Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative 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.t14 TTS g11383.t14 15878931 15878931
chr_1 g11383 g11383.t14 isoform g11383.t14 15879154 15879906
chr_1 g11383 g11383.t14 exon g11383.t14.exon1 15879154 15879261
chr_1 g11383 g11383.t14 cds g11383.t14.CDS1 15879154 15879261
chr_1 g11383 g11383.t14 exon g11383.t14.exon2 15879344 15879471
chr_1 g11383 g11383.t14 cds g11383.t14.CDS2 15879344 15879471
chr_1 g11383 g11383.t14 exon g11383.t14.exon3 15879528 15879906
chr_1 g11383 g11383.t14 cds g11383.t14.CDS3 15879528 15879591
chr_1 g11383 g11383.t14 TSS g11383.t14 15880819 15880819

Sequences

>g11383.t14 Gene=g11383 Length=615
ATGTCGTCACGAAAAACAGCAGGCCGACGTGCTACTACAAAAAAACGAGCTCAACGAGCC
ACTTCAAATGTCTTTGCCATGTTCGATCAAGCCCAGATTGCAGAGTTCAAAGTAAATATT
TTATAAGAAATTTTTTATGTTAATAGTTCTTTTATGTTAATGATTCTTATAAGAAAAATA
ATAATTTTCTGCTATAGGAAGCTTTCAATATGATTGATCAAAATCGCGATGGATTCATTG
AAAAAGAAGATCTTCATGATATGCTTGCTTCACTTGGAAAGAATCCAACAGATGACTATT
TGGAGTCAATGATGAATGAAGCTCCTGGTCCAATTAATTTTACAATGTTTCTCACTTTAT
TTGGAGAAAGATTACAAGGGCACAGACCCTGAAGATGTAATTAAAAATGCATTCGGATGC
TTTGATGAAGACAATAATGGCCATATTTCTGAGGATCGTCTGAGAGAGTTATTAACTACA
ATGGGTGATCGTTTTACTGATGAAGAGGTTGACGAAATGTATCGTGAAGCGCCAATTAAA
AACAATCTTTTTGACTATATCGAATTCACAAGAATCTTAAAACATGGCGCTAAAGACAAT
GAGAATGAACAATAA

>g11383.t14 Gene=g11383 Length=99
MKLLVQLILQCFSLYLEKDYKGTDPEDVIKNAFGCFDEDNNGHISEDRLRELLTTMGDRF
TDEEVDEMYREAPIKNNLFDYIEFTRILKHGAKDNENEQ

Protein features from InterProScan

Transcript Database ID Name Start End E.value
5 g11383.t14 Coils Coil Coil 95 99 -
4 g11383.t14 Gene3D G3DSA:1.10.238.10 - 22 89 1.7E-19
1 g11383.t14 PANTHER PTHR23049 MYOSIN REGULATORY LIGHT CHAIN 2 15 96 3.3E-34
2 g11383.t14 PANTHER PTHR23049:SF66 MYOSIN REGULATORY LIGHT POLYPEPTIDE 9 15 96 3.3E-34
8 g11383.t14 Phobius SIGNAL_PEPTIDE Signal peptide region 1 18 -
9 g11383.t14 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 2 -
10 g11383.t14 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 3 14 -
11 g11383.t14 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 15 18 -
7 g11383.t14 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 19 99 -
6 g11383.t14 ProSiteProfiles PS50222 EF-hand calcium-binding domain profile. 24 59 11.668
3 g11383.t14 SUPERFAMILY SSF47473 EF-hand 12 90 1.3E-18

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