Gene loci information

Transcript annotation

  • This transcript has been annotated as Probable pseudouridine-5’-phosphatase.

Parent gene

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.t11 TSS g16431.t11 9419926 9419926
chr_4 g16431 g16431.t11 isoform g16431.t11 9420035 9423670
chr_4 g16431 g16431.t11 exon g16431.t11.exon1 9420035 9420095
chr_4 g16431 g16431.t11 cds g16431.t11.CDS1 9420035 9420095
chr_4 g16431 g16431.t11 exon g16431.t11.exon2 9420154 9420384
chr_4 g16431 g16431.t11 cds g16431.t11.CDS2 9420154 9420384
chr_4 g16431 g16431.t11 exon g16431.t11.exon3 9420437 9420673
chr_4 g16431 g16431.t11 cds g16431.t11.CDS3 9420437 9420673
chr_4 g16431 g16431.t11 exon g16431.t11.exon4 9420734 9421132
chr_4 g16431 g16431.t11 cds g16431.t11.CDS4 9420734 9420909
chr_4 g16431 g16431.t11 exon g16431.t11.exon5 9423621 9423670
chr_4 g16431 g16431.t11 TTS g16431.t11 NA NA

Sequences

>g16431.t11 Gene=g16431 Length=978
ATGTCTTCACGTTATAAGCCAGTGACACATTGTATTTTTGATATGGATGGATTATTATTA
GACACGGAAACACTTTATACAATTGCAACTCAAAACATTCTCGATAAATATTTTCAAAAT
CCTAGAAAAATATATACTTGGGATGTAAAAGCAACTTTGATGGGATTTCAAACGGAAGAA
GTTGCAAGAAGAATTGTAAATTATTATGAAATTCCAATAACATGGCAAGAATATGTTGTA
CTGGCTAAAGAACAAATTGACATGCTCATGCCGAAATGTGAAAAGACCAAAGGTGCTGAA
AAATTAGTACGGCATCTTTACAACAACAATGTGCCGATTTGCCTTGCAACAAGTAGTTCA
AAAGAAAGCTATGACGTCAAAACGATTCAGCATAAAGAATTATTTAAATTATTCCACCAC
ATTGTTCAAGGCTCAAGCGATTGTGAGGTCAAGAATGGAAAACCAGCACCTGATATTTTT
TTAATTGCTATGAAAAGATTTGGTGATGGAGTTGAGGCTGAAAATGTTATTTTTGAAGAT
GCACCAAATGGTGTCAAAGCTGCATGTTCAGCTGGAATGCAAGTAGTGATGGTACCTGAT
CCAAATGTTCCTAAATTTCATTGTGAAAATGCAACTCAAGTGCTCGATTCACTACTAGAT
TTTAAACCTGAAGATTTTGGACTGCCAGCATTTTCTGACAAATGATTGATAATTTAGCTA
AGATGAGGAAGAAAATTTAGGGAATTAGCAAAAATAAAAAATCAAGATTTGGTACTTACA
TATTGGAAAAAAATTTGTGTCCTGCCTATCTGATATTTTTATAAATAATTTCAAAATTTT
AATTAGAATTTATGAAAAAATATTGTTAAAAATTCAAATCTAAAATCCAAAATAAAAAAA
AAAAATTTTCAAAAAATTTATTTTTCAGAAATCAAAAATTAACAAAAACTAAAAGAAATT
TTTGAAAATTTTCTCACC

>g16431.t11 Gene=g16431 Length=234
MSSRYKPVTHCIFDMDGLLLDTETLYTIATQNILDKYFQNPRKIYTWDVKATLMGFQTEE
VARRIVNYYEIPITWQEYVVLAKEQIDMLMPKCEKTKGAEKLVRHLYNNNVPICLATSSS
KESYDVKTIQHKELFKLFHHIVQGSSDCEVKNGKPAPDIFLIAMKRFGDGVEAENVIFED
APNGVKAACSAGMQVVMVPDPNVPKFHCENATQVLDSLLDFKPEDFGLPAFSDK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
4 g16431.t11 Gene3D G3DSA:3.40.50.1000 - 11 218 0
5 g16431.t11 Gene3D G3DSA:1.10.150.240 Putative phosphatase; domain 2 22 93 0
2 g16431.t11 PANTHER PTHR18901 2-DEOXYGLUCOSE-6-PHOSPHATE PHOSPHATASE 2 3 232 0
1 g16431.t11 Pfam PF13419 Haloacid dehalogenase-like hydrolase 11 198 0
7 g16431.t11 SFLD SFLDG01129 C1.5: HAD, Beta-PGM, Phosphatase Like 8 220 0
8 g16431.t11 SFLD SFLDS00003 Haloacid Dehalogenase 8 220 0
3 g16431.t11 SUPERFAMILY SSF56784 HAD-like 8 221 0
6 g16431.t11 TIGRFAM TIGR01509 HAD-SF-IA-v3: HAD hydrolase, family IA, variant 3 147 198 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

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.

Raw TPM values