Gene loci information

Transcript annotation

  • This transcript has been annotated as Ryanodine receptor.

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_1 g11391 g11391.t4 isoform g11391.t4 15905997 15909819
chr_1 g11391 g11391.t4 TSS g11391.t4 15905997 15905997
chr_1 g11391 g11391.t4 exon g11391.t4.exon1 15905997 15906056
chr_1 g11391 g11391.t4 exon g11391.t4.exon2 15906932 15907068
chr_1 g11391 g11391.t4 cds g11391.t4.CDS1 15907015 15907068
chr_1 g11391 g11391.t4 exon g11391.t4.exon3 15907133 15907336
chr_1 g11391 g11391.t4 cds g11391.t4.CDS2 15907133 15907336
chr_1 g11391 g11391.t4 exon g11391.t4.exon4 15909228 15909305
chr_1 g11391 g11391.t4 cds g11391.t4.CDS3 15909228 15909305
chr_1 g11391 g11391.t4 exon g11391.t4.exon5 15909364 15909462
chr_1 g11391 g11391.t4 cds g11391.t4.CDS4 15909364 15909462
chr_1 g11391 g11391.t4 exon g11391.t4.exon6 15909535 15909558
chr_1 g11391 g11391.t4 cds g11391.t4.CDS5 15909535 15909549
chr_1 g11391 g11391.t4 exon g11391.t4.exon7 15909620 15909689
chr_1 g11391 g11391.t4 exon g11391.t4.exon8 15909744 15909819
chr_1 g11391 g11391.t4 TTS g11391.t4 NA NA

Sequences

>g11391.t4 Gene=g11391 Length=748
CAGTCGAGTGCCAACATTCAATCGAATAACAGGTTAAAATCGTTTTGCTTCTACTTTTAG
CTATTCATATATGAATAATAATTCGAAAAAAGAGCAATAATAAAATAATATAAAAGTAAC
GAAAAGTAATTAACGGCCTCAAAATGGCCGAAGCAGATGGAGGATCCGAGCAGGATGATG
TCTCATTTCTTCGTACTGAAGACATGGTTTGCTTGTCATGTACAGCAACCGGAGAAAGAG
TGTGTTTGGCAGCTGAAGGTTTTGGCAATCGGCATTGCTTTTTGGAAAATATTGCCGACA
AAAATATTCCACCAGACCTTTCACAATGTGTTTTTGTAATTGAGCAAGCATTGTCAGTCA
GAGCTCTTCAAGAGTTAGTTACTGCTGCAGCCTCTGAATCGTCTAAAGGAACTGGTTCAG
GGCATCGTACGCTTCTATATGGCAATGCAATTTTATTACGTCACCAGAACAGTGATATGT
ACTTGGCATGTTTGTCAACATCCTCATCAAATGACAAATTATCTTTTGATGTTGGTTTAC
AAGAGCATAGTCATGGTGAAGCCTGTTGGTGGACGTTATGTACATCCAGCTAGCAAACAA
AGATCTGAAGGTGAAAAAGTGCGTGTTGGTGATGATTTGATTTTAGTTTCTGTAGCTACA
GAACGTTATTTGCACACAACAAAAGAGAATGATTTTTCAATTGTCAACGCAAGCTTCCAT
GTTACACATTGGTCTGTGCAACCATATG

>g11391.t4 Gene=g11391 Length=149
MAEADGGSEQDDVSFLRTEDMVCLSCTATGERVCLAAEGFGNRHCFLENIADKNIPPDLS
QCVFVIEQALSVRALQELVTAAASESSKGTGSGHRTLLYGNAILLRHQNSDMYLACLSTS
SSNDKLSFDVGLQEHSHGEACWWTLCTSS

Protein features from InterProScan

Transcript Database ID Name Start End E.value
6 g11391.t4 Gene3D G3DSA:2.80.10.50 - 1 149 0.000
2 g11391.t4 PANTHER PTHR12864:SF53 RYANODINE RECEPTOR 44F-LIKE PROTEIN 1 132 0.000
3 g11391.t4 PANTHER PTHR12864 RAN BINDING PROTEIN 9-RELATED 1 132 0.000
4 g11391.t4 PRINTS PR00795 Ryanodine receptor signature 56 77 0.000
5 g11391.t4 PRINTS PR00795 Ryanodine receptor signature 92 110 0.000
1 g11391.t4 Pfam PF08709 Inositol 1,4,5-trisphosphate/ryanodine receptor 12 145 0.000
7 g11391.t4 ProSiteProfiles PS50919 MIR domain profile. 94 148 9.043

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:0005219 ryanodine-sensitive calcium-release channel activity MF
GO:0006816 calcium ion transport BP
GO:0005789 endoplasmic reticulum membrane CC

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