General information for g3200.t3
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Serine/threonine-protein phosphatase 4 catalytic subunit.
Parent gene
- The parent gene g3200 is located on chr_3: 23620525..23621663 (+ 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 | g3200 | g3200.t3 | TSS | g3200.t3 | 23619663 | 23619663 |
| chr_3 | g3200 | g3200.t3 | isoform | g3200.t3 | 23619911 | 23621663 |
| chr_3 | g3200 | g3200.t3 | exon | g3200.t3.exon1 | 23619911 | 23620064 |
| chr_3 | g3200 | g3200.t3 | exon | g3200.t3.exon2 | 23620249 | 23620338 |
| chr_3 | g3200 | g3200.t3 | cds | g3200.t3.CDS1 | 23620336 | 23620338 |
| chr_3 | g3200 | g3200.t3 | exon | g3200.t3.exon3 | 23620401 | 23620463 |
| chr_3 | g3200 | g3200.t3 | cds | g3200.t3.CDS2 | 23620401 | 23620463 |
| chr_3 | g3200 | g3200.t3 | exon | g3200.t3.exon4 | 23620525 | 23621663 |
| chr_3 | g3200 | g3200.t3 | cds | g3200.t3.CDS3 | 23620525 | 23621145 |
| chr_3 | g3200 | g3200.t3 | TTS | g3200.t3 | 23621665 | 23621665 |
Sequences
>g3200.t3 Gene=g3200 Length=1446
ATGAGTGACTACAGTGATCTTGATCGTCAAATTGAGCAGCTTAAGCGATGTGAAATCATA
AAAGAGAACGAAGTAAAGGCCTTGTGTGCGAAAGCTCGAGAAATTTTGGTTGAAGAAGGA
AATGTGCAGCGAGTCGATAGTCCCGTAACAGTACGTCTCTGGTGACGTTCACGGTCAATT
TTATGATCTCAAAGAATTATTTAAAGTTGGTGGAGATGTTCCTGAAACAAATTACTTATT
CATGGGAGACTTTGTCGACAGAGGATATTATTCAGTTGAAACATTCTTACTTCTTTTGGC
ATTAAAGGTTCGATATCCAGATCGTATAACGTTAATTCGTGGCAATCACGAGTCACGTCA
AATTACTCAAGTTTATGGTTTCTATGACGAATGTCTTCGAAAATATGGCTCAATTACAGT
TTGGCGCTATTGTACAGAAGTCTTTGACTATCTTAGTCTTTCGGCTATCATCGATGGCAA
AATTTTCTGTGTACATGGCGGTTTGAGTCCTTCAATTCAGTATTTAGATCAAATTCGATC
GATTGATAGAAAACAGGAAGTTCCACATGACGGCCCTATGTGTGATTTATTATGGAGTGA
TCCAGAAGATACACATGGTTGGGGTGTTTCACCTCGCGGCGCTGGATATTTATTTGGTTC
TGATGTAGTCGCACAATTTAATGCGGCAAACGATATTGAGATGATTTGTCGAGCACATCA
ACTTGTAATGGAAGGTTACAAATGGCATTTTAATGAGACTGTCTTAACAGTGTGGTCAGC
GCCTAATTATTGCTATCGTTGTGGAAATGTCGCTGCTATACTAGAACTGAATGAAAATCT
TCAACGCGATTTTACTATATTTGAAGCGGCTCCACAAGAAAGTCGAGGGATTCCGTTGAA
AAAACCCCAAGCTGACTACTTTTTATAAACAATCAACTACTCAACGTTTCGCGTATATAC
ACAAACATATTTACACATACACACCACACACTTTTATGATTTACTAAAGTGACGACGAAT
ATAAGTTCTTTTTTTCATGTCATTATCGTCCTTTATTGTTCTCTCCCTCACTTATTTTCT
GTAATTTAAATCAATTTATTAAATATAAAAAAATTAGATTACGTAAAACAAATTATTTAG
TAATTTACAATATGTGCGCATGAATGATGCGAAAAAAATACAAGAACATAGCCAATTGTT
TATAGTGTCCCAAATTAAAGATATTTATCTTTGAAACAAAATTCTAGAACGAGTGTTAAA
AAAAATTTTTTAGTTTATAAGTTTTGCTTCATCAACTTAATATGTTCATCATTTTTATTA
TTTTAATTTCCTTTTTCTACTATCACCATCAATGATTTATACTTAACAATATATAAATGA
TAACGAATATTATAAAAGAAAAATAAAAATACGACAAGAAATAAAGTGAAAAATTTTTAG
AAAAAA
>g3200.t3 Gene=g3200 Length=228
MGDFVDRGYYSVETFLLLLALKVRYPDRITLIRGNHESRQITQVYGFYDECLRKYGSITV
WRYCTEVFDYLSLSAIIDGKIFCVHGGLSPSIQYLDQIRSIDRKQEVPHDGPMCDLLWSD
PEDTHGWGVSPRGAGYLFGSDVVAQFNAANDIEMICRAHQLVMEGYKWHFNETVLTVWSA
PNYCYRCGNVAAILELNENLQRDFTIFEAAPQESRGIPLKKPQADYFL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 11 | g3200.t3 | CDD | cd07415 | MPP_PP2A_PP4_PP6 | 1 | 211 | 1.33637E-178 |
| 10 | g3200.t3 | Gene3D | G3DSA:3.60.21.10 | - | 1 | 220 | 2.1E-100 |
| 2 | g3200.t3 | PANTHER | PTHR45619 | SERINE/THREONINE-PROTEIN PHOSPHATASE PP2A-RELATED | 1 | 228 | 1.5E-129 |
| 3 | g3200.t3 | PANTHER | PTHR45619:SF29 | SERINE/THREONINE-PROTEIN PHOSPHATASE PP-X ISOZYME 1 | 1 | 228 | 1.5E-129 |
| 8 | g3200.t3 | PRINTS | PR00114 | Serine/threonine phosphatase family signature | 31 | 55 | 2.6E-58 |
| 5 | g3200.t3 | PRINTS | PR00114 | Serine/threonine phosphatase family signature | 66 | 92 | 2.6E-58 |
| 7 | g3200.t3 | PRINTS | PR00114 | Serine/threonine phosphatase family signature | 95 | 122 | 2.6E-58 |
| 4 | g3200.t3 | PRINTS | PR00114 | Serine/threonine phosphatase family signature | 151 | 171 | 2.6E-58 |
| 6 | g3200.t3 | PRINTS | PR00114 | Serine/threonine phosphatase family signature | 173 | 189 | 2.6E-58 |
| 1 | g3200.t3 | Pfam | PF00149 | Calcineurin-like phosphoesterase | 2 | 160 | 7.2E-31 |
| 12 | g3200.t3 | ProSitePatterns | PS00125 | Serine/threonine specific protein phosphatases signature. | 32 | 37 | - |
| 13 | g3200.t3 | SMART | SM00156 | pp2a_7 | 1 | 211 | 1.8E-83 |
| 9 | g3200.t3 | SUPERFAMILY | SSF56300 | Metallo-dependent phosphatases | 1 | 214 | 6.4E-94 |
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:0016787 | hydrolase 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.
