General information for g2683.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as hypothetical.
Parent gene
- The parent gene g2683 is located on chr_3: 19708862..19709557 (- 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 | g2683 | g2683.t1 | TTS | g2683.t1 | 19708633 | 19708633 |
| chr_3 | g2683 | g2683.t1 | isoform | g2683.t1 | 19708862 | 19709557 |
| chr_3 | g2683 | g2683.t1 | exon | g2683.t1.exon1 | 19708862 | 19709557 |
| chr_3 | g2683 | g2683.t1 | cds | g2683.t1.CDS1 | 19708862 | 19709557 |
| chr_3 | g2683 | g2683.t1 | TSS | g2683.t1 | 19709637 | 19709637 |
Sequences
>g2683.t1 Gene=g2683 Length=696
ATGGAGAATGCAAGAAATAACAATAATTGGCTTGCTTTATTACGTCGAAAGATACAAAAG
AAGTTTAAAAAGACACGTCAAAAGACAACAATAGCCGAAAATCAAGAAATAGCAAATCAA
GATGAAAATGAAGAAATTCAAGCTCAAGCAGCAGTAGAACAACAGCAGCAACAATCAGAA
ACTATTAAAGAGAAAGAAATCAACAACGAATATCAAGAAATGAAAAAAGAGCTTTTTAAA
TTAGCCTGTTATTGGCCTAAATTAACTAGAGCTGGAGCTCAAAAAATTTTGAAAAACACT
CAAAATGGCTCTTTTTTAATTCGAGATTCTGGAACAGCTGATAATTCTATTACACTTTCA
TTCAGATCAAATAATAAAACATTTCACTGTCGTAATCAGTTTAATGCAATATTAAACTCA
CAGCAAACAGCTCAATATAATATAATTACTGCCATCGAGGATTCTATCAAAAAGAGTCAA
TCATCAGTTGTTGGTTTCGTTAAATGTGATAATAATGAATTATCTGTTCCAATTGCCGTT
CGTTTAATTTATCCAATTAATCGCAACGTTCCTAGTTTGCAAAATTTATGTTTAAGTCTA
GTTGTAAGCAACATCAATCAATCAACAGCTATCAATAGTTTGCCATTACCTCTAAAAATT
AAGGAAATTGTGCGTGAAAACTATAATACTTTATAA
>g2683.t1 Gene=g2683 Length=231
MENARNNNNWLALLRRKIQKKFKKTRQKTTIAENQEIANQDENEEIQAQAAVEQQQQQSE
TIKEKEINNEYQEMKKELFKLACYWPKLTRAGAQKILKNTQNGSFLIRDSGTADNSITLS
FRSNNKTFHCRNQFNAILNSQQTAQYNIITAIEDSIKKSQSSVVGFVKCDNNELSVPIAV
RLIYPINRNVPSLQNLCLSLVVSNINQSTAINSLPLPLKIKEIVRENYNTL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g2683.t1 | Coils | Coil | Coil | 38 | 58 | - |
| 7 | g2683.t1 | Gene3D | G3DSA:3.30.505.10 | SHC Adaptor Protein | 62 | 230 | 1.3E-24 |
| 2 | g2683.t1 | PANTHER | PTHR10155 | PHOSPHATIDYLINOSITOL 3-KINASE REGULATORY SUBUNIT | 5 | 229 | 2.5E-39 |
| 3 | g2683.t1 | PANTHER | PTHR10155:SF12 | LP02169P | 5 | 229 | 2.5E-39 |
| 1 | g2683.t1 | Pfam | PF00017 | SH2 domain | 84 | 135 | 1.8E-10 |
| 9 | g2683.t1 | ProSiteProfiles | PS50001 | Src homology 2 (SH2) domain profile. | 83 | 186 | 10.464 |
| 10 | g2683.t1 | ProSiteProfiles | PS50225 | SOCS box domain profile. | 173 | 226 | 10.488 |
| 6 | g2683.t1 | SMART | SM00252 | SH2_5 | 81 | 161 | 3.9E-5 |
| 5 | g2683.t1 | SUPERFAMILY | SSF55550 | SH2 domain | 60 | 131 | 1.14E-15 |
| 4 | g2683.t1 | SUPERFAMILY | SSF158235 | SOCS box-like | 180 | 222 | 9.16E-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:0035556 | intracellular signal transduction | BP |
KEGG
Orthology
- This transcript has been annotated with K04699 (suppressor of cytokine signaling 6/7)
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.
