Gene loci information

Transcript annotation

  • This transcript has been annotated as Suppressor of cytokine signaling 5.

Parent gene

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.t7 TSS g2384.t7 17489831 17489831
chr_3 g2384 g2384.t7 isoform g2384.t7 17490036 17494195
chr_3 g2384 g2384.t7 exon g2384.t7.exon1 17490036 17490535
chr_3 g2384 g2384.t7 cds g2384.t7.CDS1 17490036 17490535
chr_3 g2384 g2384.t7 exon g2384.t7.exon2 17492977 17493247
chr_3 g2384 g2384.t7 cds g2384.t7.CDS2 17492977 17493247
chr_3 g2384 g2384.t7 exon g2384.t7.exon3 17493308 17493841
chr_3 g2384 g2384.t7 cds g2384.t7.CDS3 17493308 17493835
chr_3 g2384 g2384.t7 exon g2384.t7.exon4 17493911 17494195
chr_3 g2384 g2384.t7 TTS g2384.t7 17495189 17495189

Sequences

>g2384.t7 Gene=g2384 Length=1590
ATGGAGAGTAATCATAATAATTCGTCATCGGCATCTGCCTTTCTACATCATCATCAACAG
CAGCAGCAACAACAACAACAGTCAGTTTTAGCAAATAGTAATCTTTTAAATGACACAAAT
AATACTAAAATCAACAACAATCCAGTAGCAGTAGATAATAGTGGAAATGATAAAAGCAAT
AGTGGCAAGAATGAATCAACTTTATCGTGTGGAAAGAAGGCTTTTTATAAATTAATATTT
AATAAGTCGTCGCCAGGATCAAATAATAATAATAACACTGGTAGCAATAATAATAATGAT
AACAACAATAATAGTAGTCATAACTCATCTATAATGGCGCCAACACCTCCACTCAATAAT
TCATATACAAAAGTATCAATGGAGCGGACAGGAAATGTCACAATCGAGAGCAAATTGAGC
ATCGATCAAAGTCATCCTCATTCACCATCGCAACATGGAAACTCCCTCATTGTGAGTCCA
CAATCCAACGATACAAATCGATACAACTCATCACGTGAAGAAAATCGATTGGAAGACTCA
GATCAACGTGCACGAATTAGACGCGCTATAGAAATCCAGGAAGGAATAGAAATTGATCAA
GTTACATCAAGTGATCTCATCGAAAATTTGCAACGTACACGTTTGAATGATGACTCGCAA
GAGCATTGCAGACGATGTCAGCAAAATGAATTAATGCAATATCGTCAGCAACTGCAACAA
GCGCTGTTATCGACTGCTGACGATGAAAATAATCCAAAGTATCACTCACAAGTTACATAT
TGCCACTATCTAGTGCCAGACCTTGAGAAAATCACTTCATGCTGCTATTATTGGGGAAAA
ATGGACCGATATGAAGCGGAAAAGTTACTCGATGGCAAGCCCGAGGGAACATTTCTGCTA
CGTGATTCAGCGCAGGATGATTTTCTATTCAGTGTTTCATTCCGCAAATATGGTCGATCA
TTGCATGCGCGCATCGAGCAATTTAATCACAAATTCAGTTTTGATTCACATGATCCAAGT
GTATTCATGGCATCTACAGTTACTGGTCTAGTAGAACATTATAAAGATCCTACATCAGTA
ATGTTCTTTGAACCTATGCTAACAAGTCCATTGCATCGAAATTTTGTCTTCTCATTACAA
CAATTATGTAGAGCAAATATTGTCAGTAAAACCACATATGATGGAATCAATAAGCTATGC
TTACCATTAGCAATGAAAAATTATCTAAAAGAATATCATTACAAGCTTCGAGTACGTGTC
AAGCATTTTCCTGAGGGTGTAACTTTTAGAAACTCTTAGTGCCAGGTAATAACTTGTACA
TTACCTTCATCATCGTCATCCTCAAGTAGTAATTCATCATCATCGAGTAATTTATTTTGG
CATACAACAGCGACAACATCATCGCCATTTCGTTTGAATTTTCGTCAATTTTTCGAAATT
GCAAGCACAACGTTAAATAATGAGATCGAACAACCTTCAACATCGTCAGCTGCTGCTTTG
TCAATTGACACAGATGACAATGCTAAAAAGTGTTGCAATAAGAAGAAATTGACAAAAAAA
TTACAAAATTTCTTTAGTAAATTTTGGTAA

>g2384.t7 Gene=g2384 Length=432
MESNHNNSSSASAFLHHHQQQQQQQQQSVLANSNLLNDTNNTKINNNPVAVDNSGNDKSN
SGKNESTLSCGKKAFYKLIFNKSSPGSNNNNNTGSNNNNDNNNNSSHNSSIMAPTPPLNN
SYTKVSMERTGNVTIESKLSIDQSHPHSPSQHGNSLIVSPQSNDTNRYNSSREENRLEDS
DQRARIRRAIEIQEGIEIDQVTSSDLIENLQRTRLNDDSQEHCRRCQQNELMQYRQQLQQ
ALLSTADDENNPKYHSQVTYCHYLVPDLEKITSCCYYWGKMDRYEAEKLLDGKPEGTFLL
RDSAQDDFLFSVSFRKYGRSLHARIEQFNHKFSFDSHDPSVFMASTVTGLVEHYKDPTSV
MFFEPMLTSPLHRNFVFSLQQLCRANIVSKTTYDGINKLCLPLAMKNYLKEYHYKLRVRV
KHFPEGVTFRNS

Protein features from InterProScan

Transcript Database ID Name Start End E.value
11 g2384.t7 Coils Coil Coil 224 244 -
10 g2384.t7 Gene3D G3DSA:3.30.505.10 SHC Adaptor Protein 257 426 1.0E-54
18 g2384.t7 MobiDBLite mobidb-lite consensus disorder prediction 1 28 -
15 g2384.t7 MobiDBLite mobidb-lite consensus disorder prediction 40 67 -
16 g2384.t7 MobiDBLite mobidb-lite consensus disorder prediction 141 182 -
17 g2384.t7 MobiDBLite mobidb-lite consensus disorder prediction 141 168 -
3 g2384.t7 PANTHER PTHR10155 PHOSPHATIDYLINOSITOL 3-KINASE REGULATORY SUBUNIT 249 422 3.6E-87
4 g2384.t7 PANTHER PTHR10155:SF18 SUPPRESSOR OF CYTOKINE-SIGNALING 9 249 422 3.6E-87
7 g2384.t7 PRINTS PR00401 SH2 domain signature 276 290 9.6E-5
6 g2384.t7 PRINTS PR00401 SH2 domain signature 295 305 9.6E-5
5 g2384.t7 PRINTS PR00401 SH2 domain signature 343 357 9.6E-5
2 g2384.t7 Pfam PF00017 SH2 domain 276 354 8.8E-11
1 g2384.t7 Pfam PF07525 SOCS box 376 412 2.5E-7
19 g2384.t7 ProSiteProfiles PS50001 Src homology 2 (SH2) domain profile. 276 371 15.239
20 g2384.t7 ProSiteProfiles PS50225 SOCS box domain profile. 366 415 15.342
14 g2384.t7 SMART SM00252 SH2_5 274 360 3.2E-15
12 g2384.t7 SMART SM00253 socs_2 370 413 6.2E-10
13 g2384.t7 SMART SM00969 SOCS_box_2 376 412 3.6E-9
9 g2384.t7 SUPERFAMILY SSF55550 SH2 domain 265 373 2.15E-26
8 g2384.t7 SUPERFAMILY SSF158235 SOCS box-like 376 418 6.02E-12

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

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.

Raw TPM values