Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Suppressor of cytokine signaling 7.

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 g2659 g2659.t1 TSS g2659.t1 19406435 19406435
chr_3 g2659 g2659.t1 isoform g2659.t1 19406645 19409597
chr_3 g2659 g2659.t1 exon g2659.t1.exon1 19406645 19406776
chr_3 g2659 g2659.t1 cds g2659.t1.CDS1 19406645 19406776
chr_3 g2659 g2659.t1 exon g2659.t1.exon2 19406936 19408664
chr_3 g2659 g2659.t1 cds g2659.t1.CDS2 19406936 19408664
chr_3 g2659 g2659.t1 exon g2659.t1.exon3 19408724 19408815
chr_3 g2659 g2659.t1 cds g2659.t1.CDS3 19408724 19408815
chr_3 g2659 g2659.t1 exon g2659.t1.exon4 19408876 19408939
chr_3 g2659 g2659.t1 cds g2659.t1.CDS4 19408876 19408939
chr_3 g2659 g2659.t1 exon g2659.t1.exon5 19408993 19409308
chr_3 g2659 g2659.t1 cds g2659.t1.CDS5 19408993 19409308
chr_3 g2659 g2659.t1 exon g2659.t1.exon6 19409369 19409504
chr_3 g2659 g2659.t1 cds g2659.t1.CDS6 19409369 19409504
chr_3 g2659 g2659.t1 exon g2659.t1.exon7 19409559 19409597
chr_3 g2659 g2659.t1 cds g2659.t1.CDS7 19409559 19409597
chr_3 g2659 g2659.t1 TTS g2659.t1 NA NA

Sequences

>g2659.t1 Gene=g2659 Length=2508
ATGGAAGAAATAAATTCAAACTTTAGTTACTCATCGTCAGTAATTCCATTAATAAGCAAC
AATAGTTTCGAGATCAATGCAATTTCGTTATCAGATGACTCGGGATTTACGTCGCACGCT
AGAGAAAATGAACATGCAGACTTCAACTCTGATGAGTTTGAAGAGTCACAATTTGACTCG
GATAGTGGATTGAGTGCAGAAAATTTTCATACAATCAAAAAAATTTCGAGTTCCATTATC
TATGAACCTCCACTTGAATTTCAGGATAATTACAGTAGCTCAAAATTTTTACAAAACTAT
ACGCAAACAACTACGACAGTTCCGAGCACTGTAATTCGCACCACTCACATACAAAGTTAT
GCGTCAAGACTAACACAAAATATTATTAAAAAAGCCATCAATTCCTTTCATACGCTTGCC
ACAAAAGAAGTTCATTATTGTGAAAAACATGCTGCAGCTAAATTAAGGAAACAACAGCAA
AAGAAAGAAATGAATAACGAATATTTAAAATCAAGAACGTTTGTGTCTAATAGATACAAT
GGTATTTATGGAAGTGATTCGTTCTTAAATACTTATAATAGGCAATCATGCTTGTCAAAT
GGAAAGAATAGTAATTCTAATATTAATCTAGTAGATTCAGATGAAGATGATATTTATGAT
GAACCAAATGCAGAATATGATGTTATTTATAAAGATAATAAGGATACAATTTTGTGCACA
AAAAGAATTGTTCGTTCACTTGAAAAAAAGAAAGATTCGCGATCTCATCATCTTTACTGT
AATACAGAAGAGCTATTTTATGATAAAGTACGATCAAAAGCTCATTCAACGGCAATAAAT
ATTAATGGTAATCATAGCAGTTATAGAGTACACGATGACACCAACTGTAGCAGCAATATT
AATCGTTTTCAAAGTAACAGCTTCCAGAAGAAATTTGATAAGTTCCTTCGAAGTAAATTT
CTAACAAATAATATAACGCCAACGACAACCACTTCGTCAATTTTTTATAGCTTTTGTCAT
ACAGGAGGAGCAAAATCACCAAATGTTTGTAATACATCAAATCCAAACTCCAAGAGCTCA
CTCAATAGTCGATTATCGAGCTCACACAATTCCCTAACTGTACCGACAAATAAAGCAGAT
GACTCCATTTTTATTACACAAGCTATGTCTCACGATCAACTCGGACATAATGTTGAAATA
AGTGATTTTTACAACGTACCATTGGATTCTGATATTTATACCTTGCCAATTGATGTAATT
AATAATCATGAACAACATCAATCCGCTTTTAGACATCATTATCGTGCAATGTCTGATAAC
AATTTGCTGTGTGGCAGTGGAAATAACAATAATGGTGGTAAATGTCACAAGTTTCATAGG
AGTAAAAATAAGAGAAGTAAACGTAAGAAACGTATAGATGTGATTCATGATAGTTCACGA
AAATTATCAAATGCAAGTTCAAGTGTTGTAACATCTCACTCGTTTACTATAAATCATGAA
AATCGAAAAGTGTCATCAGAAAAGGTAAAGGGAAAAGTCTTGCAATCATCATCTAGCAAT
TATACGAACGATTCAAAATTGAGGAACAGTTCAGAGAGTACAGCTATCACTAAAATAAAA
GGTGGAGATTCAAACAATAATACCAATGCAAATAATAATAAATATGGGAATACAACTGCT
GCAACCAAGAAATCACAATTTTCAATAAGCCTAAATTTAAAACAAAAATTTTGTAGCATC
TTTAGATTTAAAAAATCTCATCAAACAACATCACCATCTAGAAATGTGAATGTTACACAA
GATGAGGAGAAAAAGGTCAATTTACTTACAAGAGCTTTGCCACCTTTACCAGCTACAGAT
GATGATAAAGTCAGTGAAGATATCCAAACTGCGGATAAAAAAAAGAACAACGAAACAATG
GATTTTGCTGCTAATATTGAAAAAGTTCGCGAGTGTGGATGGTATTGGGGTCCTTTAACT
TCTGAGGCTGCTGAAAAAATTTTGTCAAATGAGCCAGATGGTAGTTTTATCGTTCGAGAC
AGTTCCGACTTGAATTATATTTTCTCATTGACTGTGAAGCTTAATGGCTGTATAAGACAT
GTAAGGATCGAACAAGAGCAGGGTACATTTTCTTTTGGCTCTTGCGCTCAAATCAAATGT
TCCTACAAGTCTAGAACAATAAAAGAGTTTATTGAAAATGCTGTGGAACACTCTAGGAGT
GGTCGGTATTTATTCTTCCTGCATCGTCGACCCGAACATGGGCCGATGCGCGTTCAACTT
CTCAATCCAGTATCAAGATTCAGACACGTCCAAAGTCTACAACATATGTGCAGATTTGTT
ATTTTAAAAGCTGTGCAACGTAAGGATTTAATTGAAACCTTGCCACTTCCAAGACGTCTC
CTCGATTATCTACAAAATAAAAATTTTCTGTCTGAACTAGTCGAAAGCGATAGCTCATCG
CAATCACAAGTATATGGCGAAAATAACAATAATTCTGATACTAACTAA

>g2659.t1 Gene=g2659 Length=835
MEEINSNFSYSSSVIPLISNNSFEINAISLSDDSGFTSHARENEHADFNSDEFEESQFDS
DSGLSAENFHTIKKISSSIIYEPPLEFQDNYSSSKFLQNYTQTTTTVPSTVIRTTHIQSY
ASRLTQNIIKKAINSFHTLATKEVHYCEKHAAAKLRKQQQKKEMNNEYLKSRTFVSNRYN
GIYGSDSFLNTYNRQSCLSNGKNSNSNINLVDSDEDDIYDEPNAEYDVIYKDNKDTILCT
KRIVRSLEKKKDSRSHHLYCNTEELFYDKVRSKAHSTAININGNHSSYRVHDDTNCSSNI
NRFQSNSFQKKFDKFLRSKFLTNNITPTTTTSSIFYSFCHTGGAKSPNVCNTSNPNSKSS
LNSRLSSSHNSLTVPTNKADDSIFITQAMSHDQLGHNVEISDFYNVPLDSDIYTLPIDVI
NNHEQHQSAFRHHYRAMSDNNLLCGSGNNNNGGKCHKFHRSKNKRSKRKKRIDVIHDSSR
KLSNASSSVVTSHSFTINHENRKVSSEKVKGKVLQSSSSNYTNDSKLRNSSESTAITKIK
GGDSNNNTNANNNKYGNTTAATKKSQFSISLNLKQKFCSIFRFKKSHQTTSPSRNVNVTQ
DEEKKVNLLTRALPPLPATDDDKVSEDIQTADKKKNNETMDFAANIEKVRECGWYWGPLT
SEAAEKILSNEPDGSFIVRDSSDLNYIFSLTVKLNGCIRHVRIEQEQGTFSFGSCAQIKC
SYKSRTIKEFIENAVEHSRSGRYLFFLHRRPEHGPMRVQLLNPVSRFRHVQSLQHMCRFV
ILKAVQRKDLIETLPLPRRLLDYLQNKNFLSELVESDSSSQSQVYGENNNNSDTN

Protein features from InterProScan

Transcript Database ID Name Start End E.value
12 g2659.t1 CDD cd10388 SH2_SOCS7 643 745 2.21346E-46
11 g2659.t1 CDD cd03741 SOCS_SOCS7 768 817 9.91678E-20
10 g2659.t1 Gene3D G3DSA:3.30.505.10 SHC Adaptor Protein 635 771 1.6E-33
9 g2659.t1 Gene3D G3DSA:1.10.750.20 - 772 806 2.3E-8
16 g2659.t1 MobiDBLite mobidb-lite consensus disorder prediction 501 551 -
17 g2659.t1 MobiDBLite mobidb-lite consensus disorder prediction 510 551 -
3 g2659.t1 PANTHER PTHR10155 PHOSPHATIDYLINOSITOL 3-KINASE REGULATORY SUBUNIT 284 570 1.1E-145
5 g2659.t1 PANTHER PTHR10155:SF26 SUPPRESSOR OF CYTOKINE SIGNALING AT 16D, ISOFORM B 284 570 1.1E-145
4 g2659.t1 PANTHER PTHR10155 PHOSPHATIDYLINOSITOL 3-KINASE REGULATORY SUBUNIT 603 824 1.1E-145
6 g2659.t1 PANTHER PTHR10155:SF26 SUPPRESSOR OF CYTOKINE SIGNALING AT 16D, ISOFORM B 603 824 1.1E-145
2 g2659.t1 Pfam PF00017 SH2 domain 654 709 2.3E-10
1 g2659.t1 Pfam PF07525 SOCS box 770 805 4.3E-10
18 g2659.t1 ProSiteProfiles PS50001 Src homology 2 (SH2) domain profile. 654 764 14.038
19 g2659.t1 ProSiteProfiles PS50225 SOCS box domain profile. 759 810 16.282
15 g2659.t1 SMART SM00252 SH2_5 652 740 2.5E-18
13 g2659.t1 SMART SM00253 socs_2 764 808 4.0E-14
14 g2659.t1 SMART SM00969 SOCS_box_2 770 807 1.6E-10
8 g2659.t1 SUPERFAMILY SSF55550 SH2 domain 640 734 6.06E-22
7 g2659.t1 SUPERFAMILY SSF158235 SOCS box-like 760 808 1.44E-10

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