Gene loci information

Transcript annotation

  • This transcript has been annotated as Calcium/calmodulin-dependent protein kinase kinase 1.

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 g11565 g11565.t1 isoform g11565.t1 17163130 17165709
chr_1 g11565 g11565.t1 exon g11565.t1.exon1 17163130 17163468
chr_1 g11565 g11565.t1 cds g11565.t1.CDS1 17163130 17163468
chr_1 g11565 g11565.t1 exon g11565.t1.exon2 17163688 17163889
chr_1 g11565 g11565.t1 cds g11565.t1.CDS2 17163688 17163889
chr_1 g11565 g11565.t1 exon g11565.t1.exon3 17163947 17164178
chr_1 g11565 g11565.t1 cds g11565.t1.CDS3 17163947 17164178
chr_1 g11565 g11565.t1 exon g11565.t1.exon4 17164264 17164392
chr_1 g11565 g11565.t1 cds g11565.t1.CDS4 17164264 17164392
chr_1 g11565 g11565.t1 exon g11565.t1.exon5 17164452 17164689
chr_1 g11565 g11565.t1 cds g11565.t1.CDS5 17164452 17164689
chr_1 g11565 g11565.t1 exon g11565.t1.exon6 17165204 17165562
chr_1 g11565 g11565.t1 cds g11565.t1.CDS6 17165204 17165562
chr_1 g11565 g11565.t1 exon g11565.t1.exon7 17165643 17165709
chr_1 g11565 g11565.t1 cds g11565.t1.CDS7 17165643 17165709
chr_1 g11565 g11565.t1 TSS g11565.t1 17166616 17166616
chr_1 g11565 g11565.t1 TTS g11565.t1 NA NA

Sequences

>g11565.t1 Gene=g11565 Length=1566
ATGGACGATAATAGTAAATTGTCAAATGAGTTTGTGCTAGCAAGTGATACAGTCTCGAGT
AAAGACGATGTTACACATCCTTATAATCGCTTGAAAACCATGTATTGTAAATTCATGCCA
AAAAAGACCCAGTCATTAGATATCGATGAGTCCACTATTGCCAATAATTTTCCCACTCAA
AATTGCTTTGAGTCAATTAATGAAGAGAAAATAATGACAGATTCATTAGGCGAGACTTCT
GATCGTCAAAAGAAGACTGTCACCGGATGTCAAACACGACCAATTTTTCCCAACTTGAGC
TATAGTCCGTTATCGAGTCCGCGAATAACAAGAAAACCAGCTAAGGAATCGAGACACATC
TCAATTGACAAAAATGGAAGTTTTATGCAACTTAATCAATATAGGTTAATGGAGCAAATT
GGAGTTGGCTCATATGGTTATGTGAAAATGGCATATAATGAAGAAGAAGATCAGCATTAT
GCAATGAAAATATTATCAAAAAAGAAGCTGATACGAAAAGCAGGAATTGGACTTAATCGA
GGGCATCCAAAAAGAGGGAATAATATTGCAACTCAAACTACTCCACTCGATAGAGTTTAT
AGGGAAATTGCTGTATTAAAGAAACTTGACCATCCAAATGTTGTTAGGCTGATTGAAGTT
TTAGATGATCCAATTGAAGATGCATTATATATGGTTTTTGAGCTTATAAGTTATGGTGAA
GTTCTTAAAATTCCTACAAACACTCCACTCTCAGAGGAACGTGCATGGTTAATATTTCGT
CAAGTTATTTTAGGTGTTGAATATTTATTTTTAAATAAAATAATTCATGGAGATTTGAAG
CCTGAAAATTTGTTACTCGCTGCCGATGATGTAGTTAAGGTAGCTGATTTAGGTGTGTGT
AATGAATTCCTAGGCGATGATGCACAAATCGATCAACGTACGGCAAGCGGTACACCAGCA
TTTCGTGCTCCCGAGACGTTGTCGGGACAAAATATGTATTTCGATGGAAAAAAAGCAGAT
ATTTGGTCCTTGGGTGTTACGCTTTTCTCATTTGTATATGGTGATATTCCATGGCGATGC
AATTCTATACCTGTTTTATATGAACAAATCAAGAATAATGAAGTAATTTTCCCACAAAAG
ATTAAAATTAGTGAAGAGCTCAAAGATTTAATTTCGCTAATGTTGGAAAAAGATCCCATA
AAGCGAATTAGTTTGGAGCTAGTGAAGGAACATAAATGGGTAACAAAATATGGACAATTT
CCAATGCCATGTCAAGATGATTGTACAAAACCTGTCGAAATTAGTCAAGAAGATATTAAT
TCCGTTGTGAAAAGCATTCCAAAGCTTGATACTCTAATTCTTATCAAAAAGATGCTGAAA
AATCATTCATTTCAAAATCCATTTTTATCGGCTGGGACAAGCGTAGCAAAGAATCTTGCT
AGTAGACTCTCAAAATTGGAGAGATTTCAAAATAACCGATCAAACTCAGCACCTGGCAAT
TATGAAGCATTATCGCCACCATCTCATTCCTCATCCACGTCTCAAAATGAGCTTAATCAA
ACCTAA

>g11565.t1 Gene=g11565 Length=521
MDDNSKLSNEFVLASDTVSSKDDVTHPYNRLKTMYCKFMPKKTQSLDIDESTIANNFPTQ
NCFESINEEKIMTDSLGETSDRQKKTVTGCQTRPIFPNLSYSPLSSPRITRKPAKESRHI
SIDKNGSFMQLNQYRLMEQIGVGSYGYVKMAYNEEEDQHYAMKILSKKKLIRKAGIGLNR
GHPKRGNNIATQTTPLDRVYREIAVLKKLDHPNVVRLIEVLDDPIEDALYMVFELISYGE
VLKIPTNTPLSEERAWLIFRQVILGVEYLFLNKIIHGDLKPENLLLAADDVVKVADLGVC
NEFLGDDAQIDQRTASGTPAFRAPETLSGQNMYFDGKKADIWSLGVTLFSFVYGDIPWRC
NSIPVLYEQIKNNEVIFPQKIKISEELKDLISLMLEKDPIKRISLELVKEHKWVTKYGQF
PMPCQDDCTKPVEISQEDINSVVKSIPKLDTLILIKKMLKNHSFQNPFLSAGTSVAKNLA
SRLSKLERFQNNRSNSAPGNYEALSPPSHSSSTSQNELNQT

Protein features from InterProScan

Transcript Database ID Name Start End E.value
5 g11565.t1 Gene3D G3DSA:3.30.200.20 Phosphorylase Kinase; domain 1 121 235 2.8E-29
6 g11565.t1 Gene3D G3DSA:1.10.510.10 Transferase(Phosphotransferase) domain 1 237 416 3.1E-52
10 g11565.t1 MobiDBLite mobidb-lite consensus disorder prediction 490 521 -
2 g11565.t1 PANTHER PTHR43895:SF26 CALCIUM/CALMODULIN-DEPENDENT PROTEIN KINASE KINASE 1, ALPHA A-RELATED 103 478 8.6E-130
3 g11565.t1 PANTHER PTHR43895 - 103 478 8.6E-130
1 g11565.t1 Pfam PF00069 Protein kinase domain 134 414 3.6E-56
8 g11565.t1 ProSitePatterns PS00107 Protein kinases ATP-binding region signature. 140 173 -
7 g11565.t1 ProSitePatterns PS00108 Serine/Threonine protein kinases active-site signature. 274 286 -
11 g11565.t1 ProSiteProfiles PS50011 Protein kinase domain profile. 134 414 44.64
9 g11565.t1 SMART SM00220 serkin_6 134 414 3.5E-80
4 g11565.t1 SUPERFAMILY SSF56112 Protein kinase-like (PK-like) 131 421 1.15E-69

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