General information for g4080.t5
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Tyrosine-protein phosphatase corkscrew .
Parent gene
- The parent gene g4080 is located on chr_3: 30486393..30487933 (+ strand)
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.t5 | TSS | g4080.t5 | 30485080 | 30485080 |
| chr_3 | g4080 | g4080.t5 | isoform | g4080.t5 | 30485305 | 30487933 |
| chr_3 | g4080 | g4080.t5 | exon | g4080.t5.exon1 | 30485305 | 30485546 |
| chr_3 | g4080 | g4080.t5 | cds | g4080.t5.CDS1 | 30485383 | 30485546 |
| chr_3 | g4080 | g4080.t5 | exon | g4080.t5.exon2 | 30485612 | 30485700 |
| chr_3 | g4080 | g4080.t5 | cds | g4080.t5.CDS2 | 30485612 | 30485700 |
| chr_3 | g4080 | g4080.t5 | exon | g4080.t5.exon3 | 30485873 | 30486522 |
| chr_3 | g4080 | g4080.t5 | cds | g4080.t5.CDS3 | 30485873 | 30486522 |
| chr_3 | g4080 | g4080.t5 | exon | g4080.t5.exon4 | 30486691 | 30486792 |
| chr_3 | g4080 | g4080.t5 | cds | g4080.t5.CDS4 | 30486691 | 30486708 |
| chr_3 | g4080 | g4080.t5 | exon | g4080.t5.exon5 | 30486886 | 30487166 |
| chr_3 | g4080 | g4080.t5 | exon | g4080.t5.exon6 | 30487634 | 30487812 |
| chr_3 | g4080 | g4080.t5 | exon | g4080.t5.exon7 | 30487884 | 30487933 |
| chr_3 | g4080 | g4080.t5 | TTS | g4080.t5 | 30488059 | 30488059 |
Sequences
>g4080.t5 Gene=g4080 Length=1593
GATAATCGATATGATGTTGGTGGTGGTGAGCAATTTTCGACTTTGAGCGAGCTTATCGAA
CACTATAAAAAGAATCCGATGGTCGAAACTTCCGGAACTGTCGTGAATCTTCGTCATCCA
TTCAATGCAACAAGAATAACAGCAGCCAGTATTGATTCCCGTGTTGAAATCCTTCAACGC
GAACATGGACCGAACTCTTGTTTTGGAAAAGGTGGTTTTTGGGAAGAATTTGAGTCATTA
CAACAACAAGAATGTCGACATTCATTTTCACGAAATGAAGGACAGCGTTTGGAAAATCGA
AGCAAAAATCGTTACAAAAACATTTTACCTTTTGATCATACGAGAGTAATTTTACGAGAT
GTTGACAACACAGTGCCCGGTGCAGAATATATAAATGCAAATTACATTCGTCCCCTCGAT
ATCGAGTCACTCGATCTAACATCGATGGCTTCATTTGAAAACTTGAGCGGATCATATGCG
ACATTAACAAATAACTCTAATGGAAAATGTGTCAATTGTCAGTTATTGAACAAAATGTGC
GTTCAATGTGCCATTGATGGAAGTTCGAGCAACAAGCACAAACGAACTGAGTCATTATCA
TCAATTCGCACCAATTTCAGCACGTTAACGAGTGCGACAACAAATGCTTCGAGAAAGGGA
GGCTGTGGTGATGAATTTATTAGCAAGACATATATTGCAACGCAAGGATGTCTACCAAAT
ACAATTGTTGATTTCTGGAACATGATTTGGCAAGAAAATACGCGTGTGATTGTCATGACA
ACAAAGGAGATTGAGCGAACGAAGAAAAAGTGCGAAAAATATTGGCCTGATAGTGGACAA
ACACAAGAGTGGGGTCATGCAAAAGTGAAATGCTTAAGTGAAACTTCTACAAATGATTAT
ACACTGCGAGAACTTTTATTTTCATGGAAAGGACAAGAAGGACGAAAAGTTTATCATTAT
CATTATTTTTTGTGGCCTGATCAATTATGTTTCCTTTAGGTGACTGATTCCGGAAGTGTT
CTCAACTTCCTGCAAGATGTTAATGTACGGCAAGAACAATTAATGAGTGATGGCGTTAAT
CCTGGTCCAATTTGTGTGCATTGCTCAGCTGGAATTGGACGTACAGGCACATTTATTGTG
ATAGACATGATTCTTGACCAAATCGATCGTGAGGGACTCGATTGTGAAATAGATATTCAT
CGTACGATCTTGATGGTTCGTTCTCAACGTTCTGGAATGGTACAGACTGAAGCTCAATAC
AAGTTTGTGTATTATGCGGTGCAACATTACATTCAAACAAAACTTCAGAGAAAGCGTGCT
GAACAACAGTCATTACAACACGGGCGAGAATATACGAATATAAAGTATGATGATGTGCGT
AGTCCGCTGCCTCAATCGATTAGCCAAATGAGTTTGTACAATAACAACAACAACACGAGT
AGCAACAACTCATATCAGCAGTCCTCGGGTATTATTGAACCATTGCCATTTCATCATCGT
CAAGTTCCCGTTCCGCCATCATTTTCTGATTTTAGTTCGTCTGCTTATGAAAATTTGGAT
TCAATACCATCAAGACCGCCAAGAAAATCTTGA
>g4080.t5 Gene=g4080 Length=306
MVETSGTVVNLRHPFNATRITAASIDSRVEILQREHGPNSCFGKGGFWEEFESLQQQECR
HSFSRNEGQRLENRSKNRYKNILPFDHTRVILRDVDNTVPGAEYINANYIRPLDIESLDL
TSMASFENLSGSYATLTNNSNGKCVNCQLLNKMCVQCAIDGSSSNKHKRTESLSSIRTNF
STLTSATTNASRKGGCGDEFISKTYIATQGCLPNTIVDFWNMIWQENTRVIVMTTKEIER
TKKKCEKYWPDSGQTQEWGHAKVKCLSETSTNDYTLRELLFSWKGQEGRKVYHYHYFLWP
DQLCFL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 2 | g4080.t5 | PANTHER | PTHR46257:SF3 | TYROSINE-PROTEIN PHOSPHATASE CORKSCREW | 1 | 303 | 0.000 |
| 3 | g4080.t5 | PANTHER | PTHR46257 | TYROSINE-PROTEIN PHOSPHATASE CORKSCREW | 1 | 303 | 0.000 |
| 6 | g4080.t5 | PRINTS | PR00700 | Protein tyrosine phosphatase signature | 103 | 110 | 0.000 |
| 5 | g4080.t5 | PRINTS | PR00700 | Protein tyrosine phosphatase signature | 205 | 225 | 0.000 |
| 4 | g4080.t5 | PRINTS | PR00700 | Protein tyrosine phosphatase signature | 289 | 306 | 0.000 |
| 1 | g4080.t5 | Pfam | PF00102 | Protein-tyrosine phosphatase | 73 | 302 | 0.000 |
| 9 | g4080.t5 | ProSiteProfiles | PS50055 | PTP type protein phosphatase family profile. | 47 | 306 | 29.757 |
| 8 | g4080.t5 | SMART | SM00194 | PTPc_3 | 46 | 306 | 0.000 |
| 7 | g4080.t5 | 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. There were no conditions that were differentially expressed