General information for g16431.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Probable pseudouridine-5’-phosphatase.
Parent gene
- The parent gene g16431 is located on chr_4: 9420035..9423670 (+ 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 | g16431 | g16431.t1 | TSS | g16431.t1 | 9419926 | 9419926 |
| chr_4 | g16431 | g16431.t1 | isoform | g16431.t1 | 9420035 | 9420909 |
| chr_4 | g16431 | g16431.t1 | exon | g16431.t1.exon1 | 9420035 | 9420095 |
| chr_4 | g16431 | g16431.t1 | cds | g16431.t1.CDS1 | 9420035 | 9420095 |
| chr_4 | g16431 | g16431.t1 | exon | g16431.t1.exon2 | 9420154 | 9420384 |
| chr_4 | g16431 | g16431.t1 | cds | g16431.t1.CDS2 | 9420154 | 9420384 |
| chr_4 | g16431 | g16431.t1 | exon | g16431.t1.exon3 | 9420437 | 9420669 |
| chr_4 | g16431 | g16431.t1 | cds | g16431.t1.CDS3 | 9420437 | 9420669 |
| chr_4 | g16431 | g16431.t1 | exon | g16431.t1.exon4 | 9420727 | 9420909 |
| chr_4 | g16431 | g16431.t1 | cds | g16431.t1.CDS4 | 9420727 | 9420909 |
| chr_4 | g16431 | g16431.t1 | TTS | g16431.t1 | 9421092 | 9421092 |
Sequences
>g16431.t1 Gene=g16431 Length=708
ATGTCTTCACGTTATAAGCCAGTGACACATTGTATTTTTGATATGGATGGATTATTATTA
GACACGGAAACACTTTATACAATTGCAACTCAAAACATTCTCGATAAATATTTTCAAAAT
CCTAGAAAAATATATACTTGGGATGTAAAAGCAACTTTGATGGGATTTCAAACGGAAGAA
GTTGCAAGAAGAATTGTAAATTATTATGAAATTCCAATAACATGGCAAGAATATGTTGTA
CTGGCTAAAGAACAAATTGACATGCTCATGCCGAAATGTGAAAAGACCAAAGGTGCTGAA
AAATTAGTACGGCATCTTTACAACAACAATGTGCCGATTTGCCTTGCAACAAGTAGTTCA
AAAGAAAGCTATGACGTCAAAACGATTCAGCATAAAGAATTATTTAAATTATTCCACCAC
ATTGTTCAAGGCTCAAGCGATTGTGAGGTCAAGAATGGAAAACCAGCACCTGATATTTTT
TTAATTGCTATGAAAAGATTTGGTGATGGAGTTGAGGCTGAAAATTGCTTAGTTTTTGAA
GATGCACCAAATGGTGTCAAAGCTGCATGTTCAGCTGGAATGCAAGTAGTGATGGTACCT
GATCCAAATGTTCCTAAATTTCATTGTGAAAATGCAACTCAAGTGCTCGATTCACTACTA
GATTTTAAACCTGAAGATTTTGGACTGCCAGCATTTTCTGACAAATGA
>g16431.t1 Gene=g16431 Length=235
MSSRYKPVTHCIFDMDGLLLDTETLYTIATQNILDKYFQNPRKIYTWDVKATLMGFQTEE
VARRIVNYYEIPITWQEYVVLAKEQIDMLMPKCEKTKGAEKLVRHLYNNNVPICLATSSS
KESYDVKTIQHKELFKLFHHIVQGSSDCEVKNGKPAPDIFLIAMKRFGDGVEAENCLVFE
DAPNGVKAACSAGMQVVMVPDPNVPKFHCENATQVLDSLLDFKPEDFGLPAFSDK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g16431.t1 | CDD | cd07529 | HAD_AtGPP-like | 8 | 201 | 0 |
| 4 | g16431.t1 | Gene3D | G3DSA:3.40.50.1000 | - | 11 | 219 | 0 |
| 5 | g16431.t1 | Gene3D | G3DSA:1.10.150.240 | Putative phosphatase; domain 2 | 22 | 93 | 0 |
| 2 | g16431.t1 | PANTHER | PTHR18901 | 2-DEOXYGLUCOSE-6-PHOSPHATE PHOSPHATASE 2 | 3 | 233 | 0 |
| 1 | g16431.t1 | Pfam | PF13419 | Haloacid dehalogenase-like hydrolase | 11 | 199 | 0 |
| 8 | g16431.t1 | SFLD | SFLDG01129 | C1.5: HAD, Beta-PGM, Phosphatase Like | 8 | 221 | 0 |
| 9 | g16431.t1 | SFLD | SFLDS00003 | Haloacid Dehalogenase | 8 | 221 | 0 |
| 3 | g16431.t1 | SUPERFAMILY | SSF56784 | HAD-like | 8 | 222 | 0 |
| 6 | g16431.t1 | TIGRFAM | TIGR01509 | HAD-SF-IA-v3: HAD hydrolase, family IA, variant 3 | 147 | 199 | 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 K17623 (pseudouridine 5’-phosphatase)
Pathway
This gene does not belong to any 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.
