Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Low molecular weight phosphotyrosine protein phosphatase 2.

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 g1851 g1851.t3 TSS g1851.t3 13347031 13347031
chr_3 g1851 g1851.t3 isoform g1851.t3 13347087 13347848
chr_3 g1851 g1851.t3 exon g1851.t3.exon1 13347087 13347356
chr_3 g1851 g1851.t3 cds g1851.t3.CDS1 13347248 13347356
chr_3 g1851 g1851.t3 exon g1851.t3.exon2 13347413 13347610
chr_3 g1851 g1851.t3 cds g1851.t3.CDS2 13347413 13347610
chr_3 g1851 g1851.t3 exon g1851.t3.exon3 13347784 13347848
chr_3 g1851 g1851.t3 cds g1851.t3.CDS3 13347784 13347848
chr_3 g1851 g1851.t3 TTS g1851.t3 13347910 13347910

Sequences

>g1851.t3 Gene=g1851 Length=533
ATGAGTGATAAAAAGAACGTACTATTTATTTGTTTAGGCAATATATGCAGGTCGCCAATC
GCTGAAGCTGTTTTCATTGATACAGTCAAGAAGAATAATGTTGCAGATAAATTTTATATT
GATTCAGCAGCTATAGGTAAATTTCTACAAAAAATTCGTACATGCAATTTATTACTGCAT
ATTTAACAGGACCTTGGCATGTCGGAAAAAAGCCAGATCGCCGTGCACTTGAAACTATGA
AAAATCATAATTTAGAATACAATAATAAAGCACGGCAATTGAAAACTGAAGATTTTCGTA
AATTTCATTATATTTTTGGTATGGATGGTGAAAACATGGCAGATTTAGAAGACATGAAAC
CAAGCGATGGAATCGCAAAATTATTACTTCTCGGAGATTTTGACCCACAAGGTGAAAGAA
TAATTCGCGATCCTTATTATGATGGAAATTCAGCTGGATTTGAGAAAGCTTATGTACAAT
CAGTGAGATGTTGCGAAGCTTTCTTGAAGAAGTTGTTGGCTGGTGAAGTTTAA

>g1851.t3 Gene=g1851 Length=123
MQFITAYLTGPWHVGKKPDRRALETMKNHNLEYNNKARQLKTEDFRKFHYIFGMDGENMA
DLEDMKPSDGIAKLLLLGDFDPQGERIIRDPYYDGNSAGFEKAYVQSVRCCEAFLKKLLA
GEV

Protein features from InterProScan

Transcript Database ID Name Start End E.value
14 g1851.t3 CDD cd16343 LMWPTP 9 116 1.07191E-41
13 g1851.t3 Coils Coil Coil 23 43 -
12 g1851.t3 Gene3D G3DSA:3.40.50.2300 - 3 122 1.9E-30
2 g1851.t3 PANTHER PTHR11717 LOW MOLECULAR WEIGHT PROTEIN TYROSINE PHOSPHATASE 9 119 5.9E-34
3 g1851.t3 PANTHER PTHR11717:SF7 LOW MOLECULAR WEIGHT PHOSPHOTYROSINE PROTEIN PHOSPHATASE 9 119 5.9E-34
6 g1851.t3 PRINTS PR00719 LMW phosphotyrosine protein phosphatase signature 14 30 2.5E-12
8 g1851.t3 PRINTS PR00720 Mammalian LMW phosphotyrosine protein phosphatase signature 33 48 1.4E-8
4 g1851.t3 PRINTS PR00719 LMW phosphotyrosine protein phosphatase signature 47 62 2.5E-12
9 g1851.t3 PRINTS PR00720 Mammalian LMW phosphotyrosine protein phosphatase signature 50 70 1.4E-8
5 g1851.t3 PRINTS PR00719 LMW phosphotyrosine protein phosphatase signature 70 83 2.5E-12
7 g1851.t3 PRINTS PR00719 LMW phosphotyrosine protein phosphatase signature 88 103 2.5E-12
10 g1851.t3 PRINTS PR00720 Mammalian LMW phosphotyrosine protein phosphatase signature 96 117 1.4E-8
1 g1851.t3 Pfam PF01451 Low molecular weight phosphotyrosine protein phosphatase 9 115 1.7E-19
15 g1851.t3 SMART SM00226 LMWPc_2 3 117 1.3E-13
11 g1851.t3 SUPERFAMILY SSF52788 Phosphotyrosine protein phosphatases I 9 118 8.9E-25

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:0004726 non-membrane spanning protein tyrosine phosphatase activity MF
GO:0006470 protein dephosphorylation BP
GO:0003993 acid phosphatase activity MF
GO:0004725 protein tyrosine phosphatase activity MF
GO:0005737 cytoplasm CC

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