Gene loci information

Transcript annotation

  • This transcript has been annotated as Myosin light chain kinase, smooth muscle.

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 g11297 g11297.t1 isoform g11297.t1 15479789 15481929
chr_1 g11297 g11297.t1 exon g11297.t1.exon1 15479789 15479843
chr_1 g11297 g11297.t1 cds g11297.t1.CDS1 15479789 15479843
chr_1 g11297 g11297.t1 exon g11297.t1.exon2 15480048 15480353
chr_1 g11297 g11297.t1 cds g11297.t1.CDS2 15480048 15480353
chr_1 g11297 g11297.t1 exon g11297.t1.exon3 15480414 15480544
chr_1 g11297 g11297.t1 cds g11297.t1.CDS3 15480414 15480544
chr_1 g11297 g11297.t1 exon g11297.t1.exon4 15480604 15480699
chr_1 g11297 g11297.t1 cds g11297.t1.CDS4 15480604 15480699
chr_1 g11297 g11297.t1 exon g11297.t1.exon5 15480780 15480883
chr_1 g11297 g11297.t1 cds g11297.t1.CDS5 15480780 15480883
chr_1 g11297 g11297.t1 exon g11297.t1.exon6 15481493 15481780
chr_1 g11297 g11297.t1 cds g11297.t1.CDS6 15481493 15481780
chr_1 g11297 g11297.t1 exon g11297.t1.exon7 15481848 15481929
chr_1 g11297 g11297.t1 cds g11297.t1.CDS7 15481848 15481929
chr_1 g11297 g11297.t1 TTS g11297.t1 15481995 15481995
chr_1 g11297 g11297.t1 TSS g11297.t1 NA NA

Sequences

>g11297.t1 Gene=g11297 Length=1062
ATGCTACTATATTTTACGGAATATTTAATTCTACGCAAGAGTTTGCACGTTAAAGACGTC
AAACCACCATTTGAATATAGAAATGTCACGATTAAAACAGATGAGAACCCAGCGGACAAA
TACAATATCCTCCCAGAATTAGGGAGAGGCAGCTTTGGAACCGTTTTTCTTTGTAAAGAA
AAAGCCTCTGATCTTGAATTGGCAGTAAAAATTGTTACATATAAAAAGAAAAAGGAGAAA
ACAATGATGGAACTAGAAATTGATATTCTCAGTTCACTTAATCATCCGGCCATTATTTCA
ATATATGATGCATTCGATTATGGCAATAAATTATATTGTTTTATGGAACTTGTTCAAGGA
GGTGAATTGTTTGAAAGAGTGATTGATGAGGACTTTGTACTTACAGAAAGAGCATGTGCA
TGTTTTATTCGTCAAATTGTTGAAGCAATTGATTATATGCACAGTAAAAGAATAATTCAT
CTTGACATGAAGCCAGAAAATGTGTTGTGCCTTTCAAAACAAGGAAACCGAATTAAAATA
ATTGATTTTGGGTTTGCTCGCAGATATGATCCACATAAGCAACTTCAAGTCATGTTTGGA
ACTGCCGAATTTTCAGCACCTGAAGTAGTAGCATTTGAAGAAATTGGACCATGGACAGAC
ATGTGGAGCATTGGAGTGATCTGTTATGTTTTATTATCGGGCTTATCACCTTTTGTGGGA
GCTGATGATTTTGAGACAATGACCAACGTATCATTTGCAAAATATTCATTCGATTATGCC
CCCTTTGAAGAGATATCAAGTACAGCTAAAGATTTCATTGAAAAATTATTAATTAAGGAG
CCAACAAAAAGAATGAAAGCCAAAAATGCACTAAAGCATGAATGGCTTACACAACTCGAT
TGTATATCAGAAAGCTCACATAAAGATATTACGCTGTCGTTGACAAAAACCAAATTAAAG
CGTTATGTAATTTTAAGACGTTGGAGAAAGGCAGCACTTTCTGTTATGTTTATTAATAAA
TTAAACAAATTGAGTAACTCACATTTACTTAATAGTTGTTAA

>g11297.t1 Gene=g11297 Length=353
MLLYFTEYLILRKSLHVKDVKPPFEYRNVTIKTDENPADKYNILPELGRGSFGTVFLCKE
KASDLELAVKIVTYKKKKEKTMMELEIDILSSLNHPAIISIYDAFDYGNKLYCFMELVQG
GELFERVIDEDFVLTERACACFIRQIVEAIDYMHSKRIIHLDMKPENVLCLSKQGNRIKI
IDFGFARRYDPHKQLQVMFGTAEFSAPEVVAFEEIGPWTDMWSIGVICYVLLSGLSPFVG
ADDFETMTNVSFAKYSFDYAPFEEISSTAKDFIEKLLIKEPTKRMKAKNALKHEWLTQLD
CISESSHKDITLSLTKTKLKRYVILRRWRKAALSVMFINKLNKLSNSHLLNSC

Protein features from InterProScan

Transcript Database ID Name Start End E.value
8 g11297.t1 Gene3D G3DSA:3.30.200.20 Phosphorylase Kinase; domain 1 14 118 2.7E-25
9 g11297.t1 Gene3D G3DSA:1.10.510.10 Transferase(Phosphotransferase) domain 1 120 333 6.2E-57
2 g11297.t1 PANTHER PTHR24347 SERINE/THREONINE-PROTEIN KINASE 23 346 7.3E-131
3 g11297.t1 PANTHER PTHR24347:SF393 MYOSIN, LIGHT CHAIN KINASE 5 23 346 7.3E-131
1 g11297.t1 Pfam PF00069 Protein kinase domain 41 296 2.7E-69
7 g11297.t1 ProSitePatterns PS00107 Protein kinases ATP-binding region signature. 47 70 -
6 g11297.t1 ProSitePatterns PS00108 Serine/Threonine protein kinases active-site signature. 158 170 -
10 g11297.t1 ProSiteProfiles PS50011 Protein kinase domain profile. 41 296 46.76
5 g11297.t1 SMART SM00220 serkin_6 41 296 5.8E-85
4 g11297.t1 SUPERFAMILY SSF56112 Protein kinase-like (PK-like) 22 309 6.61E-82

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