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.t21 TTS g11383.t21 15878931 15878931
chr_1 g11383 g11383.t21 isoform g11383.t21 15879154 15880723
chr_1 g11383 g11383.t21 exon g11383.t21.exon1 15879154 15879261
chr_1 g11383 g11383.t21 cds g11383.t21.CDS1 15879154 15879261
chr_1 g11383 g11383.t21 exon g11383.t21.exon2 15879344 15879465
chr_1 g11383 g11383.t21 cds g11383.t21.CDS2 15879344 15879465
chr_1 g11383 g11383.t21 exon g11383.t21.exon3 15879520 15879709
chr_1 g11383 g11383.t21 cds g11383.t21.CDS3 15879520 15879709
chr_1 g11383 g11383.t21 exon g11383.t21.exon4 15879796 15879915
chr_1 g11383 g11383.t21 cds g11383.t21.CDS4 15879796 15879906
chr_1 g11383 g11383.t21 exon g11383.t21.exon5 15880712 15880723
chr_1 g11383 g11383.t21 TSS g11383.t21 15880819 15880819

Sequences

>g11383.t21 Gene=g11383 Length=552
ATATTTAGGTAAAGAATCATCATGTCGTCACGAAAAACAGCAGGCCGACGTGCTACTACA
AAAAAACGAGCTCAACGAGCCACTTCAAATGTCTTTGCCATGTTCGATCAAGCCCAGATT
GCAGAGTTCAAAGAAGCTTTCAATATGATTGATCAAAATCGCGATGGATTCATTGAAAAA
GAAGATCTTCATGATATGCTTGCTTCACTTGGAAAGAATCCAACAGATGACTATTTGGAG
TCAATGATGAATGAAGCTCCTGGTCCAATTAATTTTACAATGTTTCTCACTTTATTTGGA
GAAAGATTACAAGGCAAGAATTACCCTGAAGATGTAATTAAAAATGCATTCGGATGCTTT
GATGAAGACAATAATGGCCATATTTCTGAGGATCGTCTGAGAGAGTTATTAACTACAATG
GGTGATCGTTTTACTGATGAAGAGGTTGACGAAATGTATCGTGAAGCGCCAATTAAAAAC
AATCTTTTTGACTATATCGAATTCACAAGAATCTTAAAACATGGCGCTAAAGACAATGAG
AATGAACAATAA

>g11383.t21 Gene=g11383 Length=176
MSSRKTAGRRATTKKRAQRATSNVFAMFDQAQIAEFKEAFNMIDQNRDGFIEKEDLHDML
ASLGKNPTDDYLESMMNEAPGPINFTMFLTLFGERLQGKNYPEDVIKNAFGCFDEDNNGH
ISEDRLRELLTTMGDRFTDEEVDEMYREAPIKNNLFDYIEFTRILKHGAKDNENEQ

Protein features from InterProScan

Transcript Database ID Name Start End E.value
7 g11383.t21 CDD cd00051 EFh 35 79 1.62182E-8
6 g11383.t21 Gene3D G3DSA:1.10.238.10 - 16 97 3.5E-26
5 g11383.t21 Gene3D G3DSA:1.10.238.10 - 101 166 1.1E-17
2 g11383.t21 PANTHER PTHR23049 MYOSIN REGULATORY LIGHT CHAIN 2 1 173 8.2E-89
3 g11383.t21 PANTHER PTHR23049:SF66 MYOSIN REGULATORY LIGHT POLYPEPTIDE 9 1 173 8.2E-89
1 g11383.t21 Pfam PF13405 EF-hand domain 35 64 3.1E-7
8 g11383.t21 ProSitePatterns PS00018 EF-hand calcium-binding domain. 44 56 -
11 g11383.t21 ProSiteProfiles PS50222 EF-hand calcium-binding domain profile. 31 66 15.49
12 g11383.t21 ProSiteProfiles PS50222 EF-hand calcium-binding domain profile. 101 136 11.473
10 g11383.t21 SMART SM00054 efh_1 35 63 5.6E-7
9 g11383.t21 SMART SM00054 efh_1 105 133 0.28
4 g11383.t21 SUPERFAMILY SSF47473 EF-hand 28 167 3.91E-39

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. There were no conditions that were differentially expressed