Gene loci information

Transcript annotation

  • This transcript has been annotated as Myosin regulatory light chain sqh.

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 g11383 g11383.t27 TTS g11383.t27 15878931 15878931
chr_1 g11383 g11383.t27 isoform g11383.t27 15879154 15880748
chr_1 g11383 g11383.t27 exon g11383.t27.exon1 15879154 15879261
chr_1 g11383 g11383.t27 cds g11383.t27.CDS1 15879154 15879261
chr_1 g11383 g11383.t27 exon g11383.t27.exon2 15879344 15879471
chr_1 g11383 g11383.t27 cds g11383.t27.CDS2 15879344 15879471
chr_1 g11383 g11383.t27 exon g11383.t27.exon3 15879529 15879733
chr_1 g11383 g11383.t27 cds g11383.t27.CDS3 15879529 15879697
chr_1 g11383 g11383.t27 exon g11383.t27.exon4 15879796 15879915
chr_1 g11383 g11383.t27 exon g11383.t27.exon5 15880716 15880748
chr_1 g11383 g11383.t27 TSS g11383.t27 15880819 15880819

Sequences

>g11383.t27 Gene=g11383 Length=594
ACTAATTTGTATTGAATTTAATATAATATTTAGAGAATCATCATGTCGTCACGAAAAACA
GCAGGCCGACGTGCTACTACAAAAAAACGAGCTCAACGAGCCACTTCAAATGTCTTTGCC
ATGTTCGATCAAGCCCAGATTGCAGAGTTCAAAAAAAATAATAATTTTCTGCTATAGGAA
GCTTTCAATATGATTGATCAAAATCGCGATGGATTCATTGAAAAAGAAGATCTTCATGAT
ATGCTTGCTTCACTTGGAAAGAATCCAACAGATGACTATTTGGAGTCAATGATGAATGAA
GCTCCTGGTCCAATTAATTTTACAATGTTTCTCACTTTATTTGGAGAAAGATTACAAGGC
ACAGACCCTGAAGATGTAATTAAAAATGCATTCGGATGCTTTGATGAAGACAATAATGGC
CATATTTCTGAGGATCGTCTGAGAGAGTTATTAACTACAATGGGTGATCGTTTTACTGAT
GAAGAGGTTGACGAAATGTATCGTGAAGCGCCAATTAAAAACAATCTTTTTGACTATATC
GAATTCACAAGAATCTTAAAACATGGCGCTAAAGACAATGAGAATGAACAATAA

>g11383.t27 Gene=g11383 Length=134
MIDQNRDGFIEKEDLHDMLASLGKNPTDDYLESMMNEAPGPINFTMFLTLFGERLQGTDP
EDVIKNAFGCFDEDNNGHISEDRLRELLTTMGDRFTDEEVDEMYREAPIKNNLFDYIEFT
RILKHGAKDNENEQ

Protein features from InterProScan

Transcript Database ID Name Start End E.value
10 g11383.t27 Gene3D G3DSA:1.10.238.10 - 1 56 3.1E-16
9 g11383.t27 Gene3D G3DSA:1.10.238.10 - 57 124 4.1E-19
3 g11383.t27 PANTHER PTHR23049 MYOSIN REGULATORY LIGHT CHAIN 2 1 131 1.4E-70
4 g11383.t27 PANTHER PTHR23049:SF66 MYOSIN REGULATORY LIGHT POLYPEPTIDE 9 1 131 1.4E-70
1 g11383.t27 Pfam PF13202 EF hand 1 16 0.0087
2 g11383.t27 Pfam PF13202 EF hand 65 82 0.12
8 g11383.t27 ProSitePatterns PS00018 EF-hand calcium-binding domain. 3 15 -
12 g11383.t27 ProSiteProfiles PS50222 EF-hand calcium-binding domain profile. 1 25 11.668
11 g11383.t27 ProSiteProfiles PS50222 EF-hand calcium-binding domain profile. 59 94 11.668
7 g11383.t27 SMART SM00054 efh_1 1 22 8.6
6 g11383.t27 SMART SM00054 efh_1 63 91 0.28
5 g11383.t27 SUPERFAMILY SSF47473 EF-hand 1 125 2.69E-35

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 gene did not have any KEGG ortholog annotations (KAAS, GHOSTZ).

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