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.t9 isoform g4080.t9 30486192 30487933
chr_3 g4080 g4080.t9 exon g4080.t9.exon1 30486192 30486522
chr_3 g4080 g4080.t9 exon g4080.t9.exon2 30486695 30486792
chr_3 g4080 g4080.t9 cds g4080.t9.CDS1 30486772 30486792
chr_3 g4080 g4080.t9 exon g4080.t9.exon3 30486886 30487166
chr_3 g4080 g4080.t9 cds g4080.t9.CDS2 30486886 30487166
chr_3 g4080 g4080.t9 exon g4080.t9.exon4 30487634 30487933
chr_3 g4080 g4080.t9 cds g4080.t9.CDS3 30487634 30487856
chr_3 g4080 g4080.t9 TTS g4080.t9 30488059 30488059
chr_3 g4080 g4080.t9 TSS g4080.t9 NA NA

Sequences

>g4080.t9 Gene=g4080 Length=1010
GAGAAAGGGAGGCTGTGGTGATGAATTTATTAGCAAGACATATATTGCAACGCAAGGATG
TCTACCAAATACAATTGTTGATTTCTGGAACATGATTTGGCAAGAAAATACGCGTGTGAT
TGTCATGACAACAAAGGAGATTGAGCGAACGAAGAAAAAGTGCGAAAAATATTGGCCTGA
TAGTGGACAAACACAAGAGTGGGGTCATGCAAAAGTGAAATGCTTAAGTGAAACTTCTAC
AAATGATTATACACTGCGAGAACTTTTATTTTCATGGAAAGGACAAGAAGGACGAAAAGT
TTATCATTATCATTATTTTTTGTGGCCTGATTATGTTTCCTTTAGGTGACTGATTCCGGA
AGTGTTCTCAACTTCCTGCAAGATGTTAATGTACGGCAAGAACAATTAATGAGTGATGGC
GTTAATCCTGGTCCAATTTGTGTGCATTGCTCAGCTGGAATTGGACGTACAGGCACATTT
ATTGTGATAGACATGATTCTTGACCAAATCGATCGTGAGGGACTCGATTGTGAAATAGAT
ATTCATCGTACGATCTTGATGGTTCGTTCTCAACGTTCTGGAATGGTACAGACTGAAGCT
CAATACAAGTTTGTGTATTATGCGGTGCAACATTACATTCAAACAAAACTTCAGAGAAAG
CGTGCTGAACAACAGTCATTACAACACGGGCGAGAATATACGAATATAAAGTATGATGAT
GTGCGTAGTCCGCTGCCTCAATCGATTAGCCAAATGAGTTTGTACAATAACAACAACAAC
ACGAGTAGCAACAACTCATATCAGCAGTCCTCGGGTATTATTGAACCATTGCCATTTCAT
CATCGTCAAGTTCCCGTTCCGCCATCATTTTCTGATTTTAGTTCGTCTGGTGAGTTTTTT
TTATCATTTATTATGCAATTATTTAATTTCTAAACTTGAAAAAAATCTTCCATCGTTTAG
CTTATGAAAATTTGGATTCAATACCATCAAGACCGCCAAGAAAATCTTGA

>g4080.t9 Gene=g4080 Length=174
MSDGVNPGPICVHCSAGIGRTGTFIVIDMILDQIDREGLDCEIDIHRTILMVRSQRSGMV
QTEAQYKFVYYAVQHYIQTKLQRKRAEQQSLQHGREYTNIKYDDVRSPLPQSISQMSLYN
NNNNTSSNNSYQQSSGIIEPLPFHHRQVPVPPSFSDFSSSGEFFLSFIMQLFNF

Protein features from InterProScan

Transcript Database ID Name Start End E.value
7 g4080.t9 Gene3D G3DSA:3.90.190.10 Protein tyrosine phosphatase superfamily 2 97 3.0E-31
2 g4080.t9 PANTHER PTHR46257 TYROSINE-PROTEIN PHOSPHATASE CORKSCREW 6 133 5.5E-53
4 g4080.t9 PRINTS PR00700 Protein tyrosine phosphatase signature 9 27 1.2E-18
3 g4080.t9 PRINTS PR00700 Protein tyrosine phosphatase signature 43 58 1.2E-18
5 g4080.t9 PRINTS PR00700 Protein tyrosine phosphatase signature 59 69 1.2E-18
1 g4080.t9 Pfam PF00102 Protein-tyrosine phosphatase 6 73 3.0E-22
8 g4080.t9 ProSitePatterns PS00383 Tyrosine specific protein phosphatases active site. 12 22 -
10 g4080.t9 ProSiteProfiles PS50056 Tyrosine specific protein phosphatases family profile. 1 67 20.366
11 g4080.t9 ProSiteProfiles PS50055 PTP type protein phosphatase family profile. 1 76 17.489
9 g4080.t9 SMART SM00404 ptp_7 1 75 5.3E-16
6 g4080.t9 SUPERFAMILY SSF52799 (Phosphotyrosine protein) phosphatases II 6 83 4.35E-30

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

## Warning: Removed 1 row(s) containing missing values (geom_path).

GO terms from InterProScan

GOID TERM ONTOLOGY
GO:0006470 protein dephosphorylation BP
GO:0016311 dephosphorylation BP
GO:0004725 protein tyrosine phosphatase activity MF
GO:0016791 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