Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Myosin regulatory light chain.

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_3 g533 g533.t7 TTS g533.t7 3961763 3961763
chr_3 g533 g533.t7 isoform g533.t7 3961881 3963293
chr_3 g533 g533.t7 exon g533.t7.exon1 3961881 3962067
chr_3 g533 g533.t7 exon g533.t7.exon2 3962138 3962649
chr_3 g533 g533.t7 cds g533.t7.CDS1 3962445 3962649
chr_3 g533 g533.t7 exon g533.t7.exon3 3962848 3963104
chr_3 g533 g533.t7 cds g533.t7.CDS2 3962848 3963104
chr_3 g533 g533.t7 exon g533.t7.exon4 3963162 3963293
chr_3 g533 g533.t7 cds g533.t7.CDS3 3963162 3963293
chr_3 g533 g533.t7 TSS g533.t7 3963350 3963350

Sequences

>g533.t7 Gene=g533 Length=1088
ATGGAAGAAGTGAAATTGGACAAAATTAGAGAATTTGTGAATCGACCTTATAGACCACCA
AAGCCTGTTAGTGCTGATGATCCAACTGACATTCAGGATTTGGATGAAATCAAATTGCAT
GAATTGAAAGAGTGTTTCACACTATTTGACCAAAACAATGATGGATTTATTGATGCTGAT
GATTTGCGACAAACATTTAAAACAATGGGAATGGAAGCGGATGACAAGGTGATTGAAAGT
ATGATTGCAGATGCCTCGCAACCAATTAACTTTGATAGCTTTGCCATGATGATGTGCTTT
AAAACAATGGAACTTGAACCTGAAATTGTATTGCTTGAAGCATTGTCAAAATGGGATGAG
AGAATTCAAGGCGTCATCAGTTTAGAAAGAATTTTCGCTCATTTAACCACCTACAACAAT
GATAGATTGAGTGTTGAAGAAGCGAAGGAAGTAATAAATGAAGCACCATTGATGCAAACG
AAAGAAGGATTGCGTGGGCTTGAAAGTCCAACAGACAGTTGGATCGATTATCTGTTATGG
GTTGAGAAATTTGCTGGATTCCGTAAACCACGAGCGGCAAATTATTCAATTTAAGAGAGA
GAGAAAAAATGTTTATTTTCACTTGTGTGCGTGTGTGTTTGTGTAAATAATCGAATCTCA
TAATCTCAAAGTGCTGTCGTACATTCGCATCGAAAAGATAAATCATCTCATAAATTTTAT
ACATACATGACATGCATCCCATGAAATAGTTAGTCAATAAAAATTCATAAATTCATGTTC
ATAAAAATTTCTTCTTTTTCACATTCGCACTCGCTTTTTTTGTGGCGCGCTTTGAAATTA
TGAGGTGGAAAGATATTAAGTTTATTTATAATGCGATTTCATGAAAATCATTACTATATG
ACATCAACTTTTTCAACCATAAAATGCTCCCTTCTTTCTGTCTGTCGTTCAGGGATTATT
TCTTCTGCAAATTAAAATTCGAAAGACATGTATAAGTTATTGTACTTTTTTCGATCTTTT
GTGTGTGCAAATTAAAGCTTCTTTAGCTCTCTCTCGCTCTGTGGATGTCAATAAGAATAA
ATTTATTT

>g533.t7 Gene=g533 Length=197
MEEVKLDKIREFVNRPYRPPKPVSADDPTDIQDLDEIKLHELKECFTLFDQNNDGFIDAD
DLRQTFKTMGMEADDKVIESMIADASQPINFDSFAMMMCFKTMELEPEIVLLEALSKWDE
RIQGVISLERIFAHLTTYNNDRLSVEEAKEVINEAPLMQTKEGLRGLESPTDSWIDYLLW
VEKFAGFRKPRAANYSI

Protein features from InterProScan

Transcript Database ID Name Start End E.value
5 g533.t7 CDD cd00051 EFh 41 98 1.96971E-9
4 g533.t7 Gene3D G3DSA:1.10.238.10 - 31 166 7.1E-18
2 g533.t7 PANTHER PTHR23049 MYOSIN REGULATORY LIGHT CHAIN 2 30 162 6.1E-31
1 g533.t7 Pfam PF13405 EF-hand domain 41 69 2.4E-7
6 g533.t7 ProSitePatterns PS00018 EF-hand calcium-binding domain. 50 62 -
8 g533.t7 ProSiteProfiles PS50222 EF-hand calcium-binding domain profile. 37 72 14.513
7 g533.t7 SMART SM00054 efh_1 41 69 1.6E-5
3 g533.t7 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.t7; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g533.t7.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