General information for g1848.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Low molecular weight phosphotyrosine protein phosphatase.
Parent gene
- The parent gene g1848 is located on chr_3: 13284408..13285334 (- 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 | g1848 | g1848.t1 | TTS | g1848.t1 | 13284286 | 13284286 |
| chr_3 | g1848 | g1848.t1 | isoform | g1848.t1 | 13284408 | 13285334 |
| chr_3 | g1848 | g1848.t1 | exon | g1848.t1.exon1 | 13284408 | 13284757 |
| chr_3 | g1848 | g1848.t1 | cds | g1848.t1.CDS1 | 13284408 | 13284757 |
| chr_3 | g1848 | g1848.t1 | exon | g1848.t1.exon2 | 13285136 | 13285176 |
| chr_3 | g1848 | g1848.t1 | cds | g1848.t1.CDS2 | 13285136 | 13285176 |
| chr_3 | g1848 | g1848.t1 | exon | g1848.t1.exon3 | 13285276 | 13285334 |
| chr_3 | g1848 | g1848.t1 | cds | g1848.t1.CDS3 | 13285276 | 13285334 |
| chr_3 | g1848 | g1848.t1 | TSS | g1848.t1 | 13285408 | 13285408 |
Sequences
>g1848.t1 Gene=g1848 Length=450
ATGTCATCTAATAATTCATTGATTAAAGTCCTTTTCGTTTGTTTCGGTAATACTTGCAGT
AATTTAGAATCACAATTTTTGATTGACTCTGCTGCATTAAATGATTGGCAACAAGGATGC
GATGTAAATCCAAAAGTTGATGTGATTTTGAAAAGAATAGGAATAAAAAATTTTACACAT
AAAGCTAGACCTATATCATACAAAGACTATGAAAAATTTGATTTTATGTTTGGAATGGAT
TATTTTCATATAGAAGACATGTTAAATGCTGCCGATGCATTGAAAAGTCAAACAAAAATA
TATCTTCTAGGCGAATTCAATCCAAATGAAAATGATAAAGTAATTAAAGATCCAATTGGA
AGTCCTATGTCATCATTTGAGAAATGTTATGAACAAATTTCTATTTGTTGTGAAAGATTG
TTAGAAAAAATATTGAACAAATCAATATAA
>g1848.t1 Gene=g1848 Length=149
MSSNNSLIKVLFVCFGNTCSNLESQFLIDSAALNDWQQGCDVNPKVDVILKRIGIKNFTH
KARPISYKDYEKFDFMFGMDYFHIEDMLNAADALKSQTKIYLLGEFNPNENDKVIKDPIG
SPMSSFEKCYEQISICCERLLEKILNKSI
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g1848.t1 | Gene3D | G3DSA:3.40.50.2300 | - | 2 | 148 | 0e+00 |
| 2 | g1848.t1 | PANTHER | PTHR11717 | LOW MOLECULAR WEIGHT PROTEIN TYROSINE PHOSPHATASE | 21 | 147 | 0e+00 |
| 4 | g1848.t1 | PRINTS | PR00719 | LMW phosphotyrosine protein phosphatase signature | 10 | 27 | 9e-07 |
| 3 | g1848.t1 | PRINTS | PR00719 | LMW phosphotyrosine protein phosphatase signature | 96 | 109 | 9e-07 |
| 5 | g1848.t1 | PRINTS | PR00719 | LMW phosphotyrosine protein phosphatase signature | 115 | 130 | 9e-07 |
| 1 | g1848.t1 | Pfam | PF01451 | Low molecular weight phosphotyrosine protein phosphatase | 20 | 141 | 0e+00 |
| 7 | g1848.t1 | SMART | SM00226 | LMWPc_2 | 8 | 143 | 0e+00 |
| 6 | g1848.t1 | SUPERFAMILY | SSF52788 | Phosphotyrosine protein phosphatases I | 7 | 144 | 0e+00 |
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.
