General information for g533.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Myosin regulatory light chain.
Parent gene
- The parent gene g533 is located on chr_3: 3962445..3963293 (- 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_3 | g533 | g533.t1 | TTS | g533.t1 | 3961763 | 3961763 |
| chr_3 | g533 | g533.t1 | isoform | g533.t1 | 3962445 | 3963293 |
| chr_3 | g533 | g533.t1 | exon | g533.t1.exon1 | 3962445 | 3962649 |
| chr_3 | g533 | g533.t1 | cds | g533.t1.CDS1 | 3962445 | 3962649 |
| chr_3 | g533 | g533.t1 | exon | g533.t1.exon2 | 3962848 | 3963104 |
| chr_3 | g533 | g533.t1 | cds | g533.t1.CDS2 | 3962848 | 3963104 |
| chr_3 | g533 | g533.t1 | exon | g533.t1.exon3 | 3963162 | 3963293 |
| chr_3 | g533 | g533.t1 | cds | g533.t1.CDS3 | 3963162 | 3963293 |
| chr_3 | g533 | g533.t1 | TSS | g533.t1 | 3963350 | 3963350 |
Sequences
>g533.t1 Gene=g533 Length=594
ATGGAAGAAGTGAAATTGGACAAAATTAGAGAATTTGTGAATCGACCTTATAGACCACCA
AAGCCTGTTAGTGCTGATGATCCAACTGACATTCAGGATTTGGATGAAATCAAATTGCAT
GAATTGAAAGAGTGTTTCACACTATTTGACCAAAACAATGATGGATTTATTGATGCTGAT
GATTTGCGACAAACATTTAAAACAATGGGAATGGAAGCGGATGACAAGGTGATTGAAAGT
ATGATTGCAGATGCCTCGCAACCAATTAACTTTGATAGCTTTGCCATGATGATGTGCTTT
AAAACAATGGAACTTGAACCTGAAATTGTATTGCTTGAAGCATTGTCAAAATGGGATGAG
AGAATTCAAGGCGTCATCAGTTTAGAAAGAATTTTCGCTCATTTAACCACCTACAACAAT
GATAGATTGAGTGTTGAAGAAGCGAAGGAAGTAATAAATGAAGCACCATTGATGCAAACG
AAAGAAGGATTGCGTGGGCTTGAAAGTCCAACAGACAGTTGGATCGATTATCTGTTATGG
GTTGAGAAATTTGCTGGATTCCGTAAACCACGAGCGGCAAATTATTCAATTTAA
>g533.t1 Gene=g533 Length=197
MEEVKLDKIREFVNRPYRPPKPVSADDPTDIQDLDEIKLHELKECFTLFDQNNDGFIDAD
DLRQTFKTMGMEADDKVIESMIADASQPINFDSFAMMMCFKTMELEPEIVLLEALSKWDE
RIQGVISLERIFAHLTTYNNDRLSVEEAKEVINEAPLMQTKEGLRGLESPTDSWIDYLLW
VEKFAGFRKPRAANYSI
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g533.t1 | CDD | cd00051 | EFh | 41 | 98 | 1.96971E-9 |
| 4 | g533.t1 | Gene3D | G3DSA:1.10.238.10 | - | 31 | 166 | 7.1E-18 |
| 2 | g533.t1 | PANTHER | PTHR23049 | MYOSIN REGULATORY LIGHT CHAIN 2 | 30 | 162 | 6.1E-31 |
| 1 | g533.t1 | Pfam | PF13405 | EF-hand domain | 41 | 69 | 2.4E-7 |
| 6 | g533.t1 | ProSitePatterns | PS00018 | EF-hand calcium-binding domain. | 50 | 62 | - |
| 8 | g533.t1 | ProSiteProfiles | PS50222 | EF-hand calcium-binding domain profile. | 37 | 72 | 14.513 |
| 7 | g533.t1 | SMART | SM00054 | efh_1 | 41 | 69 | 1.6E-5 |
| 3 | g533.t1 | SUPERFAMILY | SSF47473 | EF-hand | 36 | 156 | 8.34E-21 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g533/g533.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g533.t1.fa.iupred3.txt does not exist
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