Gene loci information

Transcript annotation

  • This transcript has been annotated as Serine/threonine-protein phosphatase alpha-1 isoform.

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_2 g8875 g8875.t4 isoform g8875.t4 33614312 33615366
chr_2 g8875 g8875.t4 exon g8875.t4.exon1 33614312 33614865
chr_2 g8875 g8875.t4 TTS g8875.t4 33614620 33614620
chr_2 g8875 g8875.t4 cds g8875.t4.CDS1 33614735 33614865
chr_2 g8875 g8875.t4 exon g8875.t4.exon2 33615003 33615150
chr_2 g8875 g8875.t4 cds g8875.t4.CDS2 33615003 33615150
chr_2 g8875 g8875.t4 exon g8875.t4.exon3 33615223 33615366
chr_2 g8875 g8875.t4 cds g8875.t4.CDS3 33615223 33615366
chr_2 g8875 g8875.t4 TSS g8875.t4 NA NA

Sequences

>g8875.t4 Gene=g8875 Length=846
ATGGAACAAATCAGAAGAATTATGCGCCCAACTGACGTTCCTGATCAGGGTCTATTGTGC
GATCTCCTTTGGTCAGATCCTGACAAAGACACAATGGGTTGGGGTGAGAATGATCGTGGA
GTTAGTTTTACATTTGGAGCAGAGATTGTTGCAAAATTCCTGGCAAAACACGATTTTGAT
CTAATTTGTCGTGCTCATCAAGTAGTAGAAGATGGTTATGAATTCTTTGCAAAACGACAA
CTTGTAACGCTGTTTTCGGCACCAAATTATTGTGGAGAATTTGATAACGCTGATGACACG
CTAATGTGCTCGTTCCAGATCTTAAAACCAGCCGATAAACGTAAATTTCAATATAGTAAT
CTATCGGGCGGTCGCCCTGTTACTCCACCTCGAGCCGCTAATAATAAGAATAAGAAGAAA
TAAGCAAATGATGGTGACAATATTTGAGCTTTTTATTATAAAATGCTCAATATTACACAC
CATCATTTTGCATACTATATTTTAATAAATATTAAAATAATTAAAATCATGAATACAAAC
AAAAAAAAAATATTAAATTTACATGTCTCTACGACACAACCACCACAAAAAATGTCAAAT
ATAAAACAACAAGGAGCGCACGAAAGAGAATGAACGTGACTAGGATATAATAGTTGTAGA
GTTATTCTTTTAAATGAAAGATTGAATGGTAAAACATGAGAAGCGAGAGTTGTTAGGCAA
TTAATTGATAAACGAAAATTAAAACGAAATGTGGGATAATTATGTGCATGTTGTGTCCAT
AGAACAATGACAACATCTTAAATTTAATACAAAAAAATTATTAAATAAAACAAGTATGAA
TAATAA

>g8875.t4 Gene=g8875 Length=140
MEQIRRIMRPTDVPDQGLLCDLLWSDPDKDTMGWGENDRGVSFTFGAEIVAKFLAKHDFD
LICRAHQVVEDGYEFFAKRQLVTLFSAPNYCGEFDNADDTLMCSFQILKPADKRKFQYSN
LSGGRPVTPPRAANNKNKKK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
10 g8875.t4 Gene3D G3DSA:3.60.21.10 - 1 120 6.4E-45
9 g8875.t4 MobiDBLite mobidb-lite consensus disorder prediction 119 140 -
2 g8875.t4 PANTHER PTHR11668:SF456 SERINE/THREONINE-PROTEIN PHOSPHATASE 1 134 2.3E-73
3 g8875.t4 PANTHER PTHR11668 SERINE/THREONINE PROTEIN PHOSPHATASE 1 134 2.3E-73
6 g8875.t4 PRINTS PR00114 Serine/threonine phosphatase family signature 1 28 2.4E-32
5 g8875.t4 PRINTS PR00114 Serine/threonine phosphatase family signature 58 78 2.4E-32
4 g8875.t4 PRINTS PR00114 Serine/threonine phosphatase family signature 80 96 2.4E-32
1 g8875.t4 Pfam PF00149 Calcineurin-like phosphoesterase 2 68 2.8E-6
8 g8875.t4 SMART SM00156 pp2a_7 1 112 1.2E-7
7 g8875.t4 SUPERFAMILY SSF56300 Metallo-dependent phosphatases 2 115 7.97E-37

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