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.t59 TTS g11383.t59 15878931 15878931
chr_1 g11383 g11383.t59 isoform g11383.t59 15879154 15880834
chr_1 g11383 g11383.t59 exon g11383.t59.exon1 15879154 15879239
chr_1 g11383 g11383.t59 cds g11383.t59.CDS1 15879154 15879239
chr_1 g11383 g11383.t59 exon g11383.t59.exon2 15879367 15879471
chr_1 g11383 g11383.t59 cds g11383.t59.CDS2 15879367 15879471
chr_1 g11383 g11383.t59 exon g11383.t59.exon3 15879529 15879709
chr_1 g11383 g11383.t59 cds g11383.t59.CDS3 15879529 15879709
chr_1 g11383 g11383.t59 exon g11383.t59.exon4 15879796 15879915
chr_1 g11383 g11383.t59 cds g11383.t59.CDS4 15879796 15879906
chr_1 g11383 g11383.t59 exon g11383.t59.exon5 15880716 15880834
chr_1 g11383 g11383.t59 TSS g11383.t59 15880819 15880819

Sequences

>g11383.t59 Gene=g11383 Length=611
ATGTAGTGTAGAAGTTGATTTCGAGAATAAAAACACTTTTTTTTGATTGAAAAATTTTAA
TTGATTTTGCATCTTATAGTGTTTTAACTAATTTGTATTGAATTTAATATAATATTTAGA
GAATCATCATGTCGTCACGAAAAACAGCAGGCCGACGTGCTACTACAAAAAAACGAGCTC
AACGAGCCACTTCAAATGTCTTTGCCATGTTCGATCAAGCCCAGATTGCAGAGTTCAAAG
AAGCTTTCAATATGATTGATCAAAATCGCGATGGATTCATTGAAAAAGAAGATCTTCATG
ATATGCTTGCTTCACTTGGAAAGAATCCAACAGATGACTATTTGGAGTCAATGATGAATG
AAGCTCCTGGTCCAATTAATTTTACAATGTTTCTCACTTTATTTGGAGAAAGATTACAAG
GCACAGACCCTGAAGATGTAATTAAAAATGCATTCGGATGCTTTGATGAAGACAATAATG
GCCATATTTCTGAGGATCGTCTGAGAGAGTTATTAACTACAATGGCGCCAATTAAAAACA
ATCTTTTTGACTATATCGAATTCACAAGAATCTTAAAACATGGCGCTAAAGACAATGAGA
ATGAACAATAA

>g11383.t59 Gene=g11383 Length=160
MSSRKTAGRRATTKKRAQRATSNVFAMFDQAQIAEFKEAFNMIDQNRDGFIEKEDLHDML
ASLGKNPTDDYLESMMNEAPGPINFTMFLTLFGERLQGTDPEDVIKNAFGCFDEDNNGHI
SEDRLRELLTTMAPIKNNLFDYIEFTRILKHGAKDNENEQ

Protein features from InterProScan

Transcript Database ID Name Start End E.value
8 g11383.t59 CDD cd00051 EFh 35 79 6.79255E-9
6 g11383.t59 Gene3D G3DSA:1.10.238.10 - 16 93 2.8E-26
7 g11383.t59 Gene3D G3DSA:1.10.238.10 - 94 139 2.2E-9
3 g11383.t59 PANTHER PTHR23049 MYOSIN REGULATORY LIGHT CHAIN 2 1 133 5.7E-75
4 g11383.t59 PANTHER PTHR23049:SF66 MYOSIN REGULATORY LIGHT POLYPEPTIDE 9 1 133 5.7E-75
1 g11383.t59 Pfam PF13405 EF-hand domain 35 64 2.7E-7
2 g11383.t59 Pfam PF13202 EF hand 106 123 0.15
9 g11383.t59 ProSitePatterns PS00018 EF-hand calcium-binding domain. 44 56 -
13 g11383.t59 ProSiteProfiles PS50222 EF-hand calcium-binding domain profile. 31 66 15.49
12 g11383.t59 ProSiteProfiles PS50222 EF-hand calcium-binding domain profile. 100 135 10.748
11 g11383.t59 SMART SM00054 efh_1 35 63 5.6E-7
10 g11383.t59 SMART SM00054 efh_1 104 132 0.28
5 g11383.t59 SUPERFAMILY SSF47473 EF-hand 28 151 2.24E-32

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