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[191259_s_at] SpoU rRNA Methylase family

Description Y45F3A.9 /REP_DB=WormBase Gene ID /WP=CE19170 /TR=Q9XWY8 /GB=CAA21494.1 /SUBMIT=HINXTON /CHR=3 /FEA=Sanger Annotation /DEF=SpoU rRNA Methylase family
Cluster 6grp_total > 67      4grp_total > 10      6grp_total_sub > Increase      6grp_rule_based > S6      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 14
1 2 3 4 range
A 4.9
(-3)
A 		5.7
(-2.7)
A 		6.1
(-2.5)
A 		19
(3)
A 		14
B 5
(-2.7)
A 		4.8
(-2.8)
A 		4.6
(-3)
A 		11.6
(3)
A 		7
C 5.6
(-1.8)
A 		8
(3)
A 		5
(-3)
A 		5.4
(-2.2)
A 		3
avr 5.2
(-3) 		6.2
(-2.1) 		5.2
(-3) 		12
(3) 		7

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 60
1 2 3 4 5 6 range
A 5
(-2.8)
A 		6.3
(-2.2)
A 		4.6
(-2.9)
A 		19.5
(3)
A 		4.4
(-3)
A 		8.5
(-1.4)
A 		15
B 9.8
(-2.4)
A 		4.4
(-2.9)
A 		3.6
(-3)
A 		6.3
(-2.7)
A 		6.2
(-2.7)
A 		63.5
(3)
A 		60
C 8.4
(-2.5)
A 		4
(-3)
A 		5.7
(-2.8)
A 		8.5
(-2.5)
A 		6
(-2.8)
A 		56.2
(3)
A 		52
avr 7.7
(-2.5) 		4.9
(-3) 		4.6
(-3) 		11.4
(-1.9) 		5.5
(-2.9) 		42.7
(3) 		38
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 2
1 2 3 4 range
A 1.8
(-0.8)
A 		1.2
(-3)
A 		1.6
(-1.5)
A 		2.8
(3)
A 		2
B 1.6
(-0.9)
A 		1.2
(-2.6)
A 		1.1
(-3)
A 		2.5
(3)
A 		1
C 1.9
(1.3)
A 		2.3
(3)
A 		1.8
(0.9)
A 		0.9
(-3)
A 		1
avr 1.8
(0) 		1.6
(-2) 		1.5
(-3) 		2.1
(3) 		1

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 23
1 2 3 4 5 6 range
A 0.9
(-3)
A 		2.2
(-1.1)
A 		1
(-2.9)
A 		4.9
(3)
A 		1.3
(-2.4)
A 		2.1
(-1.2)
A 		4
B 3.4
(-2.3)
A 		1.5
(-2.8)
A 		0.9
(-3)
A 		1.7
(-2.8)
A 		2.5
(-2.6)
A 		23.7
(3)
A 		23
C 3.1
(-2.4)
A 		1.2
(-3)
A 		1.5
(-2.9)
A 		1.7
(-2.8)
A 		1.9
(-2.8)
A 		18.8
(3)
A 		18
avr 2.5
(-2.4) 		1.6
(-2.8) 		1.1
(-3) 		2.8
(-2.3) 		1.9
(-2.7) 		14.9
(3) 		14
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 191259_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.6307
Sequence Type Exemplar sequence
Representative Public ID Y45F3A.9 NCBI
Target Description Y45F3A.9 /REP_DB=WormBase Gene ID /WP=CE19170 /TR=Q9XWY8 /GB=CAA21494.1 /SUBMIT=HINXTON /CHR=3 /FEA=Sanger Annotation /DEF=SpoU rRNA Methylase family
Cluster Evidence This cluster is supported by a Sanger Annotation.
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_066932(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_066932 NCBI Caenorhabditis elegans Y45F3A.9 (Y45F3A.9) mRNA, complete cds. 11/11 None
GENEFINDER00000002988 ENSEMBL cdna:GeneFinder chromosome:CEL140:III:10592704:10595039:-1 11/11 None
SNAP00000002984 ENSEMBL cdna:SNAP chromosome:CEL140:III:10592729:10595039:-1 10/11 None
Y45F3A.9 ENSEMBL cdna:known chromosome:CEL140:III:10591211:10595039:-1 gene:Y45F3A.9 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
chrIII:10592794-10595035(-) 100.0 100.0
Public Domain and Genome References
Gene Title SpoU rRNA Methylase family
Ensembl Y45F3A.9
Entrez Gene 3565184 Entrez gene
SwissProt Q9XWY8 EMBL-EBI
WormBase CE19170 Wormbase
Functional Annotations
Ortholog
ID Title Organism
CANINE_2:CFAAFFX.27317.1.S1_AT similar to Y45F3A.9 cfa
HG-U133_PLUS_2:219967_AT hypothetical protein FLJ22578 hs
HG-U133A:219967_AT hypothetical protein FLJ22578 hs
HG-U133A_2:219967_AT hypothetical protein FLJ22578 hs
U133_X3P:G13376295_3P_AT hypothetical protein FLJ22578 hs
HG-U95E:86259_F_AT hypothetical protein FLJ22578 hs
MG-U74BV2:109632_AT RIKEN cDNA A530065E19 gene mm
MG-U74BV2:165386_R_AT RIKEN cDNA A530065E19 gene mm
MOE430A:1424219_AT RIKEN cDNA A530065E19 gene mm
MOUSE430A_2:1424219_AT RIKEN cDNA A530065E19 gene mm
MOUSE430_2:1424219_AT RIKEN cDNA A530065E19 gene mm
MG-U74CV2:133897_AT RIKEN cDNA A530065E19 gene (A530065E19Rik), mRNA mm
MOE430B:1442711_AT RIKEN cDNA A530065E19 gene (A530065E19Rik), mRNA mm
MOUSE430_2:1442711_AT RIKEN cDNA A530065E19 gene (A530065E19Rik), mRNA mm
MU19KSUBC:TC35896_AT RIKEN cDNA A530065E19 gene (A530065E19Rik), mRNA mm
Gene Ontology
GO Biological Process (view graph)
ID Description Evidence Links
6396 RNA processing inferred from electronic annotation QuickGO AmiGO
GO Molecular Function (view graph)
ID Description Evidence Links
3723 RNA binding inferred from electronic annotation QuickGO AmiGO
8173 RNA methyltransferase activity inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast CAA21494 Hypothetical protein Y45F3A.9 [Caenorhabditis elegans] ref|NP_499333.1| Y45F3A.9 [Caenorhabditis elegans] 1.0E-156
blast CAA21494 Hypothetical protein Y45F3A.9 [Caenorhabditis elegans] ref|NP_499333.1| Y45F3A.9 [Caenorhabditis elegans] 1.0E-148
blast CAA21494 Hypothetical protein Y45F3A.9 [Caenorhabditis elegans] ref|NP_499333.1| Y45F3A.9 [Caenorhabditis elegans] 1.0E-116
blast AAC62129 hypothetical protein [Arabidopsis thaliana] 5.0E-22
blast AAM19346 hypothetical protein [Arabidopsis thaliana] gb|AAL32808.1| Unknown protein [Arabidopsis thaliana] ref|NP_849992.1| tRNA/rRNA methyltransferase (SpoU) family protein [Arabidopsis thaliana] 5.0E-22
blast AAC62129 hypothetical protein [Arabidopsis thaliana] 9.0E-20
blast AAM19346 hypothetical protein [Arabidopsis thaliana] gb|AAL32808.1| Unknown protein [Arabidopsis thaliana] ref|NP_849992.1| tRNA/rRNA methyltransferase (SpoU) family protein [Arabidopsis thaliana] 9.0E-20
Protein Domains
Database ID Description E-Value
Pfam IPR001537 EMBL-EBI tRNA/rRNA methyltransferase (SpoU) 1.4E-15
Pfam IPR001537 EMBL-EBI tRNA/rRNA methyltransferase (SpoU) 4.9E-12
Pfam IPR001537 EMBL-EBI tRNA/rRNA methyltransferase (SpoU) 5.9E-20
Sequence
Target Sequence 
>C. ELEGANS:191259_S_AT
aactctgctaactgatgaccaactcgatcggctcaccgagtttcagcttcacaatggaat
ctgcatggacgccagcgctctgcaattctcaaatttcgagccgaaaaccgtgtcgatttt
tgtggataaagtgttggatcctgggaatttgggtgcaatcggaagaagtgcatggtattt
tggagccgatgggcttggacttgtcaagggaagaggacccaaatcgattaccccggcaat
gatcaaatcatcgtgtggagccctggagcatcttccagtacagcaatttctcaatttcaa
cgagtttcgcgacaaaatcaaagctgccggcggtgaactcgtggcgacttgtgatcctgg
tgctgctgaaaaggctggaatttcggcaaaatcactggatcagtggacaccggaaaaacc
cgtgggcattgtgctcggcgacgagggtgtcggaattagtcgggggattctgaatctttg
tgatactgtgatatcgatttccccagtgaggaaagacggatccaatgtgacttcgttgaa
tgtttcagttgttgcaggcatcctcc

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
AACTCTGCTAACTGATGACCAACTC 675 137 297 Antisense
CTCGATCGGCTCACCGAGTTTCAGC 310 233 319 Antisense
GAGCCGATGGGCTTGGACTTGTCAA 99 385 479 Antisense
CAAATCGATTACCCCGGCAATGATC 28 193 516 Antisense
TCAAATCATCGTGTGGAGCCCTGGA 479 627 539 Antisense
GAGCATCTTCCAGTACAGCAATTTC 58 389 562 Antisense
CAAAGCTGCCGGCGGTGAACTCGTG 323 191 615 Antisense
GTGAACTCGTGGCGACTTGTGATCC 66 463 629 Antisense
ACTTGTGATCCTGGTGCTGCTGAAA 79 105 643 Antisense
AAAAACCCGTGGGCATTGTGCTCGG 566 129 710 Antisense
GTTTCAGTTGTTGCAGGCATCCTCC 462 449 838 Antisense
Sequence Source Affymetrix Proprietary Database