General information for g5931.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Tyrosine-protein phosphatase non-receptor type 7.
Parent gene
- The parent gene g5931 is located on chr_2: 12893662..12895485 (- 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 | g5931 | g5931.t2 | isoform | g5931.t2 | 12888475 | 12890030 |
| chr_2 | g5931 | g5931.t2 | exon | g5931.t2.exon1 | 12888475 | 12889098 |
| chr_2 | g5931 | g5931.t2 | cds | g5931.t2.CDS1 | 12889079 | 12889098 |
| chr_2 | g5931 | g5931.t2 | exon | g5931.t2.exon2 | 12889193 | 12890030 |
| chr_2 | g5931 | g5931.t2 | cds | g5931.t2.CDS2 | 12889193 | 12889985 |
| chr_2 | g5931 | g5931.t2 | TSS | g5931.t2 | NA | NA |
| chr_2 | g5931 | g5931.t2 | TTS | g5931.t2 | NA | NA |
Sequences
>g5931.t2 Gene=g5931 Length=1462
GGGCCAGATTATACATCTGATTGCTATATTGCAACTCAAGGACCGATGCAAAATACTGTT
TATGAATTCTGGCTAATGGTTCTACAAAATATTCAAAAGAAGAAAGATTGTGGTGTTCAA
AAAATTGCTATGCTTACCGACTTTATTGAAAGTCAGCGTCAAAAATGTGCGGTGTACTTT
CCAATAGAACAGGGAAAATGTGAAGTTTTTGCCAGTACAGGTTTGTTAAAAGATGAAAGC
TTCATTCGTGATAATTTGGATAAAATTTTGGAATCATCAACGATGGAGAATCAAGAAAAA
CTTGCAGAAATGCCAAAGATTTCATTTAATTATTTTATAATTAAGAATAATGGATTAAAA
CAGAAAAATGGATATTCAATAAGAAAACTCACACTTTATTATAGAAATATTCAGAAAGAA
AAACTACAGCAATATACAATTTATCATTATTGGTTTCCTGATTGGCCGGATCATCGTTCA
CCGCAAGACATAGATGTTCTTCTTGATATGAGCTTAGAACTTCTTGATGGCAACTGTACA
GATGATTTTCTCGAACAAGATGAAAAAAATTTAGAGGTTGTCAGCAATGTTAATGCAAAG
GAATGTATTTTTAATTCCGAGAAAAATCCTCTCCCAATAATTCATTGCTCAGCGGGAATT
GGGCGAACAGGATGTTTAGCAGCTATTTTAAATGGTCTTGGACAAATTCGAGCGAATAGT
AATGGTGAAGGAACATCAGTTGATGTATTGGGAATTGTGTGCAATTTAAGACTGCAGAGA
GGTGGAATGGTGCAGAATAGCGAGCAATATGAGCTCATTCATAGATCTTTGTGTCTCTTC
CCATTCTTAACTATTTAGATGAAAGAGTTTTGGAAATTGCTCTTTAAAAAATTTCTTCTC
ACACGAAAAAAAAGTTACACATACACATGTGAAATGTGATTTTATAACTTAAAGCTATTT
TTGTGAATCATTGTCTTCTAACACTACACTACTTTATCTTTTTACTCCTTCAGTTTGTTA
ATTTTATTTTATAACAATCAAATAGACTTTCGTAAATATTTATATATTTGCATATATACA
ACATATATGTTTTGTTAAACTACCTATATATCTCTTAGTAAAAAACTCATCAAACAAAAA
TCACGTGCTATAGTTCTCTTAATAACTTATGCAAAAATATATGCAGAAAAAAATTATAAC
AAAATGAAATAGATTGATCGAAATCTTTTCAATATAAACGACAAAAATCAGATAAAAACG
TAATGTATTGTGAAAGAAAATTTATATTTAAAAAAAAGAAGCATTGCATATTACATATTG
TGAGTGGTTTAAATTACAATTGATTTACAAATGAGAATTTAAAATGTTTATTATTTATGA
CTAAAGTGTTGAAAAATTTGAAATATACACATATAGAACTATAATAATATCTTTACATCC
CCATCTTTTTTTCTGTCATTCT
>g5931.t2 Gene=g5931 Length=270
MQNTVYEFWLMVLQNIQKKKDCGVQKIAMLTDFIESQRQKCAVYFPIEQGKCEVFASTGL
LKDESFIRDNLDKILESSTMENQEKLAEMPKISFNYFIIKNNGLKQKNGYSIRKLTLYYR
NIQKEKLQQYTIYHYWFPDWPDHRSPQDIDVLLDMSLELLDGNCTDDFLEQDEKNLEVVS
NVNAKECIFNSEKNPLPIIHCSAGIGRTGCLAAILNGLGQIRANSNGEGTSVDVLGIVCN
LRLQRGGMVQNSEQYELIHRSLCLFPFLTI
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 3 | g5931.t2 | PANTHER | PTHR19134 | RECEPTOR-TYPE TYROSINE-PROTEIN PHOSPHATASE | 1 | 260 | 2.1E-45 |
| 4 | g5931.t2 | PANTHER | PTHR19134:SF41 | TYROSINE-PROTEIN PHOSPHATASE NON-RECEPTOR TYPE 7 | 1 | 260 | 2.1E-45 |
| 5 | g5931.t2 | PRINTS | PR00700 | Protein tyrosine phosphatase signature | 130 | 147 | 1.1E-18 |
| 7 | g5931.t2 | PRINTS | PR00700 | Protein tyrosine phosphatase signature | 196 | 214 | 1.1E-18 |
| 6 | g5931.t2 | PRINTS | PR00700 | Protein tyrosine phosphatase signature | 232 | 247 | 1.1E-18 |
| 8 | g5931.t2 | PRINTS | PR00700 | Protein tyrosine phosphatase signature | 248 | 258 | 1.1E-18 |
| 2 | g5931.t2 | Pfam | PF00102 | Protein-tyrosine phosphatase | 1 | 55 | 2.4E-7 |
| 1 | g5931.t2 | Pfam | PF00102 | Protein-tyrosine phosphatase | 92 | 261 | 3.7E-24 |
| 12 | g5931.t2 | ProSitePatterns | PS00383 | Tyrosine specific protein phosphatases active site. | 199 | 209 | - |
| 14 | g5931.t2 | ProSiteProfiles | PS50055 | PTP type protein phosphatase family profile. | 1 | 265 | 23.828 |
| 13 | g5931.t2 | ProSiteProfiles | PS50056 | Tyrosine specific protein phosphatases family profile. | 173 | 256 | 16.886 |
| 11 | g5931.t2 | SMART | SM00194 | PTPc_3 | 1 | 267 | 2.9E-8 |
| 10 | g5931.t2 | SMART | SM00404 | ptp_7 | 131 | 264 | 2.0E-25 |
| 9 | g5931.t2 | SUPERFAMILY | SSF52799 | (Phosphotyrosine protein) phosphatases II | 1 | 265 | 3.68E-41 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5931/g5931.t2; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5931.t2.fa.iupred3.txt does not exist
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.
