General information for g4080.t3
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Tyrosine-protein phosphatase corkscrew.
Parent gene
- The parent gene g4080 is located on chr_3: 30486393..30487933 (+ 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 | g4080 | g4080.t3 | TSS | g4080.t3 | 30469317 | 30469317 |
| chr_3 | g4080 | g4080.t3 | isoform | g4080.t3 | 30469560 | 30471592 |
| chr_3 | g4080 | g4080.t3 | exon | g4080.t3.exon1 | 30469560 | 30469573 |
| chr_3 | g4080 | g4080.t3 | cds | g4080.t3.CDS1 | 30469560 | 30469573 |
| chr_3 | g4080 | g4080.t3 | exon | g4080.t3.exon2 | 30470983 | 30471170 |
| chr_3 | g4080 | g4080.t3 | cds | g4080.t3.CDS2 | 30470983 | 30471170 |
| chr_3 | g4080 | g4080.t3 | exon | g4080.t3.exon3 | 30471247 | 30471382 |
| chr_3 | g4080 | g4080.t3 | cds | g4080.t3.CDS3 | 30471247 | 30471382 |
| chr_3 | g4080 | g4080.t3 | exon | g4080.t3.exon4 | 30471491 | 30471592 |
| chr_3 | g4080 | g4080.t3 | cds | g4080.t3.CDS4 | 30471491 | 30471569 |
| chr_3 | g4080 | g4080.t3 | TTS | g4080.t3 | NA | NA |
Sequences
>g4080.t3 Gene=g4080 Length=440
ATGTCGACTAGAAGATGGTTTCATCAAAATATTAGTGGAGTTGAAGCTGAGCAATTGTTG
CTTGAGCGTGGCGTTGATGGCTCATTTCTTGCTCGTCTTTCATCATCAAATCCCGGTGCA
TTTACTTTAAGTGTGAGGAGAGGCCAAGAAGTTACGCATATAAAGATTCAAAACAATGGC
GATTTTTTCGATCTCTATGGAGGCGAGAAATTTGCAACATTGTCGGAATTGGTTCAGTTT
TATATGGAAAATCCTGGACAATTGCGTGAAAAGAAGACCGGTGCTGTTATTGAATTGAAG
CAACCGTTGAGCTGTGCAGTTGAACCAACTACAGAGAGAATGTTAATTTTTTGCGCATTT
TTGGAACAACAATGCCGCTTATGGGCAATTCCAAAATTGGAAAAAAATGAATTGTAAATC
TTTCTCAACTTGTTTTCGTT
>g4080.t3 Gene=g4080 Length=138
MSTRRWFHQNISGVEAEQLLLERGVDGSFLARLSSSNPGAFTLSVRRGQEVTHIKIQNNG
DFFDLYGGEKFATLSELVQFYMENPGQLREKKTGAVIELKQPLSCAVEPTTERMLIFCAF
LEQQCRLWAIPKLEKNEL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 10 | g4080.t3 | CDD | cd10340 | SH2_N-SH2_SHP_like | 5 | 103 | 0.000 |
| 9 | g4080.t3 | Gene3D | G3DSA:3.30.505.10 | SHC Adaptor Protein | 1 | 110 | 0.000 |
| 2 | g4080.t3 | PANTHER | PTHR46257 | TYROSINE-PROTEIN PHOSPHATASE CORKSCREW | 1 | 114 | 0.000 |
| 4 | g4080.t3 | PRINTS | PR00401 | SH2 domain signature | 6 | 20 | 0.000 |
| 3 | g4080.t3 | PRINTS | PR00401 | SH2 domain signature | 26 | 36 | 0.000 |
| 5 | g4080.t3 | PRINTS | PR00401 | SH2 domain signature | 38 | 49 | 0.000 |
| 7 | g4080.t3 | PRINTS | PR00401 | SH2 domain signature | 50 | 60 | 0.000 |
| 6 | g4080.t3 | PRINTS | PR00401 | SH2 domain signature | 70 | 84 | 0.000 |
| 1 | g4080.t3 | Pfam | PF00017 | SH2 domain | 6 | 81 | 0.000 |
| 12 | g4080.t3 | ProSiteProfiles | PS50001 | Src homology 2 (SH2) domain profile. | 6 | 103 | 21.304 |
| 11 | g4080.t3 | SMART | SM00252 | SH2_5 | 4 | 87 | 0.000 |
| 8 | g4080.t3 | SUPERFAMILY | SSF55550 | SH2 domain | 2 | 108 | 0.000 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
GO terms from InterProScan
There are no GO annotations for this transcript.
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