General information for g11383.t12
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.t12 | TTS | g11383.t12 | 15878931 | 15878931 |
| chr_1 | g11383 | g11383.t12 | isoform | g11383.t12 | 15879154 | 15879906 |
| chr_1 | g11383 | g11383.t12 | exon | g11383.t12.exon1 | 15879154 | 15879261 |
| chr_1 | g11383 | g11383.t12 | cds | g11383.t12.CDS1 | 15879154 | 15879261 |
| chr_1 | g11383 | g11383.t12 | exon | g11383.t12.exon2 | 15879344 | 15879471 |
| chr_1 | g11383 | g11383.t12 | cds | g11383.t12.CDS2 | 15879344 | 15879471 |
| chr_1 | g11383 | g11383.t12 | exon | g11383.t12.exon3 | 15879529 | 15879906 |
| chr_1 | g11383 | g11383.t12 | cds | g11383.t12.CDS3 | 15879529 | 15879697 |
| chr_1 | g11383 | g11383.t12 | TSS | g11383.t12 | 15880819 | 15880819 |
Sequences
>g11383.t12 Gene=g11383 Length=614
ATGTCGTCACGAAAAACAGCAGGCCGACGTGCTACTACAAAAAAACGAGCTCAACGAGCC
ACTTCAAATGTCTTTGCCATGTTCGATCAAGCCCAGATTGCAGAGTTCAAAGTAAATATT
TTATAAGAAATTTTTTATGTTAATAGTTCTTTTATGTTAATGATTCTTATAAGAAAAATA
ATAATTTTCTGCTATAGGAAGCTTTCAATATGATTGATCAAAATCGCGATGGATTCATTG
AAAAAGAAGATCTTCATGATATGCTTGCTTCACTTGGAAAGAATCCAACAGATGACTATT
TGGAGTCAATGATGAATGAAGCTCCTGGTCCAATTAATTTTACAATGTTTCTCACTTTAT
TTGGAGAAAGATTACAAGGCACAGACCCTGAAGATGTAATTAAAAATGCATTCGGATGCT
TTGATGAAGACAATAATGGCCATATTTCTGAGGATCGTCTGAGAGAGTTATTAACTACAA
TGGGTGATCGTTTTACTGATGAAGAGGTTGACGAAATGTATCGTGAAGCGCCAATTAAAA
ACAATCTTTTTGACTATATCGAATTCACAAGAATCTTAAAACATGGCGCTAAAGACAATG
AGAATGAACAATAA
>g11383.t12 Gene=g11383 Length=134
MIDQNRDGFIEKEDLHDMLASLGKNPTDDYLESMMNEAPGPINFTMFLTLFGERLQGTDP
EDVIKNAFGCFDEDNNGHISEDRLRELLTTMGDRFTDEEVDEMYREAPIKNNLFDYIEFT
RILKHGAKDNENEQ
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 10 | g11383.t12 | Gene3D | G3DSA:1.10.238.10 | - | 1 | 56 | 3.1E-16 |
| 9 | g11383.t12 | Gene3D | G3DSA:1.10.238.10 | - | 57 | 124 | 4.1E-19 |
| 3 | g11383.t12 | PANTHER | PTHR23049 | MYOSIN REGULATORY LIGHT CHAIN 2 | 1 | 131 | 1.4E-70 |
| 4 | g11383.t12 | PANTHER | PTHR23049:SF66 | MYOSIN REGULATORY LIGHT POLYPEPTIDE 9 | 1 | 131 | 1.4E-70 |
| 1 | g11383.t12 | Pfam | PF13202 | EF hand | 1 | 16 | 0.0087 |
| 2 | g11383.t12 | Pfam | PF13202 | EF hand | 65 | 82 | 0.12 |
| 8 | g11383.t12 | ProSitePatterns | PS00018 | EF-hand calcium-binding domain. | 3 | 15 | - |
| 12 | g11383.t12 | ProSiteProfiles | PS50222 | EF-hand calcium-binding domain profile. | 1 | 25 | 11.668 |
| 11 | g11383.t12 | ProSiteProfiles | PS50222 | EF-hand calcium-binding domain profile. | 59 | 94 | 11.668 |
| 7 | g11383.t12 | SMART | SM00054 | efh_1 | 1 | 22 | 8.6 |
| 6 | g11383.t12 | SMART | SM00054 | efh_1 | 63 | 91 | 0.28 |
| 5 | g11383.t12 | SUPERFAMILY | SSF47473 | EF-hand | 1 | 125 | 2.69E-35 |
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.
