Gene loci information

Transcript annotation

  • This transcript has been annotated as Casein kinase II subunit alpha.

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 g10340 g10340.t6 isoform g10340.t6 8942142 8944999
chr_1 g10340 g10340.t6 exon g10340.t6.exon1 8942142 8942377
chr_1 g10340 g10340.t6 exon g10340.t6.exon2 8942443 8942574
chr_1 g10340 g10340.t6 exon g10340.t6.exon3 8943100 8944062
chr_1 g10340 g10340.t6 cds g10340.t6.CDS1 8943237 8944062
chr_1 g10340 g10340.t6 exon g10340.t6.exon4 8944126 8944999
chr_1 g10340 g10340.t6 cds g10340.t6.CDS2 8944126 8944259
chr_1 g10340 g10340.t6 TSS g10340.t6 NA NA
chr_1 g10340 g10340.t6 TTS g10340.t6 NA NA

Sequences

>g10340.t6 Gene=g10340 Length=2205
ATGAATGTAAGTTGAATAGTTTTGCAGAATATTAGCAATAAAAATGCTGCTTTTGTTAAA
ATTAACTGAATAAAAAATTTCAAATTCCGGCTGAGCAGCAGTAAAAAAAGTTGTTTCCCC
TGTCTGCCATTTGGAGGAAAAAAATTGCCGAAAAATTAAAATTCAGTTTTTTAAAAAGTT
TTAAACATATTTTGAGCCATTTTTAATAATTTGATAGAACAAGTGGGAGCTTAATGAGCT
AATTTCTTCTGTCATCCGCGAACGAGAGAGAGTATCTAATTCGTCGTCCATTTTGCTCAT
CCCAATCGAGTTTAGAAAATTTCAATTGAATTACTGAGAAGAAGTGCAAGCTAGCCCAAC
ATAAGAAGGAACTTCAACATCTACAGTCGGGAATAATAGTTCTCCACACTATCCGTTTAT
AGTCTCATCGAGCACTACCACCACAACAGCAACTAACACCGCAACATCAACGATAAATAT
TTTTAGTTATCGTCGCAGATCAACAATGACATTACCTTCAAATGCACGAGTGTATGCTGA
TGTCAATTCGCATAAGCCGCGAGAGTATTGGGATTATGAAAACTATGTTGTAGACTGGGC
AAATCAGGATGACTATCAATTAGTTAGAAAACTCGGTCGGGGTAAATATAGTGAAGTTTT
TGAGGCAATTAACGTCACCAATAATGAAAAGTGCGTCGTAAAAATCCTTAAACCAGTAAA
GAAGAAGAAGATCAAACGAGAAATCAAAATTCTAGAAAATTTGAGAGGTGGAACTAACAT
CATTACACTTCTTGCAGTTGTCAAAGATCCAGTTTCACGTACACCAGCGCTCATTTTCGA
GCATGTCAACAATACAGATTTTAAACAGCTCTATCAAACACTCACTGACTACGACATTCG
TTTCTATCTTTATGAGCTGTTGAAAGCATTAGATTATTGTCATAGTATGGGCATTATGCA
TCGCGATGTTAAGCCACATAATGTAATGATAGACCATGAGAATCGAAAGTTGCGACTAAT
TGATTGGGGTCTCGCTGAATTTTATCATCCGGGACAAGAGTACAATGTTCGAGTTGCTAG
TCGTTATTTCAAAGGACCCGAGTTGCTCGTCGATTATCAAATGTATGATTATTCATTGGA
TATGTGGTCACTTGGCTGCATGTTGGCTTCTATGATCTTTCGTAAAGAACCGTTCTTTCA
TGGTCATGATAATTACGATCAATTGGTGAGAATTGCAAAAGTTCTTGGTACTGAGGAGTT
ATATGCTTATTTGGATAAATACAATATTGAACTTGATCCGCGTTTCAATGACATCTTATC
GAGACATTCACATTTTCTCGATAAGCTTCTTCGCTATGATCATTGTGCTCGATTAACTGC
ACGCGAAGCAATGGATCATCCATATTTTGCTGTTATCGTCAATGGACAATTACCACACGC
GGGATCATTTAAAGGCAGCAATTAATAGACTACTACTATATAAAATTATTTCTTTCTTTT
GCTACTACAACAATTTGCGCATCACTGTGCTCCTTTCGATGGCGGTCAATGATCATCATC
TTAATTCTTTATTTTGTCAATAATAATCACATAATTTTTTTCAATTTAACAAAATGAAAT
TATTTTTAAACTTTTTACTCAAGTCTATGTAGTAAAGAAAAAAGTGGGAGACATTCTCTT
TTCTATCATTTTCTTTGAAAATTGAAAAAAACTGATTATCTCATTTCATATGTGTACTTT
CCGTGAATTATTATATTATTAACAAGACAAACAGCAACAACAAATTTTATATTAATATTT
AATTATGATGAATTTTTTAATAATTGAATCAATGATTAAGAAAAAAAAATATAATTTTAT
TTTTCTCATAAAAATTTACTTTTTATTTTTCTCATAAATGCGTTGACGTCGTTGTACAAA
AACGCATATAATGAAAGTTGTAAGGAAGCAAATTTGAAATGAAATCAAAATTTACAAAAG
AAGTGAGAAAAAAAATTATCTGTTCGAAAAGCCTCTTAAGGCAAGCTGCCGATTATCATC
AATGAGAATCCTTCTTCTGTTATATTTTAAAGCATAGTTATTGTGAAATAATAAAAAAAA
AACAATTTGATTTTAATGCTAAAGCGCATAAAAATGATAAATTTGAGAGGATGTCGTAAA
TAAAATTTACGCGATGTTTCAATCTATTCATTATTATCTCTCTTG

>g10340.t6 Gene=g10340 Length=319
MTLPSNARVYADVNSHKPREYWDYENYVVDWANQDDYQLVRKLGRGKYSEVFEAINVTNN
EKCVVKILKPVKKKKIKREIKILENLRGGTNIITLLAVVKDPVSRTPALIFEHVNNTDFK
QLYQTLTDYDIRFYLYELLKALDYCHSMGIMHRDVKPHNVMIDHENRKLRLIDWGLAEFY
HPGQEYNVRVASRYFKGPELLVDYQMYDYSLDMWSLGCMLASMIFRKEPFFHGHDNYDQL
VRIAKVLGTEELYAYLDKYNIELDPRFNDILSRHSHFLDKLLRYDHCARLTAREAMDHPY
FAVIVNGQLPHAGSFKGSN

Protein features from InterProScan

Transcript Database ID Name Start End E.value
9 g10340.t6 CDD cd14132 STKc_CK2_alpha 18 301 0.0
7 g10340.t6 Gene3D G3DSA:3.30.200.20 Phosphorylase Kinase; domain 1 23 110 3.1E-40
8 g10340.t6 Gene3D G3DSA:1.10.510.10 Transferase(Phosphotransferase) domain 1 111 306 4.3E-59
3 g10340.t6 PANTHER PTHR24054 CASEIN KINASE II SUBUNIT ALPHA 3 275 1.5E-193
5 g10340.t6 PANTHER PTHR24054:SF28 CASEIN KINASE 2 ALPHA 1-RELATED 3 275 1.5E-193
2 g10340.t6 PANTHER PTHR24054 CASEIN KINASE II SUBUNIT ALPHA 276 309 1.5E-193
4 g10340.t6 PANTHER PTHR24054:SF28 CASEIN KINASE 2 ALPHA 1-RELATED 276 309 1.5E-193
1 g10340.t6 Pfam PF00069 Protein kinase domain 37 301 1.9E-67
11 g10340.t6 ProSitePatterns PS00107 Protein kinases ATP-binding region signature. 43 66 -
10 g10340.t6 ProSitePatterns PS00108 Serine/Threonine protein kinases active-site signature. 150 162 -
13 g10340.t6 ProSiteProfiles PS50011 Protein kinase domain profile. 37 301 42.393
12 g10340.t6 SMART SM00220 serkin_6 37 301 4.7E-68
6 g10340.t6 SUPERFAMILY SSF56112 Protein kinase-like (PK-like) 8 302 7.69E-74

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: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