General information for g2384.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Suppressor of cytokine signaling 4.
Parent gene
- The parent gene g2384 is located on chr_3: 17494195..17495803 (+ 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 | g2384 | g2384.t1 | TSS | g2384.t1 | 17489831 | 17489831 |
| chr_3 | g2384 | g2384.t1 | isoform | g2384.t1 | 17490036 | 17494195 |
| chr_3 | g2384 | g2384.t1 | exon | g2384.t1.exon1 | 17490036 | 17490535 |
| chr_3 | g2384 | g2384.t1 | cds | g2384.t1.CDS1 | 17490036 | 17490535 |
| chr_3 | g2384 | g2384.t1 | exon | g2384.t1.exon2 | 17492977 | 17493247 |
| chr_3 | g2384 | g2384.t1 | cds | g2384.t1.CDS2 | 17492977 | 17493247 |
| chr_3 | g2384 | g2384.t1 | exon | g2384.t1.exon3 | 17493308 | 17493787 |
| chr_3 | g2384 | g2384.t1 | cds | g2384.t1.CDS3 | 17493308 | 17493787 |
| chr_3 | g2384 | g2384.t1 | exon | g2384.t1.exon4 | 17493836 | 17493841 |
| chr_3 | g2384 | g2384.t1 | cds | g2384.t1.CDS4 | 17493836 | 17493841 |
| chr_3 | g2384 | g2384.t1 | exon | g2384.t1.exon5 | 17493911 | 17494195 |
| chr_3 | g2384 | g2384.t1 | cds | g2384.t1.CDS5 | 17493911 | 17494195 |
| chr_3 | g2384 | g2384.t1 | TTS | g2384.t1 | 17495189 | 17495189 |
Sequences
>g2384.t1 Gene=g2384 Length=1542
ATGGAGAGTAATCATAATAATTCGTCATCGGCATCTGCCTTTCTACATCATCATCAACAG
CAGCAGCAACAACAACAACAGTCAGTTTTAGCAAATAGTAATCTTTTAAATGACACAAAT
AATACTAAAATCAACAACAATCCAGTAGCAGTAGATAATAGTGGAAATGATAAAAGCAAT
AGTGGCAAGAATGAATCAACTTTATCGTGTGGAAAGAAGGCTTTTTATAAATTAATATTT
AATAAGTCGTCGCCAGGATCAAATAATAATAATAACACTGGTAGCAATAATAATAATGAT
AACAACAATAATAGTAGTCATAACTCATCTATAATGGCGCCAACACCTCCACTCAATAAT
TCATATACAAAAGTATCAATGGAGCGGACAGGAAATGTCACAATCGAGAGCAAATTGAGC
ATCGATCAAAGTCATCCTCATTCACCATCGCAACATGGAAACTCCCTCATTGTGAGTCCA
CAATCCAACGATACAAATCGATACAACTCATCACGTGAAGAAAATCGATTGGAAGACTCA
GATCAACGTGCACGAATTAGACGCGCTATAGAAATCCAGGAAGGAATAGAAATTGATCAA
GTTACATCAAGTGATCTCATCGAAAATTTGCAACGTACACGTTTGAATGATGACTCGCAA
GAGCATTGCAGACGATGTCAGCAAAATGAATTAATGCAATATCGTCAGCAACTGCAACAA
GCGCTGTTATCGACTGCTGACGATGAAAATAATCCAAAGTATCACTCACAAGTTACATAT
TGCCACTATCTAGTGCCAGACCTTGAGAAAATCACTTCATGCTGCTATTATTGGGGAAAA
ATGGACCGATATGAAGCGGAAAAGTTACTCGATGGCAAGCCCGAGGGAACATTTCTGCTA
CGTGATTCAGCGCAGGATGATTTTCTATTCAGTGTTTCATTCCGCAAATATGGTCGATCA
TTGCATGCGCGCATCGAGCAATTTAATCACAAATTCAGTTTTGATTCACATGATCCAAGT
GTATTCATGGCATCTACAGTTACTGGTCTAGTAGAACATTATAAAGATCCTACATCAGTA
ATGTTCTTTGAACCTATGCTAACAAGTCCATTGCATCGAAATTTTGTCTTCTCATTACAA
CAATTATGTAGAGCAAATATTGTCAGTAAAACCACATATGATGGAATCAATAAGCTATGC
TTACCATTAGCAATGAAAAATTATCTAAAAGAATATCATTACAAGCTTCGATGCCAGGTA
ATAACTTGTACATTACCTTCATCATCGTCATCCTCAAGTAGTAATTCATCATCATCGAGT
AATTTATTTTGGCATACAACAGCGACAACATCATCGCCATTTCGTTTGAATTTTCGTCAA
TTTTTCGAAATTGCAAGCACAACGTTAAATAATGAGATCGAACAACCTTCAACATCGTCA
GCTGCTGCTTTGTCAATTGACACAGATGACAATGCTAAAAAGTGTTGCAATAAGAAGAAA
TTGACAAAAAAATTACAAAATTTCTTTAGTAAATTTTGGTAA
>g2384.t1 Gene=g2384 Length=513
MESNHNNSSSASAFLHHHQQQQQQQQQSVLANSNLLNDTNNTKINNNPVAVDNSGNDKSN
SGKNESTLSCGKKAFYKLIFNKSSPGSNNNNNTGSNNNNDNNNNSSHNSSIMAPTPPLNN
SYTKVSMERTGNVTIESKLSIDQSHPHSPSQHGNSLIVSPQSNDTNRYNSSREENRLEDS
DQRARIRRAIEIQEGIEIDQVTSSDLIENLQRTRLNDDSQEHCRRCQQNELMQYRQQLQQ
ALLSTADDENNPKYHSQVTYCHYLVPDLEKITSCCYYWGKMDRYEAEKLLDGKPEGTFLL
RDSAQDDFLFSVSFRKYGRSLHARIEQFNHKFSFDSHDPSVFMASTVTGLVEHYKDPTSV
MFFEPMLTSPLHRNFVFSLQQLCRANIVSKTTYDGINKLCLPLAMKNYLKEYHYKLRCQV
ITCTLPSSSSSSSSNSSSSSNLFWHTTATTSSPFRLNFRQFFEIASTTLNNEIEQPSTSS
AAALSIDTDDNAKKCCNKKKLTKKLQNFFSKFW
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g2384.t1 | Coils | Coil | Coil | 224 | 244 | - |
| 7 | g2384.t1 | Gene3D | G3DSA:3.30.505.10 | SHC Adaptor Protein | 257 | 426 | 1.0E-53 |
| 15 | g2384.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 28 | - |
| 12 | g2384.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 40 | 67 | - |
| 13 | g2384.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 141 | 182 | - |
| 14 | g2384.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 141 | 168 | - |
| 3 | g2384.t1 | PANTHER | PTHR10155 | PHOSPHATIDYLINOSITOL 3-KINASE REGULATORY SUBUNIT | 249 | 420 | 5.4E-85 |
| 4 | g2384.t1 | PANTHER | PTHR10155:SF18 | SUPPRESSOR OF CYTOKINE-SIGNALING 9 | 249 | 420 | 5.4E-85 |
| 2 | g2384.t1 | Pfam | PF00017 | SH2 domain | 276 | 354 | 1.1E-10 |
| 1 | g2384.t1 | Pfam | PF07525 | SOCS box | 376 | 412 | 3.1E-7 |
| 16 | g2384.t1 | ProSiteProfiles | PS50001 | Src homology 2 (SH2) domain profile. | 276 | 371 | 15.239 |
| 17 | g2384.t1 | ProSiteProfiles | PS50225 | SOCS box domain profile. | 366 | 415 | 15.342 |
| 11 | g2384.t1 | SMART | SM00252 | SH2_5 | 274 | 360 | 3.2E-15 |
| 9 | g2384.t1 | SMART | SM00253 | socs_2 | 370 | 413 | 6.2E-10 |
| 10 | g2384.t1 | SMART | SM00969 | SOCS_box_2 | 376 | 412 | 3.6E-9 |
| 6 | g2384.t1 | SUPERFAMILY | SSF55550 | SH2 domain | 265 | 373 | 2.83E-26 |
| 5 | g2384.t1 | SUPERFAMILY | SSF158235 | SOCS box-like | 376 | 417 | 1.12E-11 |
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 K04698 (suppressor of cytokine signaling 5)
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. There were no conditions that were differentially expressed