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.t3 TSS g12215.t3 21781945 21781945
chr_1 g12215 g12215.t3 isoform g12215.t3 21782025 21782961
chr_1 g12215 g12215.t3 exon g12215.t3.exon1 21782025 21782094
chr_1 g12215 g12215.t3 exon g12215.t3.exon2 21782150 21782291
chr_1 g12215 g12215.t3 cds g12215.t3.CDS1 21782156 21782291
chr_1 g12215 g12215.t3 exon g12215.t3.exon3 21782347 21782961
chr_1 g12215 g12215.t3 cds g12215.t3.CDS2 21782347 21782960
chr_1 g12215 g12215.t3 TTS g12215.t3 21783819 21783819

Sequences

>g12215.t3 Gene=g12215 Length=827
ATGGGTAAATTAAATGTGACAGTTCTTCGTTATCTCTCAAAAGAGGATTTTAGAGTATTG
ACAGCGGTATATTGAGATGCTTTCTAAAAATCATGAATTATGTCCTGGATCAATGGTAGC
AGTAGTCGCAAACCTCAAATCAGGTGGTGTACATAAATTACTAAAAGAATTATGCAAACA
TAAGCTTGTTTCATATGAAAGAGGAGCAAAATATGACGGTTTTCGTTTGACAAACACGGG
ATACGATTATTTAGCATTAAAAGCACTCACATTACGAGGATCAATCTATTCTTTTGGTAC
TCAAATTGGCGTTGGTAAAGAATCAAATATTTACACAGTTTCAGATGAAGAAGGCAAACA
ACTTTGTCTAAAACTCCATCGTCTTGGTCGTACATGCTTCAGAAACGTTAGAAATAAGAG
AGATTATCATGGTAAAAGAAAGAAGACATCATGGCTTTATTTATCAAGAATATCAGCCAC
AAGAGAATTTGCTTATATGAAAGCACTTTATGATCGCGGCTTTCCAGTACCAAAACCAAT
TGATTTCAATCGTCATTGTGTCATTATGGAGCTCATTAATGGTTATCCTATGACTCAAAT
CAATGAAGTTATTGATATTGATCAACTCTACGATGATTTAATGAATTTAATTGTACGCTT
GGGAAATTGTGGAGTTATTCATGGCGATTTCAATGAATTTAACATTCTCGTAACTGATGA
AGCTAAACCAATTCTAATTGATTTTCCTCAAATGGTATCTACGTCACATGAAAATGCAAA
AATGTTCTTCGAGCGTGATGTCAATGGTGTTAGAGATCTATTTAAAA

>g12215.t3 Gene=g12215 Length=250
MLSKNHELCPGSMVAVVANLKSGGVHKLLKELCKHKLVSYERGAKYDGFRLTNTGYDYLA
LKALTLRGSIYSFGTQIGVGKESNIYTVSDEEGKQLCLKLHRLGRTCFRNVRNKRDYHGK
RKKTSWLYLSRISATREFAYMKALYDRGFPVPKPIDFNRHCVIMELINGYPMTQINEVID
IDQLYDDLMNLIVRLGNCGVIHGDFNEFNILVTDEAKPILIDFPQMVSTSHENAKMFFER
DVNGVRDLFK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
12 g12215.t3 CDD cd05144 RIO2_C 70 250 2.27147E-117
11 g12215.t3 Gene3D G3DSA:1.10.10.10 winged helix repressor DNA binding domain 1 68 6.7E-21
9 g12215.t3 Gene3D G3DSA:3.30.200.20 Phosphorylase Kinase; domain 1 70 169 4.2E-47
10 g12215.t3 Gene3D G3DSA:1.10.510.10 Transferase(Phosphotransferase) domain 1 170 250 2.5E-34
3 g12215.t3 PANTHER PTHR45852:SF1 SERINE/THREONINE-PROTEIN KINASE RIO2 1 250 2.7E-126
4 g12215.t3 PANTHER PTHR45852 SER/THR-PROTEIN KINASE RIO2 1 250 2.7E-126
1 g12215.t3 Pfam PF09202 Rio2, N-terminal 1 66 6.9E-20
2 g12215.t3 Pfam PF01163 RIO1 family 84 250 1.7E-52
8 g12215.t3 ProSitePatterns PS01245 RIO1/ZK632.3/MJ0444 family signature. 200 211 -
7 g12215.t3 SMART SM00090 rio_2 42 250 7.6E-46
5 g12215.t3 SUPERFAMILY SSF46785 Winged helix DNA-binding domain 2 68 2.83E-13
6 g12215.t3 SUPERFAMILY SSF56112 Protein kinase-like (PK-like) 71 246 2.29E-31

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