Gene loci information

Transcript annotation

  • This transcript has been annotated as Tyrosine-protein phosphatase corkscrew .

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 g4080 g4080.t6 TSS g4080.t6 30485080 30485080
chr_3 g4080 g4080.t6 isoform g4080.t6 30485305 30487933
chr_3 g4080 g4080.t6 exon g4080.t6.exon1 30485305 30485546
chr_3 g4080 g4080.t6 cds g4080.t6.CDS1 30485383 30485546
chr_3 g4080 g4080.t6 exon g4080.t6.exon2 30485612 30485700
chr_3 g4080 g4080.t6 cds g4080.t6.CDS2 30485612 30485700
chr_3 g4080 g4080.t6 exon g4080.t6.exon3 30485873 30486522
chr_3 g4080 g4080.t6 cds g4080.t6.CDS3 30485873 30486522
chr_3 g4080 g4080.t6 exon g4080.t6.exon4 30486695 30486792
chr_3 g4080 g4080.t6 cds g4080.t6.CDS4 30486695 30486712
chr_3 g4080 g4080.t6 exon g4080.t6.exon5 30486886 30487166
chr_3 g4080 g4080.t6 exon g4080.t6.exon6 30487634 30487812
chr_3 g4080 g4080.t6 exon g4080.t6.exon7 30487884 30487933
chr_3 g4080 g4080.t6 TTS g4080.t6 30488059 30488059

Sequences

>g4080.t6 Gene=g4080 Length=1589
GATAATCGATATGATGTTGGTGGTGGTGAGCAATTTTCGACTTTGAGCGAGCTTATCGAA
CACTATAAAAAGAATCCGATGGTCGAAACTTCCGGAACTGTCGTGAATCTTCGTCATCCA
TTCAATGCAACAAGAATAACAGCAGCCAGTATTGATTCCCGTGTTGAAATCCTTCAACGC
GAACATGGACCGAACTCTTGTTTTGGAAAAGGTGGTTTTTGGGAAGAATTTGAGTCATTA
CAACAACAAGAATGTCGACATTCATTTTCACGAAATGAAGGACAGCGTTTGGAAAATCGA
AGCAAAAATCGTTACAAAAACATTTTACCTTTTGATCATACGAGAGTAATTTTACGAGAT
GTTGACAACACAGTGCCCGGTGCAGAATATATAAATGCAAATTACATTCGTCCCCTCGAT
ATCGAGTCACTCGATCTAACATCGATGGCTTCATTTGAAAACTTGAGCGGATCATATGCG
ACATTAACAAATAACTCTAATGGAAAATGTGTCAATTGTCAGTTATTGAACAAAATGTGC
GTTCAATGTGCCATTGATGGAAGTTCGAGCAACAAGCACAAACGAACTGAGTCATTATCA
TCAATTCGCACCAATTTCAGCACGTTAACGAGTGCGACAACAAATGCTTCGAGAAAGGGA
GGCTGTGGTGATGAATTTATTAGCAAGACATATATTGCAACGCAAGGATGTCTACCAAAT
ACAATTGTTGATTTCTGGAACATGATTTGGCAAGAAAATACGCGTGTGATTGTCATGACA
ACAAAGGAGATTGAGCGAACGAAGAAAAAGTGCGAAAAATATTGGCCTGATAGTGGACAA
ACACAAGAGTGGGGTCATGCAAAAGTGAAATGCTTAAGTGAAACTTCTACAAATGATTAT
ACACTGCGAGAACTTTTATTTTCATGGAAAGGACAAGAAGGACGAAAAGTTTATCATTAT
CATTATTTTTTGTGGCCTGATTATGTTTCCTTTAGGTGACTGATTCCGGAAGTGTTCTCA
ACTTCCTGCAAGATGTTAATGTACGGCAAGAACAATTAATGAGTGATGGCGTTAATCCTG
GTCCAATTTGTGTGCATTGCTCAGCTGGAATTGGACGTACAGGCACATTTATTGTGATAG
ACATGATTCTTGACCAAATCGATCGTGAGGGACTCGATTGTGAAATAGATATTCATCGTA
CGATCTTGATGGTTCGTTCTCAACGTTCTGGAATGGTACAGACTGAAGCTCAATACAAGT
TTGTGTATTATGCGGTGCAACATTACATTCAAACAAAACTTCAGAGAAAGCGTGCTGAAC
AACAGTCATTACAACACGGGCGAGAATATACGAATATAAAGTATGATGATGTGCGTAGTC
CGCTGCCTCAATCGATTAGCCAAATGAGTTTGTACAATAACAACAACAACACGAGTAGCA
ACAACTCATATCAGCAGTCCTCGGGTATTATTGAACCATTGCCATTTCATCATCGTCAAG
TTCCCGTTCCGCCATCATTTTCTGATTTTAGTTCGTCTGCTTATGAAAATTTGGATTCAA
TACCATCAAGACCGCCAAGAAAATCTTGA

>g4080.t6 Gene=g4080 Length=306
MVETSGTVVNLRHPFNATRITAASIDSRVEILQREHGPNSCFGKGGFWEEFESLQQQECR
HSFSRNEGQRLENRSKNRYKNILPFDHTRVILRDVDNTVPGAEYINANYIRPLDIESLDL
TSMASFENLSGSYATLTNNSNGKCVNCQLLNKMCVQCAIDGSSSNKHKRTESLSSIRTNF
STLTSATTNASRKGGCGDEFISKTYIATQGCLPNTIVDFWNMIWQENTRVIVMTTKEIER
TKKKCEKYWPDSGQTQEWGHAKVKCLSETSTNDYTLRELLFSWKGQEGRKVYHYHYFLWP
DYVSFR

Protein features from InterProScan

Transcript Database ID Name Start End E.value
2 g4080.t6 PANTHER PTHR46257:SF3 TYROSINE-PROTEIN PHOSPHATASE CORKSCREW 1 302 0.000
3 g4080.t6 PANTHER PTHR46257 TYROSINE-PROTEIN PHOSPHATASE CORKSCREW 1 302 0.000
6 g4080.t6 PRINTS PR00700 Protein tyrosine phosphatase signature 103 110 0.000
5 g4080.t6 PRINTS PR00700 Protein tyrosine phosphatase signature 205 225 0.000
4 g4080.t6 PRINTS PR00700 Protein tyrosine phosphatase signature 289 306 0.000
1 g4080.t6 Pfam PF00102 Protein-tyrosine phosphatase 73 301 0.000
9 g4080.t6 ProSiteProfiles PS50055 PTP type protein phosphatase family profile. 47 306 29.978
8 g4080.t6 SMART SM00194 PTPc_3 46 304 0.000
7 g4080.t6 SUPERFAMILY SSF52799 (Phosphotyrosine protein) phosphatases II 44 302 0.000

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

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