Gene loci information

Transcript annotation

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

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 g5091 g5091.t6 TSS g5091.t6 6840236 6840236
chr_2 g5091 g5091.t6 isoform g5091.t6 6840504 6844872
chr_2 g5091 g5091.t6 exon g5091.t6.exon1 6840504 6840592
chr_2 g5091 g5091.t6 cds g5091.t6.CDS1 6840504 6840592
chr_2 g5091 g5091.t6 exon g5091.t6.exon2 6840681 6840904
chr_2 g5091 g5091.t6 cds g5091.t6.CDS2 6840681 6840904
chr_2 g5091 g5091.t6 exon g5091.t6.exon3 6840991 6841117
chr_2 g5091 g5091.t6 cds g5091.t6.CDS3 6840991 6841117
chr_2 g5091 g5091.t6 exon g5091.t6.exon4 6841175 6841368
chr_2 g5091 g5091.t6 cds g5091.t6.CDS4 6841175 6841368
chr_2 g5091 g5091.t6 exon g5091.t6.exon5 6842063 6842272
chr_2 g5091 g5091.t6 cds g5091.t6.CDS5 6842063 6842272
chr_2 g5091 g5091.t6 exon g5091.t6.exon6 6844253 6844872
chr_2 g5091 g5091.t6 cds g5091.t6.CDS6 6844253 6844872
chr_2 g5091 g5091.t6 TTS g5091.t6 6845082 6845082

Sequences

>g5091.t6 Gene=g5091 Length=1464
ATGACATCACAAGGCTCGAGCGAGGTAACTCGGGAATTTGTTGAAAATTGGAATCTATGT
CAGACCCTTGGAGAAGGAGCTTATGGAGAAGTTAAACTTTTAATTAATAAAAACACGAGT
GAAGCTATAGCTATGAAAATGGTAGATTTAGAGAGACATCCAGATGCTATGGCATCAGTT
AAGAAAGAAGTATGCATACAGAAAATTCTCTCTCATAAGCACATTTTAAAGTTCTATGGC
AAACGCTCACAAAACAATATTGAGTACATATTTCTTGAATATGCAGCGGGTGGAGAGTTG
TTTGATCGAATCGAACCTGATGTTGGCATGGAAATTACTCAAGCTCAACGATATTTCAAT
CAAATATTAGCCGGTGTTGAATATTTACACAAAAGAGGAATAGCACATCGAGATTTGAAA
CCTGAAAATATATTAATAGATGATCATAATAATATAAAGATTTGCGATTTTGGAATGGCC
ACAGTGTACAGATTAAAAGGTCGAGAACGATTGCTGGACAAGAAATGTGGAACAATGCCT
TATGTTGCGCCTGAAGTACTTGTAAAACCATACCATGCTGAGCCTGCTGATCTTTGGGCA
TGTGGCATCATTCTAGTGACTATGCTTGGTGGAGAAGAACTGCCTTGGGACTCTCCTACT
AATGGTGATCGACAATATTTATTATGGAAGGAAAACCAAGCGACAACTCTCACGCCTTGG
ACTAAATTTGATGCTTTGTCACTGAGCTTTTTGAAAAAGATACTTGTGCCAAATCCCGAA
AAAAGATTGACGTTAGAAAAAATGAAGCAGCACAAATGGTGTCAAAATCAAGGCTCAACA
ACAGGTCGATCGCGAGACGTTTGTGATGGTTTGGCGTCACCAGCAGCTAAACGACTGAAA
TCAAATCTAGATTTTTATAACACTAATCTTGACGATAGTCACGCAAGAATGTTTAGTCAT
TCGCAACCGCCACTTTCGTTCTCAAAAGATGAAGACAATGCAGATCTGCTCACGGTTGAA
GCACGTAATGACTATTGCTTTAGTCAGCCAGCTATGTTGGATGATTTATTATTATGCTCT
CAACTTAATGGAACTCAAGGTTCAAATGTTTCAACAAATCCATTCCAAAGACTTGTTAAA
CGTATGACAAGATTCTTCGTATCAACTAAATGTGATGAGACAATCAAACGTTTGACATCT
GTAGTAGATAGATTAGGATGGACATGGAAAATTAATGATAACAGTACTGTAACAATTTCA
ACTGTCGATAGAAGAAAAATTCAACTGATATTCAAGGCAATTTTATTAGAAATGGACGGA
AAACTCTTGGTTGATTTTAGACTTTCAAAAGGCTGTGGTCTCGATTTCAAACGCAATTTC
ATTAAGATAAAAGGTTCAAAAGAAATATCTGAAGCCATTCTTGATATTCCAATTAATTTT
TCATTAGCAACAGCAGTTGTATGA

>g5091.t6 Gene=g5091 Length=487
MTSQGSSEVTREFVENWNLCQTLGEGAYGEVKLLINKNTSEAIAMKMVDLERHPDAMASV
KKEVCIQKILSHKHILKFYGKRSQNNIEYIFLEYAAGGELFDRIEPDVGMEITQAQRYFN
QILAGVEYLHKRGIAHRDLKPENILIDDHNNIKICDFGMATVYRLKGRERLLDKKCGTMP
YVAPEVLVKPYHAEPADLWACGIILVTMLGGEELPWDSPTNGDRQYLLWKENQATTLTPW
TKFDALSLSFLKKILVPNPEKRLTLEKMKQHKWCQNQGSTTGRSRDVCDGLASPAAKRLK
SNLDFYNTNLDDSHARMFSHSQPPLSFSKDEDNADLLTVEARNDYCFSQPAMLDDLLLCS
QLNGTQGSNVSTNPFQRLVKRMTRFFVSTKCDETIKRLTSVVDRLGWTWKINDNSTVTIS
TVDRRKIQLIFKAILLEMDGKLLVDFRLSKGCGLDFKRNFIKIKGSKEISEAILDIPINF
SLATAVV

Protein features from InterProScan

Transcript Database ID Name Start End E.value
7 g5091.t6 CDD cd14069 STKc_Chk1 15 274 3.81919E-148
5 g5091.t6 Gene3D G3DSA:3.30.200.20 Phosphorylase Kinase; domain 1 9 105 1.1E-27
6 g5091.t6 Gene3D G3DSA:1.10.510.10 Transferase(Phosphotransferase) domain 1 107 282 3.1E-49
2 g5091.t6 PANTHER PTHR24346 MAP/MICROTUBULE AFFINITY-REGULATING KINASE 14 301 1.8E-84
3 g5091.t6 PANTHER PTHR24346:SF42 SERINE/THREONINE-PROTEIN KINASE SIK3 14 301 1.8E-84
1 g5091.t6 Pfam PF00069 Protein kinase domain 20 273 2.3E-64
9 g5091.t6 ProSitePatterns PS00107 Protein kinases ATP-binding region signature. 23 46 -
8 g5091.t6 ProSitePatterns PS00108 Serine/Threonine protein kinases active-site signature. 134 146 -
11 g5091.t6 ProSiteProfiles PS50011 Protein kinase domain profile. 17 274 43.806
10 g5091.t6 SMART SM00220 serkin_6 17 274 1.0E-76
4 g5091.t6 SUPERFAMILY SSF56112 Protein kinase-like (PK-like) 13 275 9.98E-73

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g5091/g5091.t6; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5091.t6.fa.iupred3.txt does not exist

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:0000077 DNA damage checkpoint signaling BP
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