General information for g16431.t4
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative 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.t4 | TSS | g16431.t4 | 9419926 | 9419926 |
| chr_4 | g16431 | g16431.t4 | isoform | g16431.t4 | 9420035 | 9420909 |
| chr_4 | g16431 | g16431.t4 | exon | g16431.t4.exon1 | 9420035 | 9420095 |
| chr_4 | g16431 | g16431.t4 | cds | g16431.t4.CDS1 | 9420035 | 9420095 |
| chr_4 | g16431 | g16431.t4 | exon | g16431.t4.exon2 | 9420154 | 9420384 |
| chr_4 | g16431 | g16431.t4 | cds | g16431.t4.CDS2 | 9420154 | 9420384 |
| chr_4 | g16431 | g16431.t4 | exon | g16431.t4.exon3 | 9420437 | 9420673 |
| chr_4 | g16431 | g16431.t4 | cds | g16431.t4.CDS3 | 9420437 | 9420673 |
| chr_4 | g16431 | g16431.t4 | exon | g16431.t4.exon4 | 9420727 | 9420909 |
| chr_4 | g16431 | g16431.t4 | cds | g16431.t4.CDS4 | 9420727 | 9420740 |
| chr_4 | g16431 | g16431.t4 | TTS | g16431.t4 | 9421092 | 9421092 |
Sequences
>g16431.t4 Gene=g16431 Length=712
ATGTCTTCACGTTATAAGCCAGTGACACATTGTATTTTTGATATGGATGGATTATTATTA
GACACGGAAACACTTTATACAATTGCAACTCAAAACATTCTCGATAAATATTTTCAAAAT
CCTAGAAAAATATATACTTGGGATGTAAAAGCAACTTTGATGGGATTTCAAACGGAAGAA
GTTGCAAGAAGAATTGTAAATTATTATGAAATTCCAATAACATGGCAAGAATATGTTGTA
CTGGCTAAAGAACAAATTGACATGCTCATGCCGAAATGTGAAAAGACCAAAGGTGCTGAA
AAATTAGTACGGCATCTTTACAACAACAATGTGCCGATTTGCCTTGCAACAAGTAGTTCA
AAAGAAAGCTATGACGTCAAAACGATTCAGCATAAAGAATTATTTAAATTATTCCACCAC
ATTGTTCAAGGCTCAAGCGATTGTGAGGTCAAGAATGGAAAACCAGCACCTGATATTTTT
TTAATTGCTATGAAAAGATTTGGTGATGGAGTTGAGGCTGAAAATGTTATGCTTAGTTTT
TGAAGATGCACCAAATGGTGTCAAAGCTGCATGTTCAGCTGGAATGCAAGTAGTGATGGT
ACCTGATCCAAATGTTCCTAAATTTCATTGTGAAAATGCAACTCAAGTGCTCGATTCACT
ACTAGATTTTAAACCTGAAGATTTTGGACTGCCAGCATTTTCTGACAAATGA
>g16431.t4 Gene=g16431 Length=180
MSSRYKPVTHCIFDMDGLLLDTETLYTIATQNILDKYFQNPRKIYTWDVKATLMGFQTEE
VARRIVNYYEIPITWQEYVVLAKEQIDMLMPKCEKTKGAEKLVRHLYNNNVPICLATSSS
KESYDVKTIQHKELFKLFHHIVQGSSDCEVKNGKPAPDIFLIAMKRFGDGVEAENVMLSF
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 4 | g16431.t4 | Gene3D | G3DSA:3.40.50.1000 | - | 11 | 175 | 0 |
| 5 | g16431.t4 | Gene3D | G3DSA:1.10.150.240 | Putative phosphatase; domain 2 | 22 | 93 | 0 |
| 2 | g16431.t4 | PANTHER | PTHR18901 | 2-DEOXYGLUCOSE-6-PHOSPHATE PHOSPHATASE 2 | 3 | 177 | 0 |
| 1 | g16431.t4 | Pfam | PF13419 | Haloacid dehalogenase-like hydrolase | 11 | 177 | 0 |
| 6 | g16431.t4 | SFLD | SFLDG01129 | C1.5: HAD, Beta-PGM, Phosphatase Like | 8 | 168 | 0 |
| 7 | g16431.t4 | SFLD | SFLDS00003 | Haloacid Dehalogenase | 8 | 168 | 0 |
| 3 | g16431.t4 | SUPERFAMILY | SSF56784 | HAD-like | 8 | 175 | 0 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
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.
