General information for g5701.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Tyrosine-protein phosphatase vhp-1.
Parent gene
- The parent gene g5701 is located on chr_2: 11299772..11302161 (- 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_2 | g5701 | g5701.t1 | TTS | g5701.t1 | 11299259 | 11299259 |
| chr_2 | g5701 | g5701.t1 | isoform | g5701.t1 | 11299772 | 11302161 |
| chr_2 | g5701 | g5701.t1 | exon | g5701.t1.exon1 | 11299772 | 11300505 |
| chr_2 | g5701 | g5701.t1 | cds | g5701.t1.CDS1 | 11299772 | 11300505 |
| chr_2 | g5701 | g5701.t1 | exon | g5701.t1.exon2 | 11302122 | 11302161 |
| chr_2 | g5701 | g5701.t1 | cds | g5701.t1.CDS2 | 11302122 | 11302161 |
| chr_2 | g5701 | g5701.t1 | TSS | g5701.t1 | NA | NA |
Sequences
>g5701.t1 Gene=g5701 Length=774
ATGAAATATCGATCGATAGCGACTTTTAGTCGACCACTCGAGGAAGCCCGTAAAAAAGGA
TCAACAGTGTTGTTGCATTGTCAAGCTGGAATATCACGTTCAGCGACAATTGCCATTGCC
TATGTGATGCGATACAAATCGCTTTCCCTTCTTGAGGCGTATCAACTTGTGAAAGTCGCA
CGCCCAATTATTTCGCCGAATTTAAACTTTATGGGTCAATTGCTAGAGCTAGAGCAGAGC
CTCATTGCAGATGGAATGCTAAGACCACAGCCACTTGCTAATCAAGCAGTACCACAAACG
AGTCAACATCCATTTCTTATAGAAGAGCCGCATCATCAAAGAACAACATCGTCATCGACA
CAACCACCGCCATTTCCACTAACGCTTCCGTGTCGCAATCGCAAAAATCTATTTAATAAG
AACAAATTGACACTACGAGTGCCCAACGACGACAACAATAACAATAATAATAACAACAAT
AGTAATAGCCGTAATAATAATTGTCTGATGAGATCACCTGAACCAACGAGTTCTGATGAA
GATGTTGAGATGACATCAGCAGCATCAAAGAATATGATAGTCATAAATGAGGCCTGTGAA
AATGATAATGGATCATCAACGAGTAATTGTATCAATAATAACAACAACGATGAATGTTCA
TCACCTTCAACTATGTCAACATCGAGCTTATCCTCATCATCTTTATCACCTTCATCGCTT
ACCAATTCACCGACAACCCTCACGCCAAGCGAATCAAAAATATCGCAATTCTGA
>g5701.t1 Gene=g5701 Length=257
MKYRSIATFSRPLEEARKKGSTVLLHCQAGISRSATIAIAYVMRYKSLSLLEAYQLVKVA
RPIISPNLNFMGQLLELEQSLIADGMLRPQPLANQAVPQTSQHPFLIEEPHHQRTTSSST
QPPPFPLTLPCRNRKNLFNKNKLTLRVPNDDNNNNNNNNNSNSRNNNCLMRSPEPTSSDE
DVEMTSAASKNMIVINEACENDNGSSTSNCINNNNNDECSSPSTMSTSSLSSSSLSPSSL
TNSPTTLTPSESKISQF
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g5701.t1 | Gene3D | G3DSA:3.90.190.10 | Protein tyrosine phosphatase superfamily | 4 | 103 | 1.1E-26 |
| 10 | g5701.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 111 | 131 | - |
| 9 | g5701.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 144 | 185 | - |
| 8 | g5701.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 220 | 257 | - |
| 2 | g5701.t1 | PANTHER | PTHR10159 | DUAL SPECIFICITY PROTEIN PHOSPHATASE | 13 | 120 | 2.0E-39 |
| 3 | g5701.t1 | PANTHER | PTHR10159:SF520 | PUCKERED, ISOFORM A | 13 | 120 | 2.0E-39 |
| 1 | g5701.t1 | Pfam | PF00782 | Dual specificity phosphatase, catalytic domain | 11 | 79 | 3.9E-24 |
| 6 | g5701.t1 | ProSitePatterns | PS00383 | Tyrosine specific protein phosphatases active site. | 25 | 35 | - |
| 12 | g5701.t1 | ProSiteProfiles | PS50056 | Tyrosine specific protein phosphatases family profile. | 4 | 62 | 13.937 |
| 11 | g5701.t1 | ProSiteProfiles | PS50054 | Dual specificity protein phosphatase family profile. | 13 | 82 | 29.613 |
| 7 | g5701.t1 | SMART | SM00195 | dsp_5 | 2 | 80 | 6.3E-6 |
| 4 | g5701.t1 | SUPERFAMILY | SSF52799 | (Phosphotyrosine protein) phosphatases II | 8 | 84 | 8.43E-23 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5701/g5701.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5701.t1.fa.iupred3.txt does not exist
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0008138 | protein tyrosine/serine/threonine phosphatase activity | MF |
| 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 K20216 (dual specificity phosphatase 10)
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.
