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.t7 isoform g11391.t7 15928058 15929198
chr_1 g11391 g11391.t7 exon g11391.t7.exon1 15928058 15928635
chr_1 g11391 g11391.t7 cds g11391.t7.CDS1 15928212 15928635
chr_1 g11391 g11391.t7 exon g11391.t7.exon2 15928689 15928951
chr_1 g11391 g11391.t7 cds g11391.t7.CDS2 15928689 15928951
chr_1 g11391 g11391.t7 exon g11391.t7.exon3 15929007 15929198
chr_1 g11391 g11391.t7 cds g11391.t7.CDS3 15929007 15929198
chr_1 g11391 g11391.t7 TTS g11391.t7 15929278 15929278
chr_1 g11391 g11391.t7 TSS g11391.t7 NA NA

Sequences

>g11391.t7 Gene=g11391 Length=1033
TCCTGAAGATGACGATATAAAATCACATTGGGATAAATTAGTAATTAGTTCAAAAAGCTT
CCCTGTCAATTATTGGGATAAATTTGTAAAGAAAAAGGTTCGACAAAAGTACAGCGAAAC
TTATGACTTTGATTCAATTTCAAATTTACTTGGTATGGAAAAGACAGCATTTGGCACTCA
AGAAGTCAACGAAAGCGGTGGACTTATTCATTTTATTCTCAATATTGATTGGCGTTATCA
AGTATGGAAAGCTGGTGTTACAATCACAGATAATGCTTTCCTTTATTCTCTTTGGTACTT
TACTTTCTCAATTTTGGGCAACTTTAACAACTTTTTCTTTGCTGCTCATTTACTCGATGT
TGCTGTTGGTTTCAAGACTCTAAGAACAATCTTGCAATCAGTAACACACAATGGCAAACA
ATTAGTTTTGACTGTCATGCTTCTTACAATTATTGTGTATATTTACACTGTAATTGCTTT
CAACTTTTTCCGCAAATTCTATATACAAGAGGAAGAAGATGAAGTAGATAAAAAATGTCA
TGATATGTTAACATGTTTCGTCTTCCATTTGTATAAGGGTGTAAGAGCTGGTGGTGGTAT
TGGTGATGAAATAGGAGATCCAGACGGAGATGATTATGAAGTTTATCGTATAATTTTCGA
TATTACATTCTTCTTCTTCGTTATTGTCATCTTGTTGGCCATCATTCAAGGTTTGATCAT
TGATGCTTTTGGTGAGCTTCGTGATCAATTAGAATCAGTAAAAGAAGACATGGAGTCGAA
TTGCTTTATCTGTGGCATAGGAAAAGACTACTTTGATAAAGTTCCTCATGGATTTGATAC
GCACGTTGCACAAGAACATAATCTAGCAAATTACATGTTCTTCCTGATGCACTTGATTAA
TAAACCGGATACAGAATATACGGGTCAAGAGACTTATGTGTGGAACATGTATCAACAGCG
CTGTTGGGATTTCTTCCCTGTTGGTGATTGCTTTAGGAAGCAATATGAAGATGAACTTGG
TGGAAGCCAGTAA

>g11391.t7 Gene=g11391 Length=292
MEKTAFGTQEVNESGGLIHFILNIDWRYQVWKAGVTITDNAFLYSLWYFTFSILGNFNNF
FFAAHLLDVAVGFKTLRTILQSVTHNGKQLVLTVMLLTIIVYIYTVIAFNFFRKFYIQEE
EDEVDKKCHDMLTCFVFHLYKGVRAGGGIGDEIGDPDGDDYEVYRIIFDITFFFFVIVIL
LAIIQGLIIDAFGELRDQLESVKEDMESNCFICGIGKDYFDKVPHGFDTHVAQEHNLANY
MFFLMHLINKPDTEYTGQETYVWNMYQQRCWDFFPVGDCFRKQYEDELGGSQ

Protein features from InterProScan

Transcript Database ID Name Start End E.value
7 g11391.t7 Gene3D G3DSA:1.10.287.70 - 74 196 6.4E-6
2 g11391.t7 PANTHER PTHR12864:SF53 RYANODINE RECEPTOR 44F-LIKE PROTEIN 1 290 7.0E-200
3 g11391.t7 PANTHER PTHR12864 RAN BINDING PROTEIN 9-RELATED 1 290 7.0E-200
1 g11391.t7 Pfam PF00520 Ion transport protein 55 198 9.2E-16
10 g11391.t7 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 45 -
14 g11391.t7 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 46 69 -
9 g11391.t7 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 70 89 -
13 g11391.t7 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 90 112 -
11 g11391.t7 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 113 165 -
12 g11391.t7 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 166 189 -
8 g11391.t7 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 190 292 -
5 g11391.t7 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 42 64 -
6 g11391.t7 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 90 112 -
4 g11391.t7 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 170 189 -

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:0016020 membrane CC
GO:0055085 transmembrane transport BP
GO:0005216 ion channel activity MF
GO:0006811 ion transport BP

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.

Raw TPM values