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.t1 TSS g12215.t1 21781945 21781945
chr_1 g12215 g12215.t1 isoform g12215.t1 21782025 21783767
chr_1 g12215 g12215.t1 exon g12215.t1.exon1 21782025 21782090
chr_1 g12215 g12215.t1 cds g12215.t1.CDS1 21782025 21782090
chr_1 g12215 g12215.t1 exon g12215.t1.exon2 21782150 21782291
chr_1 g12215 g12215.t1 cds g12215.t1.CDS2 21782150 21782291
chr_1 g12215 g12215.t1 exon g12215.t1.exon3 21782347 21783767
chr_1 g12215 g12215.t1 cds g12215.t1.CDS3 21782347 21783767
chr_1 g12215 g12215.t1 TTS g12215.t1 21783819 21783819

Sequences

>g12215.t1 Gene=g12215 Length=1629
ATGGGTAAATTAAATGTGACAGTTCTTCGTTATCTCTCAAAAGAGGATTTTAGAGTATTG
ACAGCGATTGAGATGCTTTCTAAAAATCATGAATTATGTCCTGGATCAATGGTAGCAGTA
GTCGCAAACCTCAAATCAGGTGGTGTACATAAATTACTAAAAGAATTATGCAAACATAAG
CTTGTTTCATATGAAAGAGGAGCAAAATATGACGGTTTTCGTTTGACAAACACGGGATAC
GATTATTTAGCATTAAAAGCACTCACATTACGAGGATCAATCTATTCTTTTGGTACTCAA
ATTGGCGTTGGTAAAGAATCAAATATTTACACAGTTTCAGATGAAGAAGGCAAACAACTT
TGTCTAAAACTCCATCGTCTTGGTCGTACATGCTTCAGAAACGTTAGAAATAAGAGAGAT
TATCATGGTAAAAGAAAGAAGACATCATGGCTTTATTTATCAAGAATATCAGCCACAAGA
GAATTTGCTTATATGAAAGCACTTTATGATCGCGGCTTTCCAGTACCAAAACCAATTGAT
TTCAATCGTCATTGTGTCATTATGGAGCTCATTAATGGTTATCCTATGACTCAAATCAAT
GAAGTTATTGATATTGATCAACTCTACGATGATTTAATGAATTTAATTGTACGCTTGGGA
AATTGTGGAGTTATTCATGGCGATTTCAATGAATTTAACATTCTCGTAACTGATGAAGCT
AAACCAATTCTAATTGATTTTCCTCAAATGGTATCTACGTCACATGAAAATGCAAAAATG
TTCTTCGAGCGTGATGTCAATGGTGTTAGAGATCTATTTAAAAAGAAGTTTGGCTATGAA
AGTGAAGATTATCCAAAATTCGAAGATTTAGAACGAGAAGATGATCTCGATATTGAAGTA
GCATGCAGTGGCTTTACAAAAGAGATGGAAAAAGATTTAATGGACGAATATCACGGAAGT
GAGCTTGATGATGAAATTGATGATGTTTCGAATAGTGATGATGGTGAAAATGAGCCAGAA
GATGATGAAGAAATGATAAATCAATATAAGAAGCAAGTTGAGAATGAAGTTAAATACTCA
GAGCAATCAGTCAAGAATAAGAGTGAGGCTGATAAGAATAATGGTATTTTAAAATACATG
GAATCTATGTCAAAACACACAGAATTCGATAAAGCTTTCAATGATGATGAAGAGGATGAA
TTTAAAGATGCTTTGAGTGAACTAAATATTAGTGATTCACCTTCTAAAAGCACTGAAACA
AATATCCTATCGAAACCTACCACTACTAAGGTTGAAAATGAAGACGATGATGCAAAATCA
ATAAGTTCAAATGAACTTGATTTACCTGAAATGGATGATGAACTTAAAGATTTAGATCCA
AATTCTAGAGAATATAGAATGAAAATGGTTCGAAAAATTCTTTCAGATGCACGAAGTCAA
AGGAGTTATTCGACCACAGCTTCTACAATTGCACCAAGTGTCATTACCGATCGTGTTAAA
AAAGTAATTGATGCAAATGCAAAGAAACAACTCAATAGAAGAATCGTTCCTAAAGGTCAA
ACAAGTGCAGTTCGTCGAATGAGAATAGAAAACAAAGATGTAATAAAAGATTTCGCTGGT
TGGATTTAA

>g12215.t1 Gene=g12215 Length=542
MGKLNVTVLRYLSKEDFRVLTAIEMLSKNHELCPGSMVAVVANLKSGGVHKLLKELCKHK
LVSYERGAKYDGFRLTNTGYDYLALKALTLRGSIYSFGTQIGVGKESNIYTVSDEEGKQL
CLKLHRLGRTCFRNVRNKRDYHGKRKKTSWLYLSRISATREFAYMKALYDRGFPVPKPID
FNRHCVIMELINGYPMTQINEVIDIDQLYDDLMNLIVRLGNCGVIHGDFNEFNILVTDEA
KPILIDFPQMVSTSHENAKMFFERDVNGVRDLFKKKFGYESEDYPKFEDLEREDDLDIEV
ACSGFTKEMEKDLMDEYHGSELDDEIDDVSNSDDGENEPEDDEEMINQYKKQVENEVKYS
EQSVKNKSEADKNNGILKYMESMSKHTEFDKAFNDDEEDEFKDALSELNISDSPSKSTET
NILSKPTTTKVENEDDDAKSISSNELDLPEMDDELKDLDPNSREYRMKMVRKILSDARSQ
RSYSTTASTIAPSVITDRVKKVIDANAKKQLNRRIVPKGQTSAVRRMRIENKDVIKDFAG
WI

Protein features from InterProScan

Transcript Database ID Name Start End E.value
10 g12215.t1 CDD cd05144 RIO2_C 94 276 8.87221E-115
9 g12215.t1 Gene3D G3DSA:1.10.10.10 winged helix repressor DNA binding domain 2 92 1.8E-33
7 g12215.t1 Gene3D G3DSA:3.30.200.20 Phosphorylase Kinase; domain 1 94 193 1.8E-46
8 g12215.t1 Gene3D G3DSA:1.10.510.10 Transferase(Phosphotransferase) domain 1 194 324 3.2E-46
15 g12215.t1 MobiDBLite mobidb-lite consensus disorder prediction 321 344 -
16 g12215.t1 MobiDBLite mobidb-lite consensus disorder prediction 321 343 -
14 g12215.t1 MobiDBLite mobidb-lite consensus disorder prediction 407 452 -
17 g12215.t1 MobiDBLite mobidb-lite consensus disorder prediction 408 428 -
13 g12215.t1 MobiDBLite mobidb-lite consensus disorder prediction 429 443 -
3 g12215.t1 PANTHER PTHR45852:SF1 SERINE/THREONINE-PROTEIN KINASE RIO2 1 417 9.7E-158
4 g12215.t1 PANTHER PTHR45852 SER/THR-PROTEIN KINASE RIO2 1 417 9.7E-158
1 g12215.t1 Pfam PF09202 Rio2, N-terminal 9 90 6.0E-30
2 g12215.t1 Pfam PF01163 RIO1 family 108 279 1.1E-53
11 g12215.t1 ProSitePatterns PS01245 RIO1/ZK632.3/MJ0444 family signature. 224 235 -
12 g12215.t1 SMART SM00090 rio_2 66 289 1.2E-55
5 g12215.t1 SUPERFAMILY SSF46785 Winged helix DNA-binding domain 6 92 3.32E-21
6 g12215.t1 SUPERFAMILY SSF56112 Protein kinase-like (PK-like) 95 270 1.37E-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