Gene loci information

Transcript annotation

  • This transcript has been annotated as Serine/threonine-protein phosphatase 4 catalytic subunit.

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_3 g3200 g3200.t4 TSS g3200.t4 23619663 23619663
chr_3 g3200 g3200.t4 isoform g3200.t4 23619911 23621663
chr_3 g3200 g3200.t4 exon g3200.t4.exon1 23619911 23620049
chr_3 g3200 g3200.t4 cds g3200.t4.CDS1 23620032 23620049
chr_3 g3200 g3200.t4 exon g3200.t4.exon2 23620249 23620338
chr_3 g3200 g3200.t4 cds g3200.t4.CDS2 23620249 23620338
chr_3 g3200 g3200.t4 exon g3200.t4.exon3 23620401 23620463
chr_3 g3200 g3200.t4 cds g3200.t4.CDS3 23620401 23620463
chr_3 g3200 g3200.t4 exon g3200.t4.exon4 23620525 23621663
chr_3 g3200 g3200.t4 cds g3200.t4.CDS4 23620525 23621145
chr_3 g3200 g3200.t4 TTS g3200.t4 23621665 23621665

Sequences

>g3200.t4 Gene=g3200 Length=1431
ATGAGTGACTACAGTGATCTTGATCGTCAAATTGAGCAGCTTAAGCGATGTGAAATCATA
AAAGAGAACGAAGTAAAGGCCTTGTGTGCGAAAGCTCGAGAAATTTTGGTTGAAGAAGGA
AATGTGCAGCGAGTCGATAGTCTCTGGTGACGTTCACGGTCAATTTTATGATCTCAAAGA
ATTATTTAAAGTTGGTGGAGATGTTCCTGAAACAAATTACTTATTCATGGGAGACTTTGT
CGACAGAGGATATTATTCAGTTGAAACATTCTTACTTCTTTTGGCATTAAAGGTTCGATA
TCCAGATCGTATAACGTTAATTCGTGGCAATCACGAGTCACGTCAAATTACTCAAGTTTA
TGGTTTCTATGACGAATGTCTTCGAAAATATGGCTCAATTACAGTTTGGCGCTATTGTAC
AGAAGTCTTTGACTATCTTAGTCTTTCGGCTATCATCGATGGCAAAATTTTCTGTGTACA
TGGCGGTTTGAGTCCTTCAATTCAGTATTTAGATCAAATTCGATCGATTGATAGAAAACA
GGAAGTTCCACATGACGGCCCTATGTGTGATTTATTATGGAGTGATCCAGAAGATACACA
TGGTTGGGGTGTTTCACCTCGCGGCGCTGGATATTTATTTGGTTCTGATGTAGTCGCACA
ATTTAATGCGGCAAACGATATTGAGATGATTTGTCGAGCACATCAACTTGTAATGGAAGG
TTACAAATGGCATTTTAATGAGACTGTCTTAACAGTGTGGTCAGCGCCTAATTATTGCTA
TCGTTGTGGAAATGTCGCTGCTATACTAGAACTGAATGAAAATCTTCAACGCGATTTTAC
TATATTTGAAGCGGCTCCACAAGAAAGTCGAGGGATTCCGTTGAAAAAACCCCAAGCTGA
CTACTTTTTATAAACAATCAACTACTCAACGTTTCGCGTATATACACAAACATATTTACA
CATACACACCACACACTTTTATGATTTACTAAAGTGACGACGAATATAAGTTCTTTTTTT
CATGTCATTATCGTCCTTTATTGTTCTCTCCCTCACTTATTTTCTGTAATTTAAATCAAT
TTATTAAATATAAAAAAATTAGATTACGTAAAACAAATTATTTAGTAATTTACAATATGT
GCGCATGAATGATGCGAAAAAAATACAAGAACATAGCCAATTGTTTATAGTGTCCCAAAT
TAAAGATATTTATCTTTGAAACAAAATTCTAGAACGAGTGTTAAAAAAAATTTTTTAGTT
TATAAGTTTTGCTTCATCAACTTAATATGTTCATCATTTTTATTATTTTAATTTCCTTTT
TCTACTATCACCATCAATGATTTATACTTAACAATATATAAATGATAACGAATATTATAA
AAGAAAAATAAAAATACGACAAGAAATAAAGTGAAAAATTTTTAGAAAAAA

>g3200.t4 Gene=g3200 Length=263
MCSESIVSGDVHGQFYDLKELFKVGGDVPETNYLFMGDFVDRGYYSVETFLLLLALKVRY
PDRITLIRGNHESRQITQVYGFYDECLRKYGSITVWRYCTEVFDYLSLSAIIDGKIFCVH
GGLSPSIQYLDQIRSIDRKQEVPHDGPMCDLLWSDPEDTHGWGVSPRGAGYLFGSDVVAQ
FNAANDIEMICRAHQLVMEGYKWHFNETVLTVWSAPNYCYRCGNVAAILELNENLQRDFT
IFEAAPQESRGIPLKKPQADYFL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
13 g3200.t4 CDD cd07415 MPP_PP2A_PP4_PP6 7 246 0.0
12 g3200.t4 Gene3D G3DSA:3.60.21.10 - 2 255 3.2E-117
2 g3200.t4 PANTHER PTHR45619 SERINE/THREONINE-PROTEIN PHOSPHATASE PP2A-RELATED 7 263 6.7E-148
3 g3200.t4 PANTHER PTHR45619:SF29 SERINE/THREONINE-PROTEIN PHOSPHATASE PP-X ISOZYME 1 7 263 6.7E-148
9 g3200.t4 PRINTS PR00114 Serine/threonine phosphatase family signature 4 31 2.2E-86
8 g3200.t4 PRINTS PR00114 Serine/threonine phosphatase family signature 33 60 2.2E-86
6 g3200.t4 PRINTS PR00114 Serine/threonine phosphatase family signature 66 90 2.2E-86
7 g3200.t4 PRINTS PR00114 Serine/threonine phosphatase family signature 101 127 2.2E-86
5 g3200.t4 PRINTS PR00114 Serine/threonine phosphatase family signature 130 157 2.2E-86
10 g3200.t4 PRINTS PR00114 Serine/threonine phosphatase family signature 186 206 2.2E-86
4 g3200.t4 PRINTS PR00114 Serine/threonine phosphatase family signature 208 224 2.2E-86
1 g3200.t4 Pfam PF00149 Calcineurin-like phosphoesterase 7 195 3.5E-38
14 g3200.t4 ProSitePatterns PS00125 Serine/threonine specific protein phosphatases signature. 67 72 -
15 g3200.t4 SMART SM00156 pp2a_7 1 246 1.2E-118
11 g3200.t4 SUPERFAMILY SSF56300 Metallo-dependent phosphatases 7 249 1.5E-107

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.

Raw TPM values