General information for g13260.t4
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Receptor-type tyrosine-protein phosphatase N2.
Parent gene
- The parent gene g13260 is located on chr_1: 28844910..28845862 (+ 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_1 | g13260 | g13260.t4 | isoform | g13260.t4 | 28844910 | 28845862 |
| chr_1 | g13260 | g13260.t4 | exon | g13260.t4.exon1 | 28844910 | 28845862 |
| chr_1 | g13260 | g13260.t4 | cds | g13260.t4.CDS1 | 28844965 | 28845300 |
| chr_1 | g13260 | g13260.t4 | TSS | g13260.t4 | NA | NA |
| chr_1 | g13260 | g13260.t4 | TTS | g13260.t4 | NA | NA |
Sequences
>g13260.t4 Gene=g13260 Length=953
TAATGGTGCTGGTAGGACGGGTGCATACATACTTCTAGATCTTGTTCTCGGCAGAATGAA
TAAAGGTGCTCGCGAAATAGATATTGCAGCAACGCTTGAACATTTAAGAGATCAGCGTGC
TGGTCTTGTTGAGACACGACAACAATTTGAATTTGTGCTCACGGCAGTGGCCGAAGAAGT
TCATGCAATTCTCAAAGCTCTACCTCAAACACAGAGTACAGAGAAACGTGATGTAGAAAA
AGAATCACCGGAGAAACAGTCGCCAGAGCAGCAGAAAAAAGCGACAGTGGCAGCAGTAAC
AACAACAACTGCTACATCTACAAAAGAGCAAGAGAATCAAAAAACTGAGAAAACTGATGA
CGACAAACCGGCTAACGAATCTAAAGGATAAGGCTAACCCAAAAAAATCTTAATATTAAT
GAATATTAATAATTATAAATGTGTAAAATATTACATTATCTATTAAGCATAAAGCATGAA
TATGCATAAACAAACTAATATATAAAAAGCATTTAGAGTGGTGAGTTTTTAGTTGAAAAT
TTTAAGTTTTCTCTCTCAAATATAAAAAGAGTAAAAAACCTTCTTTTTCTTTTTCAATTT
CCAACAAAAAAAAGAAAAGAAAAAAAATCAAAAGTATCTTTATCAAATATGAAGAAAAAA
AGTCTTAAAAATTAAAAAAAAAATTATTGACACACACAATCTTGATAATCGCATCATATT
TATGTCAATTTTGATGTTGTGCAACAAAGCAAAAGATATGTTTGTGTATAAAAAAGAACA
AATCTTAAAACTTAGCCCATAGAAAGTTAAACACTTTAAAAAAATTGAGAAAAATCCCTT
TTTGATGACCAACAACATCAGCAAAAGTAAATGGAAAGGTAAATGGTGATACTAGAAATG
ACAACATACATTACATACCTTATAAAATGACAACCCATCAAGCATCATTTAAA
>g13260.t4 Gene=g13260 Length=111
MNKGAREIDIAATLEHLRDQRAGLVETRQQFEFVLTAVAEEVHAILKALPQTQSTEKRDV
EKESPEKQSPEQQKKATVAAVTTTTATSTKEQENQKTEKTDDDKPANESKG
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g13260.t4 | Gene3D | G3DSA:3.90.190.10 | Protein tyrosine phosphatase superfamily | 1 | 51 | 1.7E-7 |
| 3 | g13260.t4 | MobiDBLite | mobidb-lite | consensus disorder prediction | 48 | 111 | - |
| 6 | g13260.t4 | MobiDBLite | mobidb-lite | consensus disorder prediction | 54 | 70 | - |
| 5 | g13260.t4 | MobiDBLite | mobidb-lite | consensus disorder prediction | 71 | 91 | - |
| 4 | g13260.t4 | MobiDBLite | mobidb-lite | consensus disorder prediction | 92 | 111 | - |
| 1 | g13260.t4 | PANTHER | PTHR46106 | IA-2 PROTEIN TYROSINE PHOSPHATASE, ISOFORM C | 1 | 51 | 5.1E-26 |
| 2 | g13260.t4 | SUPERFAMILY | SSF52799 | (Phosphotyrosine protein) phosphatases II | 6 | 47 | 7.95E-6 |
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:0030141 | secretory granule | CC |
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. There were no conditions that were differentially expressed