Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative 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.t7 TSS g4080.t7 30485080 30485080
chr_3 g4080 g4080.t7 isoform g4080.t7 30485883 30487933
chr_3 g4080 g4080.t7 exon g4080.t7.exon1 30485883 30486522
chr_3 g4080 g4080.t7 cds g4080.t7.CDS1 30485986 30486522
chr_3 g4080 g4080.t7 exon g4080.t7.exon2 30486702 30486792
chr_3 g4080 g4080.t7 cds g4080.t7.CDS2 30486702 30486716
chr_3 g4080 g4080.t7 exon g4080.t7.exon3 30486886 30487166
chr_3 g4080 g4080.t7 exon g4080.t7.exon4 30487634 30487812
chr_3 g4080 g4080.t7 exon g4080.t7.exon5 30487884 30487933
chr_3 g4080 g4080.t7 TTS g4080.t7 30488059 30488059

Sequences

>g4080.t7 Gene=g4080 Length=1241
GAGAGTAATTTTACGAGATGTTGACAACACAGTGCCCGGTGCAGAATATATAAATGCAAA
TTACATTCGTCCCCTCGATATCGAGTCACTCGATCTAACATCGATGGCTTCATTTGAAAA
CTTGAGCGGATCATATGCGACATTAACAAATAACTCTAATGGAAAATGTGTCAATTGTCA
GTTATTGAACAAAATGTGCGTTCAATGTGCCATTGATGGAAGTTCGAGCAACAAGCACAA
ACGAACTGAGTCATTATCATCAATTCGCACCAATTTCAGCACGTTAACGAGTGCGACAAC
AAATGCTTCGAGAAAGGGAGGCTGTGGTGATGAATTTATTAGCAAGACATATATTGCAAC
GCAAGGATGTCTACCAAATACAATTGTTGATTTCTGGAACATGATTTGGCAAGAAAATAC
GCGTGTGATTGTCATGACAACAAAGGAGATTGAGCGAACGAAGAAAAAGTGCGAAAAATA
TTGGCCTGATAGTGGACAAACACAAGAGTGGGGTCATGCAAAAGTGAAATGCTTAAGTGA
AACTTCTACAAATGATTATACACTGCGAGAACTTTTATTTTCATGGAAAGGACAAGAAGG
ACGAAAAGTTTATCATTATCATTATTTTTTGTGGCCTGATCCTTTAGGTGACTGATTCCG
GAAGTGTTCTCAACTTCCTGCAAGATGTTAATGTACGGCAAGAACAATTAATGAGTGATG
GCGTTAATCCTGGTCCAATTTGTGTGCATTGCTCAGCTGGAATTGGACGTACAGGCACAT
TTATTGTGATAGACATGATTCTTGACCAAATCGATCGTGAGGGACTCGATTGTGAAATAG
ATATTCATCGTACGATCTTGATGGTTCGTTCTCAACGTTCTGGAATGGTACAGACTGAAG
CTCAATACAAGTTTGTGTATTATGCGGTGCAACATTACATTCAAACAAAACTTCAGAGAA
AGCGTGCTGAACAACAGTCATTACAACACGGGCGAGAATATACGAATATAAAGTATGATG
ATGTGCGTAGTCCGCTGCCTCAATCGATTAGCCAAATGAGTTTGTACAATAACAACAACA
ACACGAGTAGCAACAACTCATATCAGCAGTCCTCGGGTATTATTGAACCATTGCCATTTC
ATCATCGTCAAGTTCCCGTTCCGCCATCATTTTCTGATTTTAGTTCGTCTGCTTATGAAA
ATTTGGATTCAATACCATCAAGACCGCCAAGAAAATCTTGA

>g4080.t7 Gene=g4080 Length=183
MASFENLSGSYATLTNNSNGKCVNCQLLNKMCVQCAIDGSSSNKHKRTESLSSIRTNFST
LTSATTNASRKGGCGDEFISKTYIATQGCLPNTIVDFWNMIWQENTRVIVMTTKEIERTK
KKCEKYWPDSGQTQEWGHAKVKCLSETSTNDYTLRELLFSWKGQEGRKVYHYHYFLWPDP
LGD

Protein features from InterProScan

Transcript Database ID Name Start End E.value
8 g4080.t7 Gene3D G3DSA:3.90.190.10 Protein tyrosine phosphatase superfamily 21 181 0.0000000
2 g4080.t7 PANTHER PTHR46257:SF3 TYROSINE-PROTEIN PHOSPHATASE CORKSCREW 72 179 0.0000000
3 g4080.t7 PANTHER PTHR46257 TYROSINE-PROTEIN PHOSPHATASE CORKSCREW 72 179 0.0000000
4 g4080.t7 PRINTS PR00700 Protein tyrosine phosphatase signature 83 103 0.0000000
5 g4080.t7 PRINTS PR00700 Protein tyrosine phosphatase signature 167 183 0.0000000
1 g4080.t7 Pfam PF00102 Protein-tyrosine phosphatase 80 179 0.0000000
9 g4080.t7 ProSiteProfiles PS50055 PTP type protein phosphatase family profile. 43 183 22.9130000
7 g4080.t7 SMART SM00194 PTPc_3 3 183 0.0000016
6 g4080.t7 SUPERFAMILY SSF52799 (Phosphotyrosine protein) phosphatases II 76 179 0.0000000

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