General information for g4080.t1
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.t1 | TSS | g4080.t1 | 30469317 | 30469317 |
| chr_3 | g4080 | g4080.t1 | isoform | g4080.t1 | 30469560 | 30487933 |
| chr_3 | g4080 | g4080.t1 | exon | g4080.t1.exon1 | 30469560 | 30469573 |
| chr_3 | g4080 | g4080.t1 | cds | g4080.t1.CDS1 | 30469560 | 30469573 |
| chr_3 | g4080 | g4080.t1 | exon | g4080.t1.exon2 | 30470983 | 30471170 |
| chr_3 | g4080 | g4080.t1 | cds | g4080.t1.CDS2 | 30470983 | 30471170 |
| chr_3 | g4080 | g4080.t1 | exon | g4080.t1.exon3 | 30471247 | 30471382 |
| chr_3 | g4080 | g4080.t1 | cds | g4080.t1.CDS3 | 30471247 | 30471382 |
| chr_3 | g4080 | g4080.t1 | exon | g4080.t1.exon4 | 30485081 | 30485243 |
| chr_3 | g4080 | g4080.t1 | cds | g4080.t1.CDS4 | 30485081 | 30485243 |
| chr_3 | g4080 | g4080.t1 | exon | g4080.t1.exon5 | 30485305 | 30485546 |
| chr_3 | g4080 | g4080.t1 | cds | g4080.t1.CDS5 | 30485305 | 30485546 |
| chr_3 | g4080 | g4080.t1 | exon | g4080.t1.exon6 | 30485612 | 30485700 |
| chr_3 | g4080 | g4080.t1 | cds | g4080.t1.CDS6 | 30485612 | 30485700 |
| chr_3 | g4080 | g4080.t1 | exon | g4080.t1.exon7 | 30485873 | 30486522 |
| chr_3 | g4080 | g4080.t1 | cds | g4080.t1.CDS7 | 30485873 | 30486522 |
| chr_3 | g4080 | g4080.t1 | exon | g4080.t1.exon8 | 30486601 | 30486615 |
| chr_3 | g4080 | g4080.t1 | cds | g4080.t1.CDS8 | 30486601 | 30486615 |
| chr_3 | g4080 | g4080.t1 | exon | g4080.t1.exon9 | 30486709 | 30486792 |
| chr_3 | g4080 | g4080.t1 | cds | g4080.t1.CDS9 | 30486709 | 30486792 |
| chr_3 | g4080 | g4080.t1 | exon | g4080.t1.exon10 | 30486886 | 30487166 |
| chr_3 | g4080 | g4080.t1 | cds | g4080.t1.CDS10 | 30486886 | 30487166 |
| chr_3 | g4080 | g4080.t1 | exon | g4080.t1.exon11 | 30487634 | 30487812 |
| chr_3 | g4080 | g4080.t1 | cds | g4080.t1.CDS11 | 30487634 | 30487812 |
| chr_3 | g4080 | g4080.t1 | exon | g4080.t1.exon12 | 30487884 | 30487933 |
| chr_3 | g4080 | g4080.t1 | cds | g4080.t1.CDS12 | 30487884 | 30487933 |
| chr_3 | g4080 | g4080.t1 | TTS | g4080.t1 | 30488059 | 30488059 |
Sequences
>g4080.t1 Gene=g4080 Length=2091
ATGTCGACTAGAAGATGGTTTCATCAAAATATTAGTGGAGTTGAAGCTGAGCAATTGTTG
CTTGAGCGTGGCGTTGATGGCTCATTTCTTGCTCGTCTTTCATCATCAAATCCCGGTGCA
TTTACTTTAAGTGTGAGGAGAGGCCAAGAAGTTACGCATATAAAGATTCAAAACAATGGC
GATTTTTTCGATCTCTATGGAGGCGAGAAATTTGCAACATTGTCGGAATTGGTTCAGTTT
TATATGGAAAATCCTGGACAATTGCGTGAAAAGAAGACCGGTGCTGTTATTGAATTGAAG
CAACCGTTGAGCTGTGCAGTTGAACCAACTACAGAGAGGTGGTTTCATGGTAATTTATCT
GGACGTGATGCTGAGAAATTAATTCTCGAACGTGGAAGGAACGGCTCGTTTTTAGTGCGA
GAATCTCAATCGAAACCCGGTGACTATGTACTATCAGTACGCAATGATGATAAAGTGACT
CATGTTATGATTCGATGGCAGGATAATCGATATGATGTTGGTGGTGGTGAGCAATTTTCG
ACTTTGAGCGAGCTTATCGAACACTATAAAAAGAATCCGATGGTCGAAACTTCCGGAACT
GTCGTGAATCTTCGTCATCCATTCAATGCAACAAGAATAACAGCAGCCAGTATTGATTCC
CGTGTTGAAATCCTTCAACGCGAACATGGACCGAACTCTTGTTTTGGAAAAGGTGGTTTT
TGGGAAGAATTTGAGTCATTACAACAACAAGAATGTCGACATTCATTTTCACGAAATGAA
GGACAGCGTTTGGAAAATCGAAGCAAAAATCGTTACAAAAACATTTTACCTTTTGATCAT
ACGAGAGTAATTTTACGAGATGTTGACAACACAGTGCCCGGTGCAGAATATATAAATGCA
AATTACATTCGTCCCCTCGATATCGAGTCACTCGATCTAACATCGATGGCTTCATTTGAA
AACTTGAGCGGATCATATGCGACATTAACAAATAACTCTAATGGAAAATGTGTCAATTGT
CAGTTATTGAACAAAATGTGCGTTCAATGTGCCATTGATGGAAGTTCGAGCAACAAGCAC
AAACGAACTGAGTCATTATCATCAATTCGCACCAATTTCAGCACGTTAACGAGTGCGACA
ACAAATGCTTCGAGAAAGGGAGGCTGTGGTGATGAATTTATTAGCAAGACATATATTGCA
ACGCAAGGATGTCTACCAAATACAATTGTTGATTTCTGGAACATGATTTGGCAAGAAAAT
ACGCGTGTGATTGTCATGACAACAAAGGAGATTGAGCGAACGAAGAAAAAGTGCGAAAAA
TATTGGCCTGATAGTGGACAAACACAAGAGTGGGGTCATGCAAAAGTGAAATGCTTAAGT
GAAACTTCTACAAATGATTATACACTGCGAGAACTTTTATTTTCATGGAAAGGACAAGAA
GGACGAAAAGTTTATCATTATCATTATTTTTTGTGGCCTGATCATGGTTGTCCACCGGTG
ACTGATTCCGGAAGTGTTCTCAACTTCCTGCAAGATGTTAATGTACGGCAAGAACAATTA
ATGAGTGATGGCGTTAATCCTGGTCCAATTTGTGTGCATTGCTCAGCTGGAATTGGACGT
ACAGGCACATTTATTGTGATAGACATGATTCTTGACCAAATCGATCGTGAGGGACTCGAT
TGTGAAATAGATATTCATCGTACGATCTTGATGGTTCGTTCTCAACGTTCTGGAATGGTA
CAGACTGAAGCTCAATACAAGTTTGTGTATTATGCGGTGCAACATTACATTCAAACAAAA
CTTCAGAGAAAGCGTGCTGAACAACAGTCATTACAACACGGGCGAGAATATACGAATATA
AAGTATGATGATGTGCGTAGTCCGCTGCCTCAATCGATTAGCCAAATGAGTTTGTACAAT
AACAACAACAACACGAGTAGCAACAACTCATATCAGCAGTCCTCGGGTATTATTGAACCA
TTGCCATTTCATCATCGTCAAGTTCCCGTTCCGCCATCATTTTCTGATTTTAGTTCGTCT
GCTTATGAAAATTTGGATTCAATACCATCAAGACCGCCAAGAAAATCTTGA
>g4080.t1 Gene=g4080 Length=696
MSTRRWFHQNISGVEAEQLLLERGVDGSFLARLSSSNPGAFTLSVRRGQEVTHIKIQNNG
DFFDLYGGEKFATLSELVQFYMENPGQLREKKTGAVIELKQPLSCAVEPTTERWFHGNLS
GRDAEKLILERGRNGSFLVRESQSKPGDYVLSVRNDDKVTHVMIRWQDNRYDVGGGEQFS
TLSELIEHYKKNPMVETSGTVVNLRHPFNATRITAASIDSRVEILQREHGPNSCFGKGGF
WEEFESLQQQECRHSFSRNEGQRLENRSKNRYKNILPFDHTRVILRDVDNTVPGAEYINA
NYIRPLDIESLDLTSMASFENLSGSYATLTNNSNGKCVNCQLLNKMCVQCAIDGSSSNKH
KRTESLSSIRTNFSTLTSATTNASRKGGCGDEFISKTYIATQGCLPNTIVDFWNMIWQEN
TRVIVMTTKEIERTKKKCEKYWPDSGQTQEWGHAKVKCLSETSTNDYTLRELLFSWKGQE
GRKVYHYHYFLWPDHGCPPVTDSGSVLNFLQDVNVRQEQLMSDGVNPGPICVHCSAGIGR
TGTFIVIDMILDQIDREGLDCEIDIHRTILMVRSQRSGMVQTEAQYKFVYYAVQHYIQTK
LQRKRAEQQSLQHGREYTNIKYDDVRSPLPQSISQMSLYNNNNNTSSNNSYQQSSGIIEP
LPFHHRQVPVPPSFSDFSSSAYENLDSIPSRPPRKS
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 23 | g4080.t1 | CDD | cd10340 | SH2_N-SH2_SHP_like | 5 | 103 | 4.37892E-58 |
| 24 | g4080.t1 | CDD | cd09931 | SH2_C-SH2_SHP_like | 113 | 210 | 1.98389E-62 |
| 21 | g4080.t1 | Gene3D | G3DSA:3.30.505.10 | SHC Adaptor Protein | 1 | 107 | 1.7E-29 |
| 22 | g4080.t1 | Gene3D | G3DSA:3.30.505.10 | SHC Adaptor Protein | 108 | 209 | 2.3E-34 |
| 5 | g4080.t1 | PANTHER | PTHR46257:SF3 | TYROSINE-PROTEIN PHOSPHATASE CORKSCREW | 4 | 655 | 1.6E-282 |
| 6 | g4080.t1 | PANTHER | PTHR46257 | TYROSINE-PROTEIN PHOSPHATASE CORKSCREW | 4 | 655 | 1.6E-282 |
| 7 | g4080.t1 | PRINTS | PR00401 | SH2 domain signature | 114 | 128 | 1.9E-17 |
| 10 | g4080.t1 | PRINTS | PR00401 | SH2 domain signature | 134 | 144 | 1.9E-17 |
| 9 | g4080.t1 | PRINTS | PR00401 | SH2 domain signature | 146 | 157 | 1.9E-17 |
| 8 | g4080.t1 | PRINTS | PR00401 | SH2 domain signature | 158 | 168 | 1.9E-17 |
| 11 | g4080.t1 | PRINTS | PR00401 | SH2 domain signature | 178 | 192 | 1.9E-17 |
| 16 | g4080.t1 | PRINTS | PR00700 | Protein tyrosine phosphatase signature | 296 | 303 | 1.6E-37 |
| 17 | g4080.t1 | PRINTS | PR00700 | Protein tyrosine phosphatase signature | 398 | 418 | 1.6E-37 |
| 15 | g4080.t1 | PRINTS | PR00700 | Protein tyrosine phosphatase signature | 482 | 499 | 1.6E-37 |
| 14 | g4080.t1 | PRINTS | PR00700 | Protein tyrosine phosphatase signature | 529 | 547 | 1.6E-37 |
| 13 | g4080.t1 | PRINTS | PR00700 | Protein tyrosine phosphatase signature | 563 | 578 | 1.6E-37 |
| 12 | g4080.t1 | PRINTS | PR00700 | Protein tyrosine phosphatase signature | 579 | 589 | 1.6E-37 |
| 2 | g4080.t1 | Pfam | PF00017 | SH2 domain | 6 | 81 | 2.5E-22 |
| 1 | g4080.t1 | Pfam | PF00017 | SH2 domain | 114 | 189 | 3.8E-26 |
| 3 | g4080.t1 | Pfam | PF00102 | Protein-tyrosine phosphatase | 266 | 304 | 7.4E-8 |
| 4 | g4080.t1 | Pfam | PF00102 | Protein-tyrosine phosphatase | 395 | 593 | 3.9E-61 |
| 25 | g4080.t1 | ProSitePatterns | PS00383 | Tyrosine specific protein phosphatases active site. | 532 | 542 | - |
| 31 | g4080.t1 | ProSiteProfiles | PS50001 | Src homology 2 (SH2) domain profile. | 6 | 103 | 21.304 |
| 32 | g4080.t1 | ProSiteProfiles | PS50001 | Src homology 2 (SH2) domain profile. | 114 | 208 | 25.472 |
| 33 | g4080.t1 | ProSiteProfiles | PS50055 | PTP type protein phosphatase family profile. | 240 | 596 | 49.772 |
| 30 | g4080.t1 | ProSiteProfiles | PS50056 | Tyrosine specific protein phosphatases family profile. | 507 | 587 | 21.509 |
| 29 | g4080.t1 | SMART | SM00252 | SH2_5 | 4 | 87 | 1.4E-28 |
| 28 | g4080.t1 | SMART | SM00252 | SH2_5 | 112 | 195 | 4.3E-34 |
| 27 | g4080.t1 | SMART | SM00194 | PTPc_3 | 239 | 598 | 1.6E-107 |
| 26 | g4080.t1 | SMART | SM00404 | ptp_7 | 483 | 595 | 7.4E-41 |
| 19 | g4080.t1 | SUPERFAMILY | SSF55550 | SH2 domain | 3 | 103 | 2.56E-26 |
| 20 | g4080.t1 | SUPERFAMILY | SSF55550 | SH2 domain | 110 | 240 | 1.62E-31 |
| 18 | g4080.t1 | SUPERFAMILY | SSF52799 | (Phosphotyrosine protein) phosphatases II | 239 | 603 | 1.61E-93 |
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:0016311 | dephosphorylation | BP |
| GO:0004725 | protein tyrosine phosphatase activity | MF |
| GO:0016791 | phosphatase activity | MF |
KEGG
Orthology
- This transcript has been annotated with K07293 (tyrosine-protein phosphatase non-receptor type 11)
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.
