Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Low molecular weight phosphotyrosine protein phosphatase 1.

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.t2 TSS g1851.t2 13347031 13347031
chr_3 g1851 g1851.t2 isoform g1851.t2 13347087 13347848
chr_3 g1851 g1851.t2 exon g1851.t2.exon1 13347087 13347222
chr_3 g1851 g1851.t2 cds g1851.t2.CDS1 13347087 13347222
chr_3 g1851 g1851.t2 exon g1851.t2.exon2 13347276 13347356
chr_3 g1851 g1851.t2 cds g1851.t2.CDS2 13347276 13347356
chr_3 g1851 g1851.t2 exon g1851.t2.exon3 13347413 13347848
chr_3 g1851 g1851.t2 cds g1851.t2.CDS3 13347413 13347693
chr_3 g1851 g1851.t2 TTS g1851.t2 13347910 13347910

Sequences

>g1851.t2 Gene=g1851 Length=653
ATGAGTGATAAAAAGAACGTACTATTTATTTGTTTAGGCAATATATGCAGGTCGCCAATC
GCTGAAGCTGTTTTCATTGATACAGTCAAGAAGAATAATGTTGCAGATAAATTTTATATT
GATTCAGCAGCTATAGGACCTTGGCATGTCGGAAAAAAGCCAGATCGCCGTGCACTTGAA
ACTATGAAAAATCATAATTTAGAATACAATAATAAAGCACGGCAATTGAAAACTGAAGAT
TTTCGTAAATTTCATTATATTTTTGGTATGGATGGTGAAAACATGGCAGATTTAGAAGAC
ATGAAACCAAGCGATGGAATCGCAAAATTATTACTTCTCGGAGATTTTGACCCACAAGGT
GAAAGAATAATTCGCGATCCTTATTATGATGGAAATTCAGCTGGATTTGAGAAAGGTAAT
TTTTCAGAATTGTTAAGTCCTTTAAACTTCAATGTTTCAAGTGCACAATATTCAATGTTT
TATGTGTTTGAATGTTGAGCACTTAATGTTTAAGTTTTTGATGTTTAGCAAACACTTAAT
GCATAAAATGAAGCACTATTCTAATAAACATTAAAATAATATTTTTAGCTTATGTACAAT
CAGTGAGATGTTGCGAAGCTTTCTTGAAGAAGTTGTTGGCTGGTGAAGTTTAA

>g1851.t2 Gene=g1851 Length=165
MSDKKNVLFICLGNICRSPIAEAVFIDTVKKNNVADKFYIDSAAIGPWHVGKKPDRRALE
TMKNHNLEYNNKARQLKTEDFRKFHYIFGMDGENMADLEDMKPSDGIAKLLLLGDFDPQG
ERIIRDPYYDGNSAGFEKGNFSELLSPLNFNVSSAQYSMFYVFEC

Protein features from InterProScan

Transcript Database ID Name Start End E.value
17 g1851.t2 CDD cd16343 LMWPTP 5 138 6.01713E-62
11 g1851.t2 Coils Coil Coil 59 79 -
10 g1851.t2 Gene3D G3DSA:3.40.50.2300 - 1 145 6.0E-48
2 g1851.t2 PANTHER PTHR11717 LOW MOLECULAR WEIGHT PROTEIN TYROSINE PHOSPHATASE 3 138 4.6E-50
3 g1851.t2 PANTHER PTHR11717:SF7 LOW MOLECULAR WEIGHT PHOSPHOTYROSINE PROTEIN PHOSPHATASE 3 138 4.6E-50
8 g1851.t2 PRINTS PR00719 LMW phosphotyrosine protein phosphatase signature 7 24 1.4E-23
7 g1851.t2 PRINTS PR00719 LMW phosphotyrosine protein phosphatase signature 50 66 1.4E-23
5 g1851.t2 PRINTS PR00719 LMW phosphotyrosine protein phosphatase signature 83 98 1.4E-23
4 g1851.t2 PRINTS PR00719 LMW phosphotyrosine protein phosphatase signature 106 119 1.4E-23
6 g1851.t2 PRINTS PR00719 LMW phosphotyrosine protein phosphatase signature 124 139 1.4E-23
1 g1851.t2 Pfam PF01451 Low molecular weight phosphotyrosine protein phosphatase 7 137 1.5E-35
13 g1851.t2 Phobius SIGNAL_PEPTIDE Signal peptide region 1 23 -
14 g1851.t2 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 6 -
15 g1851.t2 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 7 15 -
16 g1851.t2 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 16 23 -
12 g1851.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 24 165 -
18 g1851.t2 SMART SM00226 LMWPc_2 5 148 1.1E-42
9 g1851.t2 SUPERFAMILY SSF52788 Phosphotyrosine protein phosphatases I 2 137 3.01E-41

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:0006470 protein dephosphorylation BP
GO:0004725 protein tyrosine phosphatase activity MF

KEGG

Orthology

Pathway

  • This transcript belongs to the following pathways

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