General information for g12280.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Myosin-2 essential light chain.
Parent gene
- The parent gene g12280 is located on chr_1: 22120246..22124638 (- 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 | g12280 | g12280.t1 | TTS | g12280.t1 | 22120044 | 22120044 |
| chr_1 | g12280 | g12280.t1 | isoform | g12280.t1 | 22120246 | 22121995 |
| chr_1 | g12280 | g12280.t1 | exon | g12280.t1.exon1 | 22120246 | 22120476 |
| chr_1 | g12280 | g12280.t1 | cds | g12280.t1.CDS1 | 22120246 | 22120476 |
| chr_1 | g12280 | g12280.t1 | exon | g12280.t1.exon2 | 22120542 | 22120723 |
| chr_1 | g12280 | g12280.t1 | cds | g12280.t1.CDS2 | 22120542 | 22120723 |
| chr_1 | g12280 | g12280.t1 | exon | g12280.t1.exon3 | 22121897 | 22121924 |
| chr_1 | g12280 | g12280.t1 | cds | g12280.t1.CDS3 | 22121897 | 22121924 |
| chr_1 | g12280 | g12280.t1 | exon | g12280.t1.exon4 | 22121993 | 22121995 |
| chr_1 | g12280 | g12280.t1 | cds | g12280.t1.CDS4 | 22121993 | 22121995 |
| chr_1 | g12280 | g12280.t1 | TSS | g12280.t1 | 22122024 | 22122024 |
Sequences
>g12280.t1 Gene=g12280 Length=444
ATGGCAAATTATACTGAAGATCAATTAGCAGAATTCCAAGAAGCTTTTAACTTGTTTGAT
AATCGAGGAGATGGAAAAATTCAGCAGCAACAAATTGGTGAATGCCTTCGAGCATTGGGT
CAAAATCCCACAGAGAGTGATGTAAAAAAATACACTCACCAACATAAGCCAGATGAAAGA
ATAGATTTTGATACTTTTTTGCCAATTTATCAATCCATTTCGAAGCAGCGATCAACCGAT
ACAGCCGATGACTTTATTGAAGGTCTTCGCCATTTTGATAAAGATGCAAGTGGTTTCATT
TCATCTGCTGAATTGCGTCATTTACTTACAACGCTCGGTGAAAAGTTGAGCGATGAAGAA
GTTGAACAGCTTTTAACAAATCAAGAAGATTCGCAGGGAAATGTCAACTATGAAGAATTT
GTTAGAATGGTAATGAATGGTTAA
>g12280.t1 Gene=g12280 Length=147
MANYTEDQLAEFQEAFNLFDNRGDGKIQQQQIGECLRALGQNPTESDVKKYTHQHKPDER
IDFDTFLPIYQSISKQRSTDTADDFIEGLRHFDKDASGFISSAELRHLLTTLGEKLSDEE
VEQLLTNQEDSQGNVNYEEFVRMVMNG
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g12280.t1 | CDD | cd00051 | EFh | 84 | 145 | 9.99991E-12 |
| 5 | g12280.t1 | Gene3D | G3DSA:1.10.238.10 | - | 1 | 81 | 6.7E-23 |
| 6 | g12280.t1 | Gene3D | G3DSA:1.10.238.10 | - | 82 | 147 | 4.4E-20 |
| 3 | g12280.t1 | PANTHER | PTHR23048 | MYOSIN LIGHT CHAIN 1, 3 | 3 | 146 | 6.3E-55 |
| 2 | g12280.t1 | Pfam | PF13405 | EF-hand domain | 11 | 40 | 8.6E-6 |
| 1 | g12280.t1 | Pfam | PF13499 | EF-hand domain pair | 90 | 144 | 1.2E-7 |
| 8 | g12280.t1 | ProSitePatterns | PS00018 | EF-hand calcium-binding domain. | 93 | 105 | - |
| 12 | g12280.t1 | ProSiteProfiles | PS50222 | EF-hand calcium-binding domain profile. | 7 | 42 | 12.644 |
| 13 | g12280.t1 | ProSiteProfiles | PS50222 | EF-hand calcium-binding domain profile. | 80 | 115 | 12.644 |
| 11 | g12280.t1 | ProSiteProfiles | PS50222 | EF-hand calcium-binding domain profile. | 130 | 147 | 5.698 |
| 9 | g12280.t1 | SMART | SM00054 | efh_1 | 11 | 39 | 0.18 |
| 10 | g12280.t1 | SMART | SM00054 | efh_1 | 84 | 112 | 0.07 |
| 4 | g12280.t1 | SUPERFAMILY | SSF47473 | EF-hand | 5 | 146 | 4.58E-37 |
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:0005509 | calcium ion binding | MF |
KEGG
Orthology
- This transcript has been annotated with K12751 (myosin light chain 6)
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.
