Gene loci information

Transcript annotation

  • This transcript has been annotated as Serine/threonine-protein kinase RIO2.

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_1 g12215 g12215.t4 TSS g12215.t4 21781945 21781945
chr_1 g12215 g12215.t4 isoform g12215.t4 21782025 21783767
chr_1 g12215 g12215.t4 exon g12215.t4.exon1 21782025 21782291
chr_1 g12215 g12215.t4 cds g12215.t4.CDS1 21782156 21782291
chr_1 g12215 g12215.t4 exon g12215.t4.exon2 21782347 21783767
chr_1 g12215 g12215.t4 cds g12215.t4.CDS2 21782347 21783767
chr_1 g12215 g12215.t4 TTS g12215.t4 21783819 21783819

Sequences

>g12215.t4 Gene=g12215 Length=1688
ATGGGTAAATTAAATGTGACAGTTCTTCGTTATCTCTCAAAAGAGGATTTTAGAGTATTG
ACAGCGGTATGTAACTTGTTAGATTGTGAATTTTAATATTTTCTCATAAGCACATGTTTA
TACAGATTGAGATGCTTTCTAAAAATCATGAATTATGTCCTGGATCAATGGTAGCAGTAG
TCGCAAACCTCAAATCAGGTGGTGTACATAAATTACTAAAAGAATTATGCAAACATAAGC
TTGTTTCATATGAAAGAGGAGCAAAATATGACGGTTTTCGTTTGACAAACACGGGATACG
ATTATTTAGCATTAAAAGCACTCACATTACGAGGATCAATCTATTCTTTTGGTACTCAAA
TTGGCGTTGGTAAAGAATCAAATATTTACACAGTTTCAGATGAAGAAGGCAAACAACTTT
GTCTAAAACTCCATCGTCTTGGTCGTACATGCTTCAGAAACGTTAGAAATAAGAGAGATT
ATCATGGTAAAAGAAAGAAGACATCATGGCTTTATTTATCAAGAATATCAGCCACAAGAG
AATTTGCTTATATGAAAGCACTTTATGATCGCGGCTTTCCAGTACCAAAACCAATTGATT
TCAATCGTCATTGTGTCATTATGGAGCTCATTAATGGTTATCCTATGACTCAAATCAATG
AAGTTATTGATATTGATCAACTCTACGATGATTTAATGAATTTAATTGTACGCTTGGGAA
ATTGTGGAGTTATTCATGGCGATTTCAATGAATTTAACATTCTCGTAACTGATGAAGCTA
AACCAATTCTAATTGATTTTCCTCAAATGGTATCTACGTCACATGAAAATGCAAAAATGT
TCTTCGAGCGTGATGTCAATGGTGTTAGAGATCTATTTAAAAAGAAGTTTGGCTATGAAA
GTGAAGATTATCCAAAATTCGAAGATTTAGAACGAGAAGATGATCTCGATATTGAAGTAG
CATGCAGTGGCTTTACAAAAGAGATGGAAAAAGATTTAATGGACGAATATCACGGAAGTG
AGCTTGATGATGAAATTGATGATGTTTCGAATAGTGATGATGGTGAAAATGAGCCAGAAG
ATGATGAAGAAATGATAAATCAATATAAGAAGCAAGTTGAGAATGAAGTTAAATACTCAG
AGCAATCAGTCAAGAATAAGAGTGAGGCTGATAAGAATAATGGTATTTTAAAATACATGG
AATCTATGTCAAAACACACAGAATTCGATAAAGCTTTCAATGATGATGAAGAGGATGAAT
TTAAAGATGCTTTGAGTGAACTAAATATTAGTGATTCACCTTCTAAAAGCACTGAAACAA
ATATCCTATCGAAACCTACCACTACTAAGGTTGAAAATGAAGACGATGATGCAAAATCAA
TAAGTTCAAATGAACTTGATTTACCTGAAATGGATGATGAACTTAAAGATTTAGATCCAA
ATTCTAGAGAATATAGAATGAAAATGGTTCGAAAAATTCTTTCAGATGCACGAAGTCAAA
GGAGTTATTCGACCACAGCTTCTACAATTGCACCAAGTGTCATTACCGATCGTGTTAAAA
AAGTAATTGATGCAAATGCAAAGAAACAACTCAATAGAAGAATCGTTCCTAAAGGTCAAA
CAAGTGCAGTTCGTCGAATGAGAATAGAAAACAAAGATGTAATAAAAGATTTCGCTGGTT
GGATTTAA

>g12215.t4 Gene=g12215 Length=518
MLSKNHELCPGSMVAVVANLKSGGVHKLLKELCKHKLVSYERGAKYDGFRLTNTGYDYLA
LKALTLRGSIYSFGTQIGVGKESNIYTVSDEEGKQLCLKLHRLGRTCFRNVRNKRDYHGK
RKKTSWLYLSRISATREFAYMKALYDRGFPVPKPIDFNRHCVIMELINGYPMTQINEVID
IDQLYDDLMNLIVRLGNCGVIHGDFNEFNILVTDEAKPILIDFPQMVSTSHENAKMFFER
DVNGVRDLFKKKFGYESEDYPKFEDLEREDDLDIEVACSGFTKEMEKDLMDEYHGSELDD
EIDDVSNSDDGENEPEDDEEMINQYKKQVENEVKYSEQSVKNKSEADKNNGILKYMESMS
KHTEFDKAFNDDEEDEFKDALSELNISDSPSKSTETNILSKPTTTKVENEDDDAKSISSN
ELDLPEMDDELKDLDPNSREYRMKMVRKILSDARSQRSYSTTASTIAPSVITDRVKKVID
ANAKKQLNRRIVPKGQTSAVRRMRIENKDVIKDFAGWI

Protein features from InterProScan

Transcript Database ID Name Start End E.value
10 g12215.t4 CDD cd05144 RIO2_C 70 252 3.69336E-115
9 g12215.t4 Gene3D G3DSA:1.10.10.10 winged helix repressor DNA binding domain 1 68 2.2E-20
7 g12215.t4 Gene3D G3DSA:3.30.200.20 Phosphorylase Kinase; domain 1 70 169 1.7E-46
8 g12215.t4 Gene3D G3DSA:1.10.510.10 Transferase(Phosphotransferase) domain 1 170 300 3.0E-46
14 g12215.t4 MobiDBLite mobidb-lite consensus disorder prediction 297 320 -
17 g12215.t4 MobiDBLite mobidb-lite consensus disorder prediction 297 319 -
16 g12215.t4 MobiDBLite mobidb-lite consensus disorder prediction 383 428 -
15 g12215.t4 MobiDBLite mobidb-lite consensus disorder prediction 384 404 -
13 g12215.t4 MobiDBLite mobidb-lite consensus disorder prediction 405 419 -
3 g12215.t4 PANTHER PTHR45852:SF1 SERINE/THREONINE-PROTEIN KINASE RIO2 1 393 1.5E-144
4 g12215.t4 PANTHER PTHR45852 SER/THR-PROTEIN KINASE RIO2 1 393 1.5E-144
1 g12215.t4 Pfam PF09202 Rio2, N-terminal 1 66 2.2E-19
2 g12215.t4 Pfam PF01163 RIO1 family 84 255 9.9E-54
11 g12215.t4 ProSitePatterns PS01245 RIO1/ZK632.3/MJ0444 family signature. 200 211 -
12 g12215.t4 SMART SM00090 rio_2 42 265 1.2E-55
5 g12215.t4 SUPERFAMILY SSF46785 Winged helix DNA-binding domain 2 68 1.33E-12
6 g12215.t4 SUPERFAMILY SSF56112 Protein kinase-like (PK-like) 71 246 1.24E-30

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:0005524 ATP binding MF
GO:0004674 protein serine/threonine kinase activity MF
GO:0004672 protein kinase activity MF
GO:0006468 protein phosphorylation 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