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.t7 TSS g16431.t7 9419926 9419926
chr_4 g16431 g16431.t7 isoform g16431.t7 9420035 9420909
chr_4 g16431 g16431.t7 exon g16431.t7.exon1 9420035 9420384
chr_4 g16431 g16431.t7 cds g16431.t7.CDS1 9420252 9420384
chr_4 g16431 g16431.t7 exon g16431.t7.exon2 9420437 9420673
chr_4 g16431 g16431.t7 cds g16431.t7.CDS2 9420437 9420673
chr_4 g16431 g16431.t7 exon g16431.t7.exon3 9420734 9420909
chr_4 g16431 g16431.t7 cds g16431.t7.CDS3 9420734 9420909
chr_4 g16431 g16431.t7 TTS g16431.t7 9421092 9421092

Sequences

>g16431.t7 Gene=g16431 Length=763
ATGTCTTCACGTTATAAGCCAGTGACACATTGTATTTTTGATATGGATGGATTATTATTA
GGTAAAAATTTTAAAAACATTCTCTCTCCTCTAAAAATTGAAATTTTATTTTTTCTCAGA
CACGGAAACACTTTATACAATTGCAACTCAAAACATTCTCGATAAATATTTTCAAAATCC
TAGAAAAATATATACTTGGGATGTAAAAGCAACTTTGATGGGATTTCAAACGGAAGAAGT
TGCAAGAAGAATTGTAAATTATTATGAAATTCCAATAACATGGCAAGAATATGTTGTACT
GGCTAAAGAACAAATTGACATGCTCATGCCGAAATGTGAAAAGACCAAAGGTGCTGAAAA
ATTAGTACGGCATCTTTACAACAACAATGTGCCGATTTGCCTTGCAACAAGTAGTTCAAA
AGAAAGCTATGACGTCAAAACGATTCAGCATAAAGAATTATTTAAATTATTCCACCACAT
TGTTCAAGGCTCAAGCGATTGTGAGGTCAAGAATGGAAAACCAGCACCTGATATTTTTTT
AATTGCTATGAAAAGATTTGGTGATGGAGTTGAGGCTGAAAATGTTATTTTTGAAGATGC
ACCAAATGGTGTCAAAGCTGCATGTTCAGCTGGAATGCAAGTAGTGATGGTACCTGATCC
AAATGTTCCTAAATTTCATTGTGAAAATGCAACTCAAGTGCTCGATTCACTACTAGATTT
TAAACCTGAAGATTTTGGACTGCCAGCATTTTCTGACAAATGA

>g16431.t7 Gene=g16431 Length=181
MGFQTEEVARRIVNYYEIPITWQEYVVLAKEQIDMLMPKCEKTKGAEKLVRHLYNNNVPI
CLATSSSKESYDVKTIQHKELFKLFHHIVQGSSDCEVKNGKPAPDIFLIAMKRFGDGVEA
ENVIFEDAPNGVKAACSAGMQVVMVPDPNVPKFHCENATQVLDSLLDFKPEDFGLPAFSD
K

Protein features from InterProScan

Transcript Database ID Name Start End E.value
5 g16431.t7 Gene3D G3DSA:1.10.150.240 Putative phosphatase; domain 2 1 40 0
4 g16431.t7 Gene3D G3DSA:3.40.50.1000 - 41 165 0
2 g16431.t7 PANTHER PTHR18901 2-DEOXYGLUCOSE-6-PHOSPHATE PHOSPHATASE 2 1 179 0
1 g16431.t7 Pfam PF13419 Haloacid dehalogenase-like hydrolase 1 145 0
3 g16431.t7 SUPERFAMILY SSF56784 HAD-like 2 168 0
6 g16431.t7 TIGRFAM TIGR01509 HAD-SF-IA-v3: HAD hydrolase, family IA, variant 3 94 145 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. There were no conditions that were differentially expressed