General information for g16431.t10
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.t10 | TSS | g16431.t10 | 9419926 | 9419926 |
| chr_4 | g16431 | g16431.t10 | isoform | g16431.t10 | 9420035 | 9421132 |
| chr_4 | g16431 | g16431.t10 | exon | g16431.t10.exon1 | 9420035 | 9420384 |
| chr_4 | g16431 | g16431.t10 | cds | g16431.t10.CDS1 | 9420252 | 9420384 |
| chr_4 | g16431 | g16431.t10 | exon | g16431.t10.exon2 | 9420437 | 9420669 |
| chr_4 | g16431 | g16431.t10 | cds | g16431.t10.CDS2 | 9420437 | 9420669 |
| chr_4 | g16431 | g16431.t10 | exon | g16431.t10.exon3 | 9420727 | 9421132 |
| chr_4 | g16431 | g16431.t10 | cds | g16431.t10.CDS3 | 9420727 | 9420909 |
| chr_4 | g16431 | g16431.t10 | TTS | g16431.t10 | 9421092 | 9421092 |
Sequences
>g16431.t10 Gene=g16431 Length=989
ATGTCTTCACGTTATAAGCCAGTGACACATTGTATTTTTGATATGGATGGATTATTATTA
GGTAAAAATTTTAAAAACATTCTCTCTCCTCTAAAAATTGAAATTTTATTTTTTCTCAGA
CACGGAAACACTTTATACAATTGCAACTCAAAACATTCTCGATAAATATTTTCAAAATCC
TAGAAAAATATATACTTGGGATGTAAAAGCAACTTTGATGGGATTTCAAACGGAAGAAGT
TGCAAGAAGAATTGTAAATTATTATGAAATTCCAATAACATGGCAAGAATATGTTGTACT
GGCTAAAGAACAAATTGACATGCTCATGCCGAAATGTGAAAAGACCAAAGGTGCTGAAAA
ATTAGTACGGCATCTTTACAACAACAATGTGCCGATTTGCCTTGCAACAAGTAGTTCAAA
AGAAAGCTATGACGTCAAAACGATTCAGCATAAAGAATTATTTAAATTATTCCACCACAT
TGTTCAAGGCTCAAGCGATTGTGAGGTCAAGAATGGAAAACCAGCACCTGATATTTTTTT
AATTGCTATGAAAAGATTTGGTGATGGAGTTGAGGCTGAAAATTGCTTAGTTTTTGAAGA
TGCACCAAATGGTGTCAAAGCTGCATGTTCAGCTGGAATGCAAGTAGTGATGGTACCTGA
TCCAAATGTTCCTAAATTTCATTGTGAAAATGCAACTCAAGTGCTCGATTCACTACTAGA
TTTTAAACCTGAAGATTTTGGACTGCCAGCATTTTCTGACAAATGATTGATAATTTAGCT
AAGATGAGGAAGAAAATTTAGGGAATTAGCAAAAATAAAAAATCAAGATTTGGTACTTAC
ATATTGGAAAAAAATTTGTGTCCTGCCTATCTGATATTTTTATAAATAATTTCAAAATTT
TAATTAGAATTTATGAAAAAATATTGTTAAAAATTCAAATCTAAAATCCAAAATAAAAAA
AAAAAATTTTCAAAAAATTTATTTTTCAG
>g16431.t10 Gene=g16431 Length=182
MGFQTEEVARRIVNYYEIPITWQEYVVLAKEQIDMLMPKCEKTKGAEKLVRHLYNNNVPI
CLATSSSKESYDVKTIQHKELFKLFHHIVQGSSDCEVKNGKPAPDIFLIAMKRFGDGVEA
ENCLVFEDAPNGVKAACSAGMQVVMVPDPNVPKFHCENATQVLDSLLDFKPEDFGLPAFS
DK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g16431.t10 | Gene3D | G3DSA:1.10.150.240 | Putative phosphatase; domain 2 | 1 | 40 | 0 |
| 4 | g16431.t10 | Gene3D | G3DSA:3.40.50.1000 | - | 41 | 166 | 0 |
| 2 | g16431.t10 | PANTHER | PTHR18901 | 2-DEOXYGLUCOSE-6-PHOSPHATE PHOSPHATASE 2 | 1 | 180 | 0 |
| 1 | g16431.t10 | Pfam | PF13419 | Haloacid dehalogenase-like hydrolase | 1 | 146 | 0 |
| 3 | g16431.t10 | SUPERFAMILY | SSF56784 | HAD-like | 2 | 169 | 0 |
| 6 | g16431.t10 | TIGRFAM | TIGR01509 | HAD-SF-IA-v3: HAD hydrolase, family IA, variant 3 | 94 | 146 | 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 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.
