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.t54 TTS g11383.t54 15878931 15878931
chr_1 g11383 g11383.t54 isoform g11383.t54 15879154 15880834
chr_1 g11383 g11383.t54 exon g11383.t54.exon1 15879154 15879261
chr_1 g11383 g11383.t54 cds g11383.t54.CDS1 15879257 15879261
chr_1 g11383 g11383.t54 exon g11383.t54.exon2 15879367 15879465
chr_1 g11383 g11383.t54 cds g11383.t54.CDS2 15879367 15879465
chr_1 g11383 g11383.t54 exon g11383.t54.exon3 15879520 15879709
chr_1 g11383 g11383.t54 cds g11383.t54.CDS3 15879520 15879709
chr_1 g11383 g11383.t54 exon g11383.t54.exon4 15879796 15879915
chr_1 g11383 g11383.t54 cds g11383.t54.CDS4 15879796 15879906
chr_1 g11383 g11383.t54 exon g11383.t54.exon5 15880716 15880834
chr_1 g11383 g11383.t54 TSS g11383.t54 15880819 15880819

Sequences

>g11383.t54 Gene=g11383 Length=636
ATGTAGTGTAGAAGTTGATTTCGAGAATAAAAACACTTTTTTTTGATTGAAAAATTTTAA
TTGATTTTGCATCTTATAGTGTTTTAACTAATTTGTATTGAATTTAATATAATATTTAGA
GAATCATCATGTCGTCACGAAAAACAGCAGGCCGACGTGCTACTACAAAAAAACGAGCTC
AACGAGCCACTTCAAATGTCTTTGCCATGTTCGATCAAGCCCAGATTGCAGAGTTCAAAG
AAGCTTTCAATATGATTGATCAAAATCGCGATGGATTCATTGAAAAAGAAGATCTTCATG
ATATGCTTGCTTCACTTGGAAAGAATCCAACAGATGACTATTTGGAGTCAATGATGAATG
AAGCTCCTGGTCCAATTAATTTTACAATGTTTCTCACTTTATTTGGAGAAAGATTACAAG
GCAAGAATTACCCTGAAGATGTAATTAAAAATGCATTCGGATGCTTTGATGAAGACAATA
ATGGCCATATTTCTGAGGATCGTCTGAGAGAGTTATTAACTACAATGGGTTGACGAAATG
TATCGTGAAGCGCCAATTAAAAACAATCTTTTTGACTATATCGAATTCACAAGAATCTTA
AAACATGGCGCTAAAGACAATGAGAATGAACAATAA

>g11383.t54 Gene=g11383 Length=134
MSSRKTAGRRATTKKRAQRATSNVFAMFDQAQIAEFKEAFNMIDQNRDGFIEKEDLHDML
ASLGKNPTDDYLESMMNEAPGPINFTMFLTLFGERLQGKNYPEDVIKNAFGCFDEDNNGH
ISEDRLRELLTTMG

Protein features from InterProScan

Transcript Database ID Name Start End E.value
8 g11383.t54 CDD cd00051 EFh 35 79 2.72419E-9
6 g11383.t54 Gene3D G3DSA:1.10.238.10 - 16 93 1.7E-26
7 g11383.t54 Gene3D G3DSA:1.10.238.10 - 94 134 1.7E-8
3 g11383.t54 PANTHER PTHR23049 MYOSIN REGULATORY LIGHT CHAIN 2 1 134 7.2E-68
4 g11383.t54 PANTHER PTHR23049:SF57 MYOSIN REGULATORY LIGHT CHAIN 12A 1 134 7.2E-68
1 g11383.t54 Pfam PF13405 EF-hand domain 35 64 2.0E-7
2 g11383.t54 Pfam PF13202 EF hand 107 124 0.12
9 g11383.t54 ProSitePatterns PS00018 EF-hand calcium-binding domain. 44 56 -
12 g11383.t54 ProSiteProfiles PS50222 EF-hand calcium-binding domain profile. 31 66 15.49
13 g11383.t54 ProSiteProfiles PS50222 EF-hand calcium-binding domain profile. 101 134 11.808
11 g11383.t54 SMART SM00054 efh_1 35 63 5.6E-7
10 g11383.t54 SMART SM00054 efh_1 105 133 0.28
5 g11383.t54 SUPERFAMILY SSF47473 EF-hand 28 134 2.67E-30

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