General information for g11383.t17
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Myosin regulatory light chain sqh.
Parent gene
- The parent gene g11383 is located on chr_1: 15879728..15880963 (- strand)
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.t17 | TTS | g11383.t17 | 15878931 | 15878931 |
| chr_1 | g11383 | g11383.t17 | isoform | g11383.t17 | 15879154 | 15879906 |
| chr_1 | g11383 | g11383.t17 | exon | g11383.t17.exon1 | 15879154 | 15879261 |
| chr_1 | g11383 | g11383.t17 | cds | g11383.t17.CDS1 | 15879154 | 15879261 |
| chr_1 | g11383 | g11383.t17 | exon | g11383.t17.exon2 | 15879344 | 15879465 |
| chr_1 | g11383 | g11383.t17 | cds | g11383.t17.CDS2 | 15879344 | 15879465 |
| chr_1 | g11383 | g11383.t17 | exon | g11383.t17.exon3 | 15879520 | 15879733 |
| chr_1 | g11383 | g11383.t17 | cds | g11383.t17.CDS3 | 15879520 | 15879697 |
| chr_1 | g11383 | g11383.t17 | exon | g11383.t17.exon4 | 15879796 | 15879906 |
| chr_1 | g11383 | g11383.t17 | TSS | g11383.t17 | 15880819 | 15880819 |
Sequences
>g11383.t17 Gene=g11383 Length=555
ATGTCGTCACGAAAAACAGCAGGCCGACGTGCTACTACAAAAAAACGAGCTCAACGAGCC
ACTTCAAATGTCTTTGCCATGTTCGATCAAGCCCAGATTGCAGAGTTCAAAAAAAATAAT
AATTTTCTGCTATAGGAAGCTTTCAATATGATTGATCAAAATCGCGATGGATTCATTGAA
AAAGAAGATCTTCATGATATGCTTGCTTCACTTGGAAAGAATCCAACAGATGACTATTTG
GAGTCAATGATGAATGAAGCTCCTGGTCCAATTAATTTTACAATGTTTCTCACTTTATTT
GGAGAAAGATTACAAGGCAAGAATTACCCTGAAGATGTAATTAAAAATGCATTCGGATGC
TTTGATGAAGACAATAATGGCCATATTTCTGAGGATCGTCTGAGAGAGTTATTAACTACA
ATGGGTGATCGTTTTACTGATGAAGAGGTTGACGAAATGTATCGTGAAGCGCCAATTAAA
AACAATCTTTTTGACTATATCGAATTCACAAGAATCTTAAAACATGGCGCTAAAGACAAT
GAGAATGAACAATAA
>g11383.t17 Gene=g11383 Length=135
MIDQNRDGFIEKEDLHDMLASLGKNPTDDYLESMMNEAPGPINFTMFLTLFGERLQGKNY
PEDVIKNAFGCFDEDNNGHISEDRLRELLTTMGDRFTDEEVDEMYREAPIKNNLFDYIEF
TRILKHGAKDNENEQ
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 10 | g11383.t17 | Gene3D | G3DSA:1.10.238.10 | - | 1 | 56 | 3.1E-16 |
| 9 | g11383.t17 | Gene3D | G3DSA:1.10.238.10 | - | 60 | 125 | 5.8E-18 |
| 3 | g11383.t17 | PANTHER | PTHR23049 | MYOSIN REGULATORY LIGHT CHAIN 2 | 1 | 132 | 2.0E-67 |
| 4 | g11383.t17 | PANTHER | PTHR23049:SF66 | MYOSIN REGULATORY LIGHT POLYPEPTIDE 9 | 1 | 132 | 2.0E-67 |
| 1 | g11383.t17 | Pfam | PF13202 | EF hand | 1 | 16 | 0.0088 |
| 2 | g11383.t17 | Pfam | PF13202 | EF hand | 66 | 83 | 0.12 |
| 8 | g11383.t17 | ProSitePatterns | PS00018 | EF-hand calcium-binding domain. | 3 | 15 | - |
| 12 | g11383.t17 | ProSiteProfiles | PS50222 | EF-hand calcium-binding domain profile. | 1 | 25 | 11.668 |
| 11 | g11383.t17 | ProSiteProfiles | PS50222 | EF-hand calcium-binding domain profile. | 60 | 95 | 11.473 |
| 6 | g11383.t17 | SMART | SM00054 | efh_1 | 1 | 22 | 8.6 |
| 7 | g11383.t17 | SMART | SM00054 | efh_1 | 64 | 92 | 0.28 |
| 5 | g11383.t17 | SUPERFAMILY | SSF47473 | EF-hand | 1 | 126 | 1.11E-33 |
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