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[173827_at] ryanodine receptor

Description CEK003H7R_rc /REP_DB=TREMBL Accession /5_PRIME_EXT_ID=K11C4.5 /5_PRIME_EXT_DB=WormBase Gene ID /GB=D27189 /WB_GENE_ID=K11C4.5 /WP=CE12116 /CHR=5 /FEA=Genomic Cluster /GEN=unc-68 /DEF=ryanodine receptor; C.elegans cDNA clone yk3h7 : 3prime end, single read.
Cluster 6grp_highest_10_10 > 30      6grp_high1_10_10 > 04      4grp_highest_8_8 > 41      4grp_high_8_8 > 49      6grp_highest_nonorm > 41      6grp_total > 15      4grp_total > 62      6grp_highest_sub > De      6grp_cgc > 32      6grp_high1_sub > De      6grp_cgc_sub > De      6grp_total_sub > Decrease      6grp_rule_based > S1      4grp_rule_based > L1      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 963
1 2 3 4 range
A 1032.8
(3)
P 		632.8
(0.1)
P 		545.1
(-0.5)
P 		191.3
(-3)
P 		842
B 959.9
(3)
P 		779
(1.5)
P 		586.2
(-0.1)
P 		236.2
(-3)
P 		724
C 1153.9
(3)
P 		635
(-0.4)
P 		681.2
(-0.1)
P 		246
(-3)
P 		908
avr 1048.9
(3) 		682.3
(0.3) 		604.2
(-0.2) 		224.5
(-3) 		824

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 755
1 2 3 4 5 6 range
A 792.8
(1.8)
P 		909.7
(3)
P 		613.8
(-0.1)
P 		385.7
(-2.4)
P 		709.7
(0.9)
P 		330.8
(-3)
P 		579
B 1085.6
(3)
P 		819.5
(0.8)
P 		810.9
(0.7)
P 		705
(-0.1)
P 		560.6
(-1.3)
P 		359.7
(-3)
P 		726
C 865.9
(1.8)
P 		963.8
(3)
P 		663
(-0.7)
P 		732.9
(0.2)
P 		528.9
(-2.3)
P 		472.6
(-3)
P 		491
avr 914.8
(3) 		897.7
(2.8) 		695.9
(0.5) 		607.9
(-0.5) 		599.7
(-0.6) 		387.7
(-3) 		527
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 354
1 2 3 4 range
A 376
(3)
P 		137.4
(-1.1)
P 		142.5
(-1)
P 		28
(-3)
P 		348
B 306.1
(3)
P 		192.4
(0.3)
P 		135.8
(-1)
P 		50.3
(-3)
P 		256
C 382
(3)
P 		182.6
(-0.5)
P 		237.4
(0.5)
P 		41.5
(-3)
P 		341
avr 354.7
(3) 		170.8
(-0.5) 		171.9
(-0.5) 		39.9
(-3) 		315

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 297
1 2 3 4 5 6 range
A 146.1
(-1.4)
P 		323.5
(3)
P 		133.7
(-1.7)
P 		97.8
(-2.6)
P 		214.2
(0.3)
P 		80.5
(-3)
P 		243
B 377.7
(3)
P 		272.8
(0.4)
P 		196.9
(-1.5)
P 		186.7
(-1.7)
P 		227.8
(-0.7)
P 		134.1
(-3)
P 		244
C 320.9
(3)
P 		294.1
(2.1)
P 		168.8
(-2.3)
P 		147.4
(-3)
P 		171.2
(-2.2)
P 		158.2
(-2.6)
P 		174
avr 281.6
(2.5) 		296.8
(3) 		166.5
(-1.5) 		144
(-2.3) 		204.4
(-0.2) 		124.3
(-3) 		173
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 173827_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.25208
Sequence Type Exemplar sequence
Representative Public ID CEK003H7R NCBI
Target Description CEK003H7R_rc /REP_DB=TREMBL Accession /5_PRIME_EXT_ID=K11C4.5 /5_PRIME_EXT_DB=WormBase Gene ID /GB=D27189 /WB_GENE_ID=K11C4.5 /WP=CE12116 /CHR=5 /FEA=Genomic Cluster /GEN=unc-68 /DEF=ryanodine receptor; C.elegans cDNA clone yk3h7 : 3prime end, single read.
Cluster Evidence This cluster is supported by a Genomic Cluster.
Annotation Method Description
Annotation Description This probe set was annotated using the Matching Probes based pipeline to a RefSeq identifier using 1 transcript(s).
Annotation Grade This is a grade A annotation.
Annotation Transcript Cluster (# of Matching Probes) NM_072352(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_072352 NCBI Caenorhabditis elegans UNCoordinated family member (unc-68) (unc-68) mRNA, complete cds. 11/11 None
K11C4.5 ENSEMBL cdna:known chromosome:CEL140:V:6904281:6926786:-1 gene:K11C4.5 11/11 A 
Annotation Notes
There are no noteworthy cross hybridizing mRNAs found for this probe set.
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrV:6904309-6926788(-) 99.92 100.0
Public Domain and Genome References
Gene Title ryanodine receptor
Gene Symbol unc-68
Ensembl K11C4.5
Entrez Gene 179080 Entrez gene
SwissProt Q94279 EMBL-EBI
WormBase CE12116 Wormbase
Functional Annotations
Ortholog
ID Title Organism
CANINE:1606135_AT ryanodine receptor 2 (cardiac) cfa
CANINE:1604423_AT ryanodine receptor 2 (cardiac) cfa
CANINE:1587427_AT ryanodine receptor 2 (cardiac) cfa
CANINE:1582933_AT ryanodine receptor 2 (cardiac) cfa
CANINE_2:CFA.269.1.A1_AT ryanodine receptor 2 (cardiac) cfa
CANINE_2:CFA.3475.1.S1_S_AT ryanodine receptor 2 (cardiac) cfa
CANINE_2:CFA.9100.1.A1_AT ryanodine receptor 2 (cardiac) cfa
CANINE_2:CFAAFFX.15723.1.S1_S_AT ryanodine receptor 2 (cardiac) cfa
CANINE_2:CFAAFFX.15743.1.S1_AT ryanodine receptor 2 (cardiac) cfa
CANINE:1582932_AT ryanodine receptor 2 (cardiac) cfa
DROSOPHILA_2:1633452_A_AT Ryanodine receptor 44F dm
DROSGENOME1:143650_AT Ryanodine receptor 44F dm
CHICKEN:GGAAFFX.6834.2.S1_S_AT similar to Ryanodine receptor 2 (Cardiac muscle-type ryanodine receptor) (RyR2) (RYR-2) (Cardiac muscle ryanodine receptor-calcium release channel) (hRYR-2) gga
CHICKEN:GGAAFFX.6834.4.S1_S_AT similar to Ryanodine receptor 2 (Cardiac muscle-type ryanodine receptor) (RyR2) (RYR-2) (Cardiac muscle ryanodine receptor-calcium release channel) (hRYR-2) gga
HG-U133_PLUS_2:207557_S_AT ryanodine receptor 2 (cardiac) hs
HG-U133A:207557_S_AT ryanodine receptor 2 (cardiac) hs
HG-FOCUS:207557_S_AT ryanodine receptor 2 (cardiac) hs
HG-U133A_2:207557_S_AT ryanodine receptor 2 (cardiac) hs
HU35KSUBA:X98330_AT ryanodine receptor 2 (cardiac) hs
HUGENEFL:X98330_AT ryanodine receptor 2 (cardiac) hs
HU35KSUBC:RC_F02154_S_AT ryanodine receptor 2 (cardiac) hs
U133_X3P:G4506756_3P_S_AT ryanodine receptor 2 (cardiac) hs
U133_X3P:HS.332699.0.A1_3P_AT ryanodine receptor 2 (cardiac) hs
HG-U133A_2:214044_AT ryanodine receptor 2 (cardiac) hs
HG-U133_PLUS_2:214044_AT ryanodine receptor 2 (cardiac) hs
HG-U133A:214044_AT ryanodine receptor 2 (cardiac) hs
HG-U95AV2:38263_AT ryanodine receptor 2 (cardiac) hs
HG-U133_PLUS_2:243447_AT Ryanodine receptor 2 (cardiac) hs
HG-U133B:243447_AT Ryanodine receptor 2 (cardiac) hs
HG-U95B:42351_AT Ryanodine receptor 2 (cardiac) hs
HG-U95E:78861_F_AT Ryanodine receptor 2 (cardiac) hs
HU35KSUBD:RC_W86038_AT Ryanodine receptor 2 (cardiac) hs
U133_X3P:HS.109514.0.A1_3P_AT Ryanodine receptor 2 (cardiac) hs
MOUSE430_2:1421126_AT ryanodine receptor 2, cardiac mm
MOE430A:1421126_AT ryanodine receptor 2, cardiac mm
MOUSE430A_2:1421126_AT ryanodine receptor 2, cardiac mm
MU11KSUBB:X83933_S_AT ryanodine receptor 2, cardiac mm
MG-U74AV2:102653_AT ryanodine receptor 2, cardiac mm
MOE430A:1450123_AT ryanodine receptor 2, cardiac mm
MOUSE430A_2:1450123_AT ryanodine receptor 2, cardiac mm
MOUSE430_2:1450123_AT ryanodine receptor 2, cardiac mm
MG-U74CV2:140190_AT Ryanodine receptor 2, cardiac (Ryr2), mRNA mm
MOUSE430_2:1445498_AT Ryanodine receptor 2, cardiac (Ryr2), mRNA mm
MOE430B:1445498_AT Ryanodine receptor 2, cardiac (Ryr2), mRNA mm
Gene Ontology
GO Biological Process (view graph)
ID Description Evidence Links
6811 ion transport inferred from electronic annotation QuickGO AmiGO
6816 calcium ion transport inferred from electronic annotation QuickGO AmiGO
9058 biosynthesis inferred from electronic annotation QuickGO AmiGO
GO Cellular Component (view graph)
ID Description Evidence Links
16020 membrane inferred from electronic annotation QuickGO AmiGO
GO Molecular Function (view graph)
ID Description Evidence Links
4420 hydroxymethylglutaryl-CoA reductase (NADPH) activity inferred from electronic annotation QuickGO AmiGO
5216 ion channel activity inferred from electronic annotation QuickGO AmiGO
5262 calcium channel activity inferred from electronic annotation QuickGO AmiGO
5509 calcium ion binding inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast AAB18318 Uncoordinated protein 68 [Caenorhabditis elegans] ref|NP_504753.1| UNCoordinated family member (unc-68) [Caenorhabditis elegans] 0.0
blast CAE71970 Hypothetical protein CBG19042 [Caenorhabditis briggsae] 0.0
blast BAA08309.1 ryanodine receptor [Caenorhabditis elegans] 0.0
Protein Domains
Database ID Description E-Value
scop a.4.5.Forkhead DNA-binding domain All alpha proteins; DNA/RNA-binding 3-helical bundle; "Winged helix" DNA-binding domain; Forkhead DNA-binding domain 1.5
Pfam IPR005821 EMBL-EBI Ion transport protein 2.1E-12
Pfam IPR002048 EMBL-EBI Calcium-binding EF-hand 1.8E-6
Pfam IPR002048 EMBL-EBI Calcium-binding EF-hand 0.047
Pfam IPR003608 EMBL-EBI MIR domain 5.7E-4
Pfam IPR003608 EMBL-EBI MIR domain 1.7E-7
Pfam IPR003608 EMBL-EBI MIR domain 2.0E-10
Pfam IPR003032 EMBL-EBI Ryanodine receptor Ryr 1.1E-26
Pfam IPR003032 EMBL-EBI Ryanodine receptor Ryr 2.3E-24
Pfam IPR003032 EMBL-EBI Ryanodine receptor Ryr 4.5E-23
Pfam IPR003032 EMBL-EBI Ryanodine receptor Ryr 2.8E-14
Pfam IPR003877 EMBL-EBI SPla/RYanodine receptor SPRY 1.1E-33
Pfam IPR003877 EMBL-EBI SPla/RYanodine receptor SPRY 1.9E-40
Pfam IPR003877 EMBL-EBI SPla/RYanodine receptor SPRY 1.5E-28
Pfam IPR009460 EMBL-EBI Ryanodine Receptor TM 4-6 1.0E-126
Pfam IPR000699 EMBL-EBI Intracellular calcium-release channel 1.1E-93
Pfam IPR000699 EMBL-EBI Intracellular calcium-release channel 3.2E-95
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_504753.1 6 4473-4495,4658-4675,4721-4743,4859-4881,4904-4926,4986-5005
K11C4.5 6 4473-4495,4658-4675,4721-4743,4859-4881,4904-4926,4986-5005
Sequence
Target Sequence 
>C. ELEGANS:173827_AT
aaaatctttcatcagcagaattcttaatagaacaaatgtttcgggtcaactcaatgttta
ggtgttattcgttccaattctcatcactagtatttttcgattctgatattctttttcaat
tttttatggaatatgtcgttcttcgttattattcagaattgagcgacgtttttagtctgt
ttaattgttatattttttcaacgtttcaaacaaccaaatcataacttcaaacgtgcctta
gcgaaccactttg

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
AAAATCTTTCATCAGCAGAATTCTT 553 133 15338 Antisense
AAATGTTTCGGGTCAACTCAATGTT 512 119 15371 Antisense
CAATGTTTAGGTGTTATTCGTTCCA 256 181 15389 Antisense
ATTCGTTCCAATTCTCATCACTAGT 680 9 15404 Antisense
AATTCTCATCACTAGTATTTTTCGA 365 177 15413 Antisense
ATTTTTCGATTCTGATATTCTTTTT 386 15 15429 Antisense
ATATGTCGTTCTTCGTTATTATTCA 221 21 15468 Antisense
TTGAGCGACGTTTTTAGTCTGTTTA 353 681 15496 Antisense
CAACGTTTCAAACAACCAAATCATA 529 145 15536 Antisense
CAAATCATAACTTCAAACGTGCCTT 684 193 15552 Antisense
AAACGTGCCTTAGCGAACCACTTTG 437 115 15566 Antisense
Sequence Source Affymetrix Proprietary Database