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.t25 TTS g11383.t25 15878931 15878931
chr_1 g11383 g11383.t25 isoform g11383.t25 15879154 15880748
chr_1 g11383 g11383.t25 exon g11383.t25.exon1 15879154 15879261
chr_1 g11383 g11383.t25 cds g11383.t25.CDS1 15879154 15879261
chr_1 g11383 g11383.t25 exon g11383.t25.exon2 15879344 15879465
chr_1 g11383 g11383.t25 cds g11383.t25.CDS2 15879344 15879465
chr_1 g11383 g11383.t25 exon g11383.t25.exon3 15879520 15879709
chr_1 g11383 g11383.t25 cds g11383.t25.CDS3 15879520 15879709
chr_1 g11383 g11383.t25 exon g11383.t25.exon4 15879822 15879915
chr_1 g11383 g11383.t25 cds g11383.t25.CDS4 15879822 15879839
chr_1 g11383 g11383.t25 exon g11383.t25.exon5 15880716 15880748
chr_1 g11383 g11383.t25 TSS g11383.t25 15880819 15880819

Sequences

>g11383.t25 Gene=g11383 Length=547
ACTAATTTGTATTGAATTTAATATAATATTTAGAGAATCATCATGTCGTCACGAAAAACA
GCAGGCCGACGTGCTACTACAAAAAAACGAGCTCAACGAGCCACTTCAAATGTCTTTGCC
ATGTTCGGAAGCTTTCAATATGATTGATCAAAATCGCGATGGATTCATTGAAAAAGAAGA
TCTTCATGATATGCTTGCTTCACTTGGAAAGAATCCAACAGATGACTATTTGGAGTCAAT
GATGAATGAAGCTCCTGGTCCAATTAATTTTACAATGTTTCTCACTTTATTTGGAGAAAG
ATTACAAGGCAAGAATTACCCTGAAGATGTAATTAAAAATGCATTCGGATGCTTTGATGA
AGACAATAATGGCCATATTTCTGAGGATCGTCTGAGAGAGTTATTAACTACAATGGGTGA
TCGTTTTACTGATGAAGAGGTTGACGAAATGTATCGTGAAGCGCCAATTAAAAACAATCT
TTTTGACTATATCGAATTCACAAGAATCTTAAAACATGGCGCTAAAGACAATGAGAATGA
ACAATAA

>g11383.t25 Gene=g11383 Length=145
MSLPCSEAFNMIDQNRDGFIEKEDLHDMLASLGKNPTDDYLESMMNEAPGPINFTMFLTL
FGERLQGKNYPEDVIKNAFGCFDEDNNGHISEDRLRELLTTMGDRFTDEEVDEMYREAPI
KNNLFDYIEFTRILKHGAKDNENEQ

Protein features from InterProScan

Transcript Database ID Name Start End E.value
8 g11383.t25 CDD cd00051 EFh 5 48 4.46148E-7
7 g11383.t25 Gene3D G3DSA:1.10.238.10 - 4 66 1.3E-19
6 g11383.t25 Gene3D G3DSA:1.10.238.10 - 70 135 6.9E-18
3 g11383.t25 PANTHER PTHR23049 MYOSIN REGULATORY LIGHT CHAIN 2 6 142 9.4E-71
4 g11383.t25 PANTHER PTHR23049:SF66 MYOSIN REGULATORY LIGHT POLYPEPTIDE 9 6 142 9.4E-71
1 g11383.t25 Pfam PF00036 EF hand 6 32 3.7E-6
2 g11383.t25 Pfam PF13202 EF hand 76 93 0.13
9 g11383.t25 ProSitePatterns PS00018 EF-hand calcium-binding domain. 13 25 -
12 g11383.t25 ProSiteProfiles PS50222 EF-hand calcium-binding domain profile. 7 35 12.365
13 g11383.t25 ProSiteProfiles PS50222 EF-hand calcium-binding domain profile. 70 105 11.473
11 g11383.t25 SMART SM00054 efh_1 4 32 0.0016
10 g11383.t25 SMART SM00054 efh_1 74 102 0.28
5 g11383.t25 SUPERFAMILY SSF47473 EF-hand 6 136 1.54E-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

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. There were no conditions that were differentially expressed