General information for g11383.t43
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.t43 | TTS | g11383.t43 | 15878931 | 15878931 |
| chr_1 | g11383 | g11383.t43 | isoform | g11383.t43 | 15879154 | 15880834 |
| chr_1 | g11383 | g11383.t43 | exon | g11383.t43.exon1 | 15879154 | 15879261 |
| chr_1 | g11383 | g11383.t43 | cds | g11383.t43.CDS1 | 15879154 | 15879261 |
| chr_1 | g11383 | g11383.t43 | exon | g11383.t43.exon2 | 15879344 | 15879471 |
| chr_1 | g11383 | g11383.t43 | cds | g11383.t43.CDS2 | 15879344 | 15879471 |
| chr_1 | g11383 | g11383.t43 | exon | g11383.t43.exon3 | 15879520 | 15879709 |
| chr_1 | g11383 | g11383.t43 | cds | g11383.t43.CDS3 | 15879520 | 15879697 |
| chr_1 | g11383 | g11383.t43 | exon | g11383.t43.exon4 | 15880716 | 15880834 |
| chr_1 | g11383 | g11383.t43 | TSS | g11383.t43 | 15880819 | 15880819 |
Sequences
>g11383.t43 Gene=g11383 Length=545
ATGTAGTGTAGAAGTTGATTTCGAGAATAAAAACACTTTTTTTTGATTGAAAAATTTTAA
TTGATTTTGCATCTTATAGTGTTTTAACTAATTTGTATTGAATTTAATATAATATTTAGG
AAGCTTTCAATATGATTGATCAAAATCGCGATGGATTCATTGAAAAAGAAGATCTTCATG
ATATGCTTGCTTCACTTGGAAAGAATCCAACAGATGACTATTTGGAGTCAATGATGAATG
AAGCTCCTGGTCCAATTAATTTTACAATGTTTCTCACTTTATTTGGAGAAAGATTACAAG
GCAAGAATTGCACAGACCCTGAAGATGTAATTAAAAATGCATTCGGATGCTTTGATGAAG
ACAATAATGGCCATATTTCTGAGGATCGTCTGAGAGAGTTATTAACTACAATGGGTGATC
GTTTTACTGATGAAGAGGTTGACGAAATGTATCGTGAAGCGCCAATTAAAAACAATCTTT
TTGACTATATCGAATTCACAAGAATCTTAAAACATGGCGCTAAAGACAATGAGAATGAAC
AATAA
>g11383.t43 Gene=g11383 Length=137
MIDQNRDGFIEKEDLHDMLASLGKNPTDDYLESMMNEAPGPINFTMFLTLFGERLQGKNC
TDPEDVIKNAFGCFDEDNNGHISEDRLRELLTTMGDRFTDEEVDEMYREAPIKNNLFDYI
EFTRILKHGAKDNENEQ
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 10 | g11383.t43 | Gene3D | G3DSA:1.10.238.10 | - | 1 | 56 | 3.3E-16 |
| 9 | g11383.t43 | Gene3D | G3DSA:1.10.238.10 | - | 60 | 127 | 6.7E-19 |
| 3 | g11383.t43 | PANTHER | PTHR23049 | MYOSIN REGULATORY LIGHT CHAIN 2 | 1 | 134 | 2.5E-68 |
| 4 | g11383.t43 | PANTHER | PTHR23049:SF66 | MYOSIN REGULATORY LIGHT POLYPEPTIDE 9 | 1 | 134 | 2.5E-68 |
| 1 | g11383.t43 | Pfam | PF13202 | EF hand | 1 | 16 | 0.009 |
| 2 | g11383.t43 | Pfam | PF13202 | EF hand | 68 | 85 | 0.12 |
| 8 | g11383.t43 | ProSitePatterns | PS00018 | EF-hand calcium-binding domain. | 3 | 15 | - |
| 12 | g11383.t43 | ProSiteProfiles | PS50222 | EF-hand calcium-binding domain profile. | 1 | 25 | 11.668 |
| 11 | g11383.t43 | ProSiteProfiles | PS50222 | EF-hand calcium-binding domain profile. | 62 | 97 | 11.668 |
| 7 | g11383.t43 | SMART | SM00054 | efh_1 | 1 | 22 | 8.6 |
| 6 | g11383.t43 | SMART | SM00054 | efh_1 | 66 | 94 | 0.28 |
| 5 | g11383.t43 | SUPERFAMILY | SSF47473 | EF-hand | 1 | 128 | 2.78E-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