cds | g5609.t4.CDS1 | 10598114 | 10598617 |
| chr_2 | g5609 | g5609.t4 | TTS | g5609.t4 | 10598682 | 10598682 |
| chr_2 | g5609 | g5609.t4 | TSS | g5609.t4 | NA | NA |
Sequences
>g5609.t4 Gene=g5609 Length=732
TATCGTGGAATAATTTTCCCTGGAGGTTTCAGTTATGCCGACACACTTGGTTCAGCAAAA
GGATGGGCTGCAAGCATACGATTTAGTGACTTATTACAACCACAGTTTGAAAACTTTAAG
ATTCGAAAAGACACATTTTCACTTGGTGTATGCAATGGTTGTCAATTGATGAGCTTGATA
GGATGGATTGATTATGAAGAAAATTCTACAAATGATGATGTTCCTTCGATCGCTCTATTG
CATAATAAATCTGGTAGATTTGAATGTCGTTGGAGCACATTGAAAGTTGCTTCAAGTAAT
GCAATAATGTTAAGACGAATGCAAGGAAGCGTTTTGGGATGTTGGGTCGCACATGGAGAA
GGTCGATTCTCATTCAAAAATCAACAGGTGCTGAAAAATCTCAAAGCATCAAATTCAATT
GCTCTTCATTATGTAGATGACGATATGAAACCTACTGAAAAATATCCATTAAATCCAAAC
GGTAGTGTTGAAGGAATTGCTGCAATTTGCTCAAAAGATGGTCGTCATTTGGCTATGATG
CCTCATCCAGAGAGATGTTGTGAAATGTTCCAATGGCCATTTTTACCATCAGATTTTAAA
ACTGAAAATTGCCCATGGCAATCAATGTTCAATGAAGCAAATATTTGGTGTTGCGAAAAC
AAACAAAACTAAAGTGCCAATAATTTTTATAAAATTTATAATAATAATGAAAGAATAAAA
GACATTTTTTAC
>g5609.t4 Gene=g5609 Length=167
MSLIGWIDYEENSTNDDVPSIALLHNKSGRFECRWSTLKVASSNAIMLRRMQGSVLGCWV
AHGEGRFSFKNQQVLKNLKASNSIALHYVDDDMKPTEKYPLNPNGSVEGIAAICSKDGRH
LAMMPHPERCCEMFQWPFLPSDFKTENCPWQSMFNEANIWCCENKQN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g5609.t4 | Gene3D | G3DSA:3.40.50.880 | - | 1 | 162 | 0 |
| 2 | g5609.t4 | PANTHER | PTHR10099 | PHOSPHORIBOSYLFORMYLGLYCINAMIDINE SYNTHASE | 1 | 161 | 0 |
| 1 | g5609.t4 | Pfam | PF13507 | CobB/CobQ-like glutamine amidotransferase domain | 1 | 161 | 0 |
| 4 | g5609.t4 | SMART | SM01211 | GATase_5_2 | 1 | 161 | 0 |
| 3 | g5609.t4 | SUPERFAMILY | SSF52317 | Class I glutamine amidotransferase-like | 17 | 161 | 0 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5609/g5609.t4; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5609.t4.fa.iupred3.txt does not exist
GO terms from InterProScan
There are no GO annotations for this transcript.
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.
