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.t3 TSS g16431.t3 9419926 9419926
chr_4 g16431 g16431.t3 isoform g16431.t3 9420035 9420909
chr_4 g16431 g16431.t3 exon g16431.t3.exon1 9420035 9420095
chr_4 g16431 g16431.t3 cds g16431.t3.CDS1 9420035 9420095
chr_4 g16431 g16431.t3 exon g16431.t3.exon2 9420154 9420344
chr_4 g16431 g16431.t3 cds g16431.t3.CDS2 9420154 9420344
chr_4 g16431 g16431.t3 exon g16431.t3.exon3 9420487 9420673
chr_4 g16431 g16431.t3 cds g16431.t3.CDS3 9420487 9420673
chr_4 g16431 g16431.t3 exon g16431.t3.exon4 9420734 9420909
chr_4 g16431 g16431.t3 cds g16431.t3.CDS4 9420734 9420909
chr_4 g16431 g16431.t3 TTS g16431.t3 9421092 9421092

Sequences

>g16431.t3 Gene=g16431 Length=615
ATGTCTTCACGTTATAAGCCAGTGACACATTGTATTTTTGATATGGATGGATTATTATTA
GACACGGAAACACTTTATACAATTGCAACTCAAAACATTCTCGATAAATATTTTCAAAAT
CCTAGAAAAATATATACTTGGGATGTAAAAGCAACTTTGATGGGATTTCAAACGGAAGAA
GTTGCAAGAAGAATTGTAAATTATTATGAAATTCCAATAACATGGCAAGAATATGTTGTA
CTGGCTAAAGAACTTGCAACAAGTAGTTCAAAAGAAAGCTATGACGTCAAAACGATTCAG
CATAAAGAATTATTTAAATTATTCCACCACATTGTTCAAGGCTCAAGCGATTGTGAGGTC
AAGAATGGAAAACCAGCACCTGATATTTTTTTAATTGCTATGAAAAGATTTGGTGATGGA
GTTGAGGCTGAAAATGTTATTTTTGAAGATGCACCAAATGGTGTCAAAGCTGCATGTTCA
GCTGGAATGCAAGTAGTGATGGTACCTGATCCAAATGTTCCTAAATTTCATTGTGAAAAT
GCAACTCAAGTGCTCGATTCACTACTAGATTTTAAACCTGAAGATTTTGGACTGCCAGCA
TTTTCTGACAAATGA

>g16431.t3 Gene=g16431 Length=204
MSSRYKPVTHCIFDMDGLLLDTETLYTIATQNILDKYFQNPRKIYTWDVKATLMGFQTEE
VARRIVNYYEIPITWQEYVVLAKELATSSSKESYDVKTIQHKELFKLFHHIVQGSSDCEV
KNGKPAPDIFLIAMKRFGDGVEAENVIFEDAPNGVKAACSAGMQVVMVPDPNVPKFHCEN
ATQVLDSLLDFKPEDFGLPAFSDK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
7 g16431.t3 Gene3D G3DSA:1.10.150.240 Putative phosphatase; domain 2 22 86 0.0e+00
6 g16431.t3 Gene3D G3DSA:3.40.50.1000 - 87 197 0.0e+00
3 g16431.t3 PANTHER PTHR18901 2-DEOXYGLUCOSE-6-PHOSPHATE PHOSPHATASE 2 3 82 0.0e+00
4 g16431.t3 PANTHER PTHR18901 2-DEOXYGLUCOSE-6-PHOSPHATE PHOSPHATASE 2 85 202 0.0e+00
1 g16431.t3 Pfam PF13419 Haloacid dehalogenase-like hydrolase 11 78 1.4e-05
2 g16431.t3 Pfam PF13419 Haloacid dehalogenase-like hydrolase 87 168 1.0e-07
9 g16431.t3 SFLD SFLDG01129 C1.5: HAD, Beta-PGM, Phosphatase Like 8 190 0.0e+00
10 g16431.t3 SFLD SFLDS00003 Haloacid Dehalogenase 8 190 0.0e+00
5 g16431.t3 SUPERFAMILY SSF56784 HAD-like 8 191 0.0e+00
8 g16431.t3 TIGRFAM TIGR01509 HAD-SF-IA-v3: HAD hydrolase, family IA, variant 3 10 168 0.0e+00

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