Gene loci information

Transcript annotation

  • This transcript has been annotated as Myosin-2 essential light chain.

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 g12280 g12280.t2 TTS g12280.t2 22120044 22120044
chr_1 g12280 g12280.t2 isoform g12280.t2 22120246 22120825
chr_1 g12280 g12280.t2 exon g12280.t2.exon1 22120246 22120476
chr_1 g12280 g12280.t2 cds g12280.t2.CDS1 22120246 22120476
chr_1 g12280 g12280.t2 exon g12280.t2.exon2 22120542 22120723
chr_1 g12280 g12280.t2 cds g12280.t2.CDS2 22120542 22120723
chr_1 g12280 g12280.t2 exon g12280.t2.exon3 22120780 22120825
chr_1 g12280 g12280.t2 cds g12280.t2.CDS3 22120780 22120825
chr_1 g12280 g12280.t2 TSS g12280.t2 22120908 22120908

Sequences

>g12280.t2 Gene=g12280 Length=459
ATGTACGAACAACCACATAAGAAACACTCATTTTCATCTGTTGATGAATTCCAAGAAGCT
TTTAACTTGTTTGATAATCGAGGAGATGGAAAAATTCAGCAGCAACAAATTGGTGAATGC
CTTCGAGCATTGGGTCAAAATCCCACAGAGAGTGATGTAAAAAAATACACTCACCAACAT
AAGCCAGATGAAAGAATAGATTTTGATACTTTTTTGCCAATTTATCAATCCATTTCGAAG
CAGCGATCAACCGATACAGCCGATGACTTTATTGAAGGTCTTCGCCATTTTGATAAAGAT
GCAAGTGGTTTCATTTCATCTGCTGAATTGCGTCATTTACTTACAACGCTCGGTGAAAAG
TTGAGCGATGAAGAAGTTGAACAGCTTTTAACAAATCAAGAAGATTCGCAGGGAAATGTC
AACTATGAAGAATTTGTTAGAATGGTAATGAATGGTTAA

>g12280.t2 Gene=g12280 Length=152
MYEQPHKKHSFSSVDEFQEAFNLFDNRGDGKIQQQQIGECLRALGQNPTESDVKKYTHQH
KPDERIDFDTFLPIYQSISKQRSTDTADDFIEGLRHFDKDASGFISSAELRHLLTTLGEK
LSDEEVEQLLTNQEDSQGNVNYEEFVRMVMNG

Protein features from InterProScan

Transcript Database ID Name Start End E.value
7 g12280.t2 CDD cd00051 EFh 89 150 8.36578E-12
5 g12280.t2 Gene3D G3DSA:1.10.238.10 - 10 86 9.2E-21
6 g12280.t2 Gene3D G3DSA:1.10.238.10 - 87 152 4.8E-20
3 g12280.t2 PANTHER PTHR23048 MYOSIN LIGHT CHAIN 1, 3 13 151 4.8E-53
2 g12280.t2 Pfam PF13405 EF-hand domain 16 45 9.1E-6
1 g12280.t2 Pfam PF13499 EF-hand domain pair 95 149 1.3E-7
8 g12280.t2 ProSitePatterns PS00018 EF-hand calcium-binding domain. 98 110 -
11 g12280.t2 ProSiteProfiles PS50222 EF-hand calcium-binding domain profile. 12 47 12.7
13 g12280.t2 ProSiteProfiles PS50222 EF-hand calcium-binding domain profile. 85 120 12.644
12 g12280.t2 ProSiteProfiles PS50222 EF-hand calcium-binding domain profile. 135 152 5.698
10 g12280.t2 SMART SM00054 efh_1 16 44 0.18
9 g12280.t2 SMART SM00054 efh_1 89 117 0.07
4 g12280.t2 SUPERFAMILY SSF47473 EF-hand 14 150 4.39E-36

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

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