General information for g5703.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as hypothetical.
Parent gene
- The parent gene g5703 is located on chr_2: 11315273..11316700 (- 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 | g5703 | g5703.t1 | isoform | g5703.t1 | 11307337 | 11315796 |
| chr_2 | g5703 | g5703.t1 | exon | g5703.t1.exon1 | 11307337 | 11307386 |
| chr_2 | g5703 | g5703.t1 | cds | g5703.t1.CDS1 | 11307337 | 11307386 |
| chr_2 | g5703 | g5703.t1 | exon | g5703.t1.exon2 | 11309281 | 11309511 |
| chr_2 | g5703 | g5703.t1 | cds | g5703.t1.CDS2 | 11309281 | 11309511 |
| chr_2 | g5703 | g5703.t1 | exon | g5703.t1.exon3 | 11313508 | 11313645 |
| chr_2 | g5703 | g5703.t1 | cds | g5703.t1.CDS3 | 11313508 | 11313645 |
| chr_2 | g5703 | g5703.t1 | exon | g5703.t1.exon4 | 11315778 | 11315796 |
| chr_2 | g5703 | g5703.t1 | cds | g5703.t1.CDS4 | 11315778 | 11315796 |
| chr_2 | g5703 | g5703.t1 | TSS | g5703.t1 | 11316700 | 11316700 |
| chr_2 | g5703 | g5703.t1 | TTS | g5703.t1 | NA | NA |
Sequences
>g5703.t1 Gene=g5703 Length=438
ATGCCGATCAAATTGCCTAATAACAACAATGCATCAAATTCAAATTGCGGCACATCAACG
AGCATGAATAAAAGACACTGTGATGATTCGTCTCTGACACCAAATAGCTCAAGGATTCCT
CTATCACGCAGTTGCTCTAGTCCAGCAGTTTCACATGATATTGAAACACATCCAGCGTCA
CCAGTTTTTCCACATCTTCTACTAGGTAATGGACGAGATGCCATCGATCCATCGAGTGTC
GGTGCCAATTGTGTCCTTAATGTAACATGTCAGTCACCATCAAATACAACACAAATAACG
CCTGGCGTCAAGTACAAACAGATTCCTGCAAATGATACACCACATCAGAACATTAAGCAA
TACTTTCAAGAGGCATTTGAATTTATCGATAAACAGCAGCGAACAATAGCTTGTTTGATT
ATTCATTTGGAGGTGTAA
>g5703.t1 Gene=g5703 Length=145
MPIKLPNNNNASNSNCGTSTSMNKRHCDDSSLTPNSSRIPLSRSCSSPAVSHDIETHPAS
PVFPHLLLGNGRDAIDPSSVGANCVLNVTCQSPSNTTQITPGVKYKQIPANDTPHQNIKQ
YFQEAFEFIDKQQRTIACLIIHLEV
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g5703.t1 | Gene3D | G3DSA:3.90.190.10 | Protein tyrosine phosphatase superfamily | 41 | 142 | 5.5E-13 |
| 5 | g5703.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 51 | - |
| 2 | g5703.t1 | PANTHER | PTHR10159 | DUAL SPECIFICITY PROTEIN PHOSPHATASE | 9 | 140 | 4.4E-25 |
| 3 | g5703.t1 | PANTHER | PTHR10159:SF520 | PUCKERED, ISOFORM A | 9 | 140 | 4.4E-25 |
| 1 | g5703.t1 | Pfam | PF00782 | Dual specificity phosphatase, catalytic domain | 81 | 135 | 5.4E-6 |
| 4 | g5703.t1 | SUPERFAMILY | SSF52799 | (Phosphotyrosine protein) phosphatases II | 54 | 133 | 5.14E-8 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5703/g5703.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5703.t1.fa.iupred3.txt does not exist
GO terms from InterProScan
There are no GO annotations for this transcript.
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.
