Gene loci information

Transcript annotation

  • This transcript has been annotated as Raf homolog serine/threonine-protein kinase Raf.

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_2 g8869 g8869.t1 TSS g8869.t1 33596669 33596669
chr_2 g8869 g8869.t1 isoform g8869.t1 33596943 33599263
chr_2 g8869 g8869.t1 exon g8869.t1.exon1 33596943 33597028
chr_2 g8869 g8869.t1 cds g8869.t1.CDS1 33596943 33597028
chr_2 g8869 g8869.t1 exon g8869.t1.exon2 33597098 33597751
chr_2 g8869 g8869.t1 cds g8869.t1.CDS2 33597098 33597751
chr_2 g8869 g8869.t1 exon g8869.t1.exon3 33597814 33598166
chr_2 g8869 g8869.t1 cds g8869.t1.CDS3 33597814 33598166
chr_2 g8869 g8869.t1 exon g8869.t1.exon4 33598241 33598506
chr_2 g8869 g8869.t1 cds g8869.t1.CDS4 33598241 33598506
chr_2 g8869 g8869.t1 exon g8869.t1.exon5 33598565 33598655
chr_2 g8869 g8869.t1 cds g8869.t1.CDS5 33598565 33598655
chr_2 g8869 g8869.t1 exon g8869.t1.exon6 33598714 33598783
chr_2 g8869 g8869.t1 cds g8869.t1.CDS6 33598714 33598783
chr_2 g8869 g8869.t1 exon g8869.t1.exon7 33598840 33599263
chr_2 g8869 g8869.t1 cds g8869.t1.CDS7 33598840 33599263
chr_2 g8869 g8869.t1 TTS g8869.t1 33599741 33599741

Sequences

>g8869.t1 Gene=g8869 Length=1944
ATGGATCAAAATGGAGAAAGCAGCTCTTTGGCTGAGATGCAGATTGAATTAGAGAATGTT
CAGAGCATTATTAAATTCACAATAAGTGCAATCGATGCTCTCAATGATCGATTTAGTAAA
TTTAAGCCGCCACCAAAAATTTATGTCGAGGAATATAAAGATTTGACGAGCAAGTTGCAT
CAATTTAAGACAGTTGAACAAAATCTTATTGAGAAAATTCAGTCCTTAGAAGCAGAGTTG
GAGAGTAAATTGCATCCAAAGCAACAGAAGTTATTTTTGCGAGCTCATCTGCCCAATCAA
CAACGTACATCAGTGCAAATTGTTCAAGGACAAAGACTTCGGGATGCTTTAGCAAAAGCA
TTGAGTCGTCGAAATATGAATTTTGAAATGTGTGAAGTTTATCAAACAGGAGGTGAAGGT
GAAGACATTCCAATTCCATGGGATACTGACATAAGCACACTTAAGTGTGATGAAATTAGT
GTAAAAATTTTGGATATTGTTGGATTTCCGACTTATATTTCACATCAATTTATTCGCAAA
ACATTCTTTTCGCTTGCATTTTGCGAATGCTGCCGTCGATTACTTTTTACTGGATTTTAT
TGCAATCAATGCAACTACAGATTTCATCAAAGATGTGTCGATAAAGTTCCTCCATTATGC
AGTAAATTACAAATGGACACTTATTATCAATTATTGCTTTCTGAAACACTCGGCTCAAGT
GGTTCTAGTGGATTTCATAGACATCCAAAGACATTAAATTTTGAGAATCGATCAAATTCA
GCGCCAAATGTATGCGTAAATAGTGTTTTAAAGCCATTACTTGGGAGTGATCAAAAGATT
TTGGCTAATTCAAAGTGTCCCATTCCATTGCAAACTTACTCAGAACATTCACATTCCACT
CAGGCATCGCCAACAAATACATTAAAGCATGCAAAAAGAAAACAACGTGCACGAGCAAGA
TCTGCTGATGAAAGTAACAAAATTTTATCTCCACGAGATCAAATTCAAACAGGAGAGGAT
TGGAATATTGATGCTAGTGAAATTTTGATGGGACCAAGAATTGGTAGTGGTTCATTTGGG
ACTGTATATAAAGCTCATTGGCATGGTCCGATTGCAGTAAAAACTTTAAATGTCAAAACG
CCTACTCCTTCGCAATTACAGGCGTTTAAAAATGAAGTTGCGATGCTCAAGAAGACTCGT
CACTGCAATATTTTGCTCTTCATGGGATGTGTTAGTAAGCCATCTTTAGCTATAGTAACA
CAATGGTGTGAAGGCAGTAGTCTTTACAAGCATATTCATGTACTTGAAACCAAATTTAAA
TTAAATACTTTAATCGATATTGCACGTCAAGTAGCACAGGGAATGGATTATTTACATGCA
AAAAATATAATCCATCGTGATTTAAAATCAAATAATATTTTCTTGCATGATGATCTCACA
GTAAAAATAGGCGATTTTGGACTGGCTACTGCCAAAGTAAGAATCACAGGACAAAATCAG
CCAACAGGATCAATTTTATGGATGGCACCAGAAATAATTCGAATGGATGACACAAATCCA
TATTCATTCCATTCTGATGTCTACTCATTTGGCATAGTATTGTATGAATTGTTGACCGAA
CAATTACCATATTCACATATTAATAACAAAGATCAAATACTCTATTTGGTTGGAAGAGGT
ATTCTGAGACCAGATTTATCAAAAGTTAGATCAGATTGTCCACAAGCACTGAAACGTTGC
GCTGAAGACTGTATTAAATTTGATAGAAATGAGCGACCCGTTTTTCGATTACTTCTTAAC
ATGTTGGAAAATATTTTGAAAAATTTACCGAAAATTCATCGAAGTGCAAGTGAGCCAAAT
TTGACTCAATCTCAATTACAAAACGATGATTTCTTATTTGCTTGCTCGAGCCCAAAGACT
CCTGTAAACATAACATTTAAATGA

>g8869.t1 Gene=g8869 Length=647
MDQNGESSSLAEMQIELENVQSIIKFTISAIDALNDRFSKFKPPPKIYVEEYKDLTSKLH
QFKTVEQNLIEKIQSLEAELESKLHPKQQKLFLRAHLPNQQRTSVQIVQGQRLRDALAKA
LSRRNMNFEMCEVYQTGGEGEDIPIPWDTDISTLKCDEISVKILDIVGFPTYISHQFIRK
TFFSLAFCECCRRLLFTGFYCNQCNYRFHQRCVDKVPPLCSKLQMDTYYQLLLSETLGSS
GSSGFHRHPKTLNFENRSNSAPNVCVNSVLKPLLGSDQKILANSKCPIPLQTYSEHSHST
QASPTNTLKHAKRKQRARARSADESNKILSPRDQIQTGEDWNIDASEILMGPRIGSGSFG
TVYKAHWHGPIAVKTLNVKTPTPSQLQAFKNEVAMLKKTRHCNILLFMGCVSKPSLAIVT
QWCEGSSLYKHIHVLETKFKLNTLIDIARQVAQGMDYLHAKNIIHRDLKSNNIFLHDDLT
VKIGDFGLATAKVRITGQNQPTGSILWMAPEIIRMDDTNPYSFHSDVYSFGIVLYELLTE
QLPYSHINNKDQILYLVGRGILRPDLSKVRSDCPQALKRCAEDCIKFDRNERPVFRLLLN
MLENILKNLPKIHRSASEPNLTQSQLQNDDFLFACSSPKTPVNITFK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
19 g8869.t1 CDD cd01816 RBD_RAF 92 164 1.62641E-31
20 g8869.t1 CDD cd00029 C1 175 220 2.87493E-12
18 g8869.t1 CDD cd14062 STKc_Raf 354 603 0.0
17 g8869.t1 Coils Coil Coil 59 79 -
13 g8869.t1 Gene3D G3DSA:3.10.20.90 - 92 175 3.4E-25
15 g8869.t1 Gene3D G3DSA:3.30.60.20 - 176 221 1.4E-13
14 g8869.t1 Gene3D G3DSA:3.30.200.20 Phosphorylase Kinase; domain 1 340 424 4.1E-32
16 g8869.t1 Gene3D G3DSA:1.10.510.10 Transferase(Phosphotransferase) domain 1 425 614 3.3E-56
27 g8869.t1 MobiDBLite mobidb-lite consensus disorder prediction 293 308 -
28 g8869.t1 MobiDBLite mobidb-lite consensus disorder prediction 293 327 -
5 g8869.t1 PANTHER PTHR44329:SF193 RAF HOMOLOG SERINE/THREONINE-PROTEIN KINASE RAF 18 76 5.7E-261
8 g8869.t1 PANTHER PTHR44329 SERINE/THREONINE-PROTEIN KINASE TNNI3K-RELATED 18 76 5.7E-261
6 g8869.t1 PANTHER PTHR44329:SF193 RAF HOMOLOG SERINE/THREONINE-PROTEIN KINASE RAF 83 272 5.7E-261
9 g8869.t1 PANTHER PTHR44329 SERINE/THREONINE-PROTEIN KINASE TNNI3K-RELATED 83 272 5.7E-261
4 g8869.t1 PANTHER PTHR44329:SF193 RAF HOMOLOG SERINE/THREONINE-PROTEIN KINASE RAF 284 646 5.7E-261
7 g8869.t1 PANTHER PTHR44329 SERINE/THREONINE-PROTEIN KINASE TNNI3K-RELATED 284 646 5.7E-261
1 g8869.t1 Pfam PF02196 Raf-like Ras-binding domain 93 161 7.6E-23
3 g8869.t1 Pfam PF00130 Phorbol esters/diacylglycerol binding domain (C1 domain) 175 221 3.6E-9
2 g8869.t1 Pfam PF07714 Protein tyrosine and serine/threonine kinase 351 601 7.1E-58
25 g8869.t1 ProSitePatterns PS00479 Zinc finger phorbol-ester/DAG-type signature. 175 220 -
26 g8869.t1 ProSitePatterns PS00107 Protein kinases ATP-binding region signature. 354 374 -
24 g8869.t1 ProSitePatterns PS00108 Serine/Threonine protein kinases active-site signature. 463 475 -
29 g8869.t1 ProSiteProfiles PS50898 Ras-binding domain (RBD) profile. 91 164 22.176
30 g8869.t1 ProSiteProfiles PS50081 Zinc finger phorbol-ester/DAG-type profile. 174 220 13.49
31 g8869.t1 ProSiteProfiles PS50011 Protein kinase domain profile. 348 606 42.746
21 g8869.t1 SMART SM00455 RBD_5 91 164 2.0E-16
23 g8869.t1 SMART SM00109 c1_12 175 220 2.3E-9
22 g8869.t1 SMART SM00220 serkin_6 348 606 4.2E-53
11 g8869.t1 SUPERFAMILY SSF54236 Ubiquitin-like 91 163 2.38E-19
10 g8869.t1 SUPERFAMILY SSF57889 Cysteine-rich domain 156 221 1.94E-12
12 g8869.t1 SUPERFAMILY SSF56112 Protein kinase-like (PK-like) 340 608 1.01E-72

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:0007165 signal transduction BP
GO:0005524 ATP binding MF
GO:0004672 protein kinase activity MF
GO:0006468 protein phosphorylation BP
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