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.t26 TTS g11383.t26 15878931 15878931
chr_1 g11383 g11383.t26 isoform g11383.t26 15879154 15880748
chr_1 g11383 g11383.t26 exon g11383.t26.exon1 15879154 15879261
chr_1 g11383 g11383.t26 cds g11383.t26.CDS1 15879154 15879261
chr_1 g11383 g11383.t26 exon g11383.t26.exon2 15879344 15879465
chr_1 g11383 g11383.t26 cds g11383.t26.CDS2 15879344 15879465
chr_1 g11383 g11383.t26 exon g11383.t26.exon3 15879520 15879709
chr_1 g11383 g11383.t26 cds g11383.t26.CDS3 15879520 15879709
chr_1 g11383 g11383.t26 exon g11383.t26.exon4 15879808 15879915
chr_1 g11383 g11383.t26 cds g11383.t26.CDS4 15879808 15879906
chr_1 g11383 g11383.t26 exon g11383.t26.exon5 15880716 15880748
chr_1 g11383 g11383.t26 TSS g11383.t26 15880819 15880819

Sequences

>g11383.t26 Gene=g11383 Length=561
ACTAATTTGTATTGAATTTAATATAATATTTAGAGAATCATCATGTCGTCACGAAAAACA
GCAGGCCGACGTGCTACTACAAAAAAACGAGCTCAACGAGCCACTTCAAATGTCTTTGCC
ATGTTCGATCAAGCCCAGATTGAAGCTTTCAATATGATTGATCAAAATCGCGATGGATTC
ATTGAAAAAGAAGATCTTCATGATATGCTTGCTTCACTTGGAAAGAATCCAACAGATGAC
TATTTGGAGTCAATGATGAATGAAGCTCCTGGTCCAATTAATTTTACAATGTTTCTCACT
TTATTTGGAGAAAGATTACAAGGCAAGAATTACCCTGAAGATGTAATTAAAAATGCATTC
GGATGCTTTGATGAAGACAATAATGGCCATATTTCTGAGGATCGTCTGAGAGAGTTATTA
ACTACAATGGGTGATCGTTTTACTGATGAAGAGGTTGACGAAATGTATCGTGAAGCGCCA
ATTAAAAACAATCTTTTTGACTATATCGAATTCACAAGAATCTTAAAACATGGCGCTAAA
GACAATGAGAATGAACAATAA

>g11383.t26 Gene=g11383 Length=172
MSSRKTAGRRATTKKRAQRATSNVFAMFDQAQIEAFNMIDQNRDGFIEKEDLHDMLASLG
KNPTDDYLESMMNEAPGPINFTMFLTLFGERLQGKNYPEDVIKNAFGCFDEDNNGHISED
RLRELLTTMGDRFTDEEVDEMYREAPIKNNLFDYIEFTRILKHGAKDNENEQ

Protein features from InterProScan

Transcript Database ID Name Start End E.value
7 g11383.t26 CDD cd00051 EFh 34 75 5.31587E-7
6 g11383.t26 Gene3D G3DSA:1.10.238.10 - 16 93 1.3E-20
5 g11383.t26 Gene3D G3DSA:1.10.238.10 - 97 162 1.0E-17
2 g11383.t26 PANTHER PTHR23049 MYOSIN REGULATORY LIGHT CHAIN 2 1 169 1.5E-83
3 g11383.t26 PANTHER PTHR23049:SF66 MYOSIN REGULATORY LIGHT POLYPEPTIDE 9 1 169 1.5E-83
1 g11383.t26 Pfam PF13405 EF-hand domain 34 60 3.6E-6
8 g11383.t26 ProSitePatterns PS00018 EF-hand calcium-binding domain. 40 52 -
12 g11383.t26 ProSiteProfiles PS50222 EF-hand calcium-binding domain profile. 27 62 12.393
11 g11383.t26 ProSiteProfiles PS50222 EF-hand calcium-binding domain profile. 97 132 11.473
10 g11383.t26 SMART SM00054 efh_1 31 59 0.0046
9 g11383.t26 SMART SM00054 efh_1 101 129 0.28
4 g11383.t26 SUPERFAMILY SSF47473 EF-hand 33 163 7.32E-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