General information for g13953.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Myosin light chain kinase, smooth muscle.
Parent gene
- The parent gene g13953 is located on chr_1: 33586738..33590149 (+ strand)
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 | g13953 | g13953.t1 | isoform | g13953.t1 | 33581251 | 33590149 |
| chr_1 | g13953 | g13953.t1 | exon | g13953.t1.exon1 | 33581251 | 33581284 |
| chr_1 | g13953 | g13953.t1 | cds | g13953.t1.CDS1 | 33581251 | 33581284 |
| chr_1 | g13953 | g13953.t1 | exon | g13953.t1.exon2 | 33585602 | 33585692 |
| chr_1 | g13953 | g13953.t1 | cds | g13953.t1.CDS2 | 33585602 | 33585692 |
| chr_1 | g13953 | g13953.t1 | exon | g13953.t1.exon3 | 33585750 | 33585953 |
| chr_1 | g13953 | g13953.t1 | cds | g13953.t1.CDS3 | 33585750 | 33585953 |
| chr_1 | g13953 | g13953.t1 | exon | g13953.t1.exon4 | 33586009 | 33586350 |
| chr_1 | g13953 | g13953.t1 | cds | g13953.t1.CDS4 | 33586009 | 33586350 |
| chr_1 | g13953 | g13953.t1 | exon | g13953.t1.exon5 | 33586465 | 33586738 |
| chr_1 | g13953 | g13953.t1 | cds | g13953.t1.CDS5 | 33586465 | 33586738 |
| chr_1 | g13953 | g13953.t1 | exon | g13953.t1.exon6 | 33587173 | 33587305 |
| chr_1 | g13953 | g13953.t1 | cds | g13953.t1.CDS6 | 33587173 | 33587305 |
| chr_1 | g13953 | g13953.t1 | exon | g13953.t1.exon7 | 33589161 | 33590149 |
| chr_1 | g13953 | g13953.t1 | cds | g13953.t1.CDS7 | 33589161 | 33590149 |
| chr_1 | g13953 | g13953.t1 | TSS | g13953.t1 | NA | NA |
| chr_1 | g13953 | g13953.t1 | TTS | g13953.t1 | NA | NA |
Sequences
>g13953.t1 Gene=g13953 Length=2067
ATGATTAAAGTTGATGAAACGGATCCTGTGGGAGATATTGAGCCGCAATTTCCCTATCGT
CAAGTGAGCGTAAAACGAGGCGTCGATATAAAAGAATTCTATGATTTAAAAGAGGAAATC
GGAAGAGGAAAATTCGGAACAGTTTACAAATGCAAAGAAAAATCAACTGGATTATGTTTA
GCGGCAAAATTTATTTCAGTGCCAAATCGAAAAGAAAGAAAAAATGTTGAAAGTGAATTG
GACATGATGAATCGTCTACAACATCCAAAAATCATTCAACTATACGATGCCTATGAATTC
AACAAGACTGTCTGTGTGGTACTAGAATTAATCGAGGGTGGTGAATTATTTGATCGCGTA
CTCGACGATAAATTTATACTTACCGAGAAAGCCTGCTCGATATTCATGCGTCAGATATGT
GAAGCAATGGATTACATTCATGAACACAACATCATTCATTTGGACTTGAAACCTGAAAAT
ATTTTATGTCTAACAGAGTCAGGAAATCGCATTAAAATTATCGACTTTGGCCTCGCTCGT
GAATTCGATCCGTCATCGAAACTGCAGGTGCTATTTGGTACGCCAGAGTTTGTTGCACCA
GAGGTCGTGAACTTTGATGCAATCACTTTTGCCACTGATATGTGGTCAGTTGGTGTTATT
GCATATGTCCTTGTAAGTGGTCTTTCACCGTTTGCGGGCGAATGTGATGTTGAGACGATG
GGTAACGTAACAGTTGGCAAATACGATTTCAACGATGAAGCATTCGATAATGTATCGTCT
GAGTGCATTGATTTCATCACAAAGTTGTTGGTAAAAGAACAGGATGATAGAATGACAGCA
AAACAAGCACTACGACATAAATGGATAAAAAAGAAACCACAATATACACCAACTAATGCT
AAACCATCAAATCCACTTTCGTTTAAAGCAGTTTACATGGACAAAGACAACTCACTGTCA
ACAGCAAAAGACAATTTACGGAATTGTGTGGACAGATGGAATGACAGCACACCGTATGTA
TTTGATAAGCATGCGAATGCAATAACACCAGTACACGCGAGCATCTCATCATCAATAGAC
ACATCACCATCGTCACCAGCTGACTCATTGAATAGCTCAACAGTAAGTTTACCTGCGAGC
GATGATACTGAAAATGATAGCGAACAATCGTCACCCAAATCACTGTCATTGCACGATTGT
GATAAAATCATGAATACAAACAACATTAACTCACCATCACCAAAATTAACCACAAATCAG
CATTATCCATTGCCATCGATTATGCGCTTAAAAGATTATTTGCACACACTTGATCGACAT
AAGTCGATAGATAATTGCTTTCTTGGACCATGTGCTGATGATACTATGCACACGGGTTTG
TGTTATTATAATGATGATGAAATTAAGAAATTAACAAATCATTTATTCGAAATCACCACA
AAACATTATTCAGAGACACCAGAAGAAGATGCTGCAGAAAAGGATTTGAATCTGTGCAAG
ACAACGACAAATGGCTCGGTAAGAGAGATTGATGGAGATGATGGCGATACGAGAAGAAAG
AGTCACAATCAATTTTCTGAAATTTTCGAAAAGTTTACAAAACTCGCTGACAGCGGTTCA
GTTGTAAGCAATGTGCCGTGGATAGTCACAAAGCGTACAAAATTTCGCATCAATCAAACA
AGCAGTCGTGATGTGCCGATTGTGAAGACAGATAGGCCCGCAAGGCTGACAAAACAGAAT
GCCATTGATGATGCCACTGACATGAACCTATTTGATGAGACCGTCAACCGCATTTCAAAT
TCGGGTGGCAATGGTATTTTGAGAAATACGCTTGTAGATATTTTTGATGAAAAATTTACA
AATAAAAATCATCGTCACATGTTTCAATCGCATGTATTACGACATGAAACATTTATGAAC
GGAAATTCACTCTCATTTGATTGCGGTCAACTTGGTGTAGAGAAAAGATCGATAAATACG
ATACGAGCACTATTGCATCTTCATGCAACAACAGGCACGAGTGTGAGACAAATTCAGGCA
CAGATTGAGTCAAAAAACAAAATATAA
>g13953.t1 Gene=g13953 Length=688
MIKVDETDPVGDIEPQFPYRQVSVKRGVDIKEFYDLKEEIGRGKFGTVYKCKEKSTGLCL
AAKFISVPNRKERKNVESELDMMNRLQHPKIIQLYDAYEFNKTVCVVLELIEGGELFDRV
LDDKFILTEKACSIFMRQICEAMDYIHEHNIIHLDLKPENILCLTESGNRIKIIDFGLAR
EFDPSSKLQVLFGTPEFVAPEVVNFDAITFATDMWSVGVIAYVLVSGLSPFAGECDVETM
GNVTVGKYDFNDEAFDNVSSECIDFITKLLVKEQDDRMTAKQALRHKWIKKKPQYTPTNA
KPSNPLSFKAVYMDKDNSLSTAKDNLRNCVDRWNDSTPYVFDKHANAITPVHASISSSID
TSPSSPADSLNSSTVSLPASDDTENDSEQSSPKSLSLHDCDKIMNTNNINSPSPKLTTNQ
HYPLPSIMRLKDYLHTLDRHKSIDNCFLGPCADDTMHTGLCYYNDDEIKKLTNHLFEITT
KHYSETPEEDAAEKDLNLCKTTTNGSVREIDGDDGDTRRKSHNQFSEIFEKFTKLADSGS
VVSNVPWIVTKRTKFRINQTSSRDVPIVKTDRPARLTKQNAIDDATDMNLFDETVNRISN
SGGNGILRNTLVDIFDEKFTNKNHRHMFQSHVLRHETFMNGNSLSFDCGQLGVEKRSINT
IRALLHLHATTGTSVRQIQAQIESKNKI
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g13953.t1 | CDD | cd14103 | STKc_MLCK | 40 | 289 | 2.94591E-162 |
| 5 | g13953.t1 | Gene3D | G3DSA:3.30.200.20 | Phosphorylase Kinase; domain 1 | 2 | 111 | 1.1E-29 |
| 6 | g13953.t1 | Gene3D | G3DSA:1.10.510.10 | Transferase(Phosphotransferase) domain 1 | 113 | 344 | 1.3E-61 |
| 11 | g13953.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 359 | 399 | - |
| 2 | g13953.t1 | PANTHER | PTHR24347 | SERINE/THREONINE-PROTEIN KINASE | 17 | 397 | 9.5E-151 |
| 3 | g13953.t1 | PANTHER | PTHR24347:SF393 | MYOSIN, LIGHT CHAIN KINASE 5 | 17 | 397 | 9.5E-151 |
| 1 | g13953.t1 | Pfam | PF00069 | Protein kinase domain | 34 | 289 | 4.9E-74 |
| 9 | g13953.t1 | ProSitePatterns | PS00107 | Protein kinases ATP-binding region signature. | 40 | 63 | - |
| 8 | g13953.t1 | ProSitePatterns | PS00108 | Serine/Threonine protein kinases active-site signature. | 151 | 163 | - |
| 12 | g13953.t1 | ProSiteProfiles | PS50011 | Protein kinase domain profile. | 34 | 289 | 47.368 |
| 10 | g13953.t1 | SMART | SM00220 | serkin_6 | 34 | 289 | 9.3E-95 |
| 4 | g13953.t1 | SUPERFAMILY | SSF56112 | Protein kinase-like (PK-like) | 9 | 311 | 2.43E-85 |
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
- This transcript has been annotated with K00907 (myosin-light-chain kinase)
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.
