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[188174_s_at]

Description Y49F6B.4 /REP_DB=WormBase Gene ID /WP=CE25338 /GEN=smu-2 /TR=Q9N4U5 /GB=AAF60731.1 /SUBMIT=ST.LOUIS /CHR=2 /FEA=Sanger Annotation
Cluster 6grp_highest_10_10 > 94      6grp_high1_10_10 > 58      4grp_highest_8_8 > 46      4grp_high_8_8 > 02      6grp_highest_nonorm > 82      6grp_total > 47      4grp_total > 14      6grp_highest_sub > Cu      6grp_cgc > 27      6grp_high1_sub > Cu      6grp_cgc_sub > Cu      6grp_total_sub > Cup      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 239
1 2 3 4 range
A 323.3
(-3)
P 		378.8
(-0.7)
P 		328.9
(-2.8)
P 		470.1
(3)
P 		147
B 395.1
(3)
P 		262.6
(-3)
P 		290.6
(-1.7)
P 		344.2
(0.7)
P 		133
C 364
(3)
P 		231.4
(-3)
P 		248.7
(-2.2)
P 		349
(2.3)
P 		133
avr 360.8
(1.4) 		290.9
(-2.9) 		289.4
(-3) 		387.8
(3) 		98

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 275
1 2 3 4 5 6 range
A 464.1
(0.8)
P 		531.8
(2.6)
P 		320.9
(-3)
P 		336.7
(-2.6)
P 		323.8
(-2.9)
P 		547.9
(3)
P 		227
B 441.9
(0.9)
P 		400.9
(-0.1)
P 		272.7
(-3)
P 		369.7
(-0.8)
P 		343.9
(-1.4)
P 		534.5
(3)
P 		262
C 374.6
(-0.7)
P 		410.5
(0.3)
P 		293.2
(-3)
P 		352.8
(-1.3)
P 		360.2
(-1.1)
P 		506.4
(3)
P 		213
avr 426.9
(0.4) 		447.7
(0.9) 		295.6
(-3) 		353.1
(-1.5) 		342.6
(-1.8) 		529.6
(3) 		234
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 67
1 2 3 4 range
A 117.7
(3)
P 		82.2
(-1.4)
P 		86
(-0.9)
P 		68.8
(-3)
P 		49
B 126
(3)
P 		64.9
(-3)
P 		67.3
(-2.8)
P 		73.3
(-2.2)
P 		61
C 120.5
(3)
P 		66.5
(-2.3)
P 		86.7
(-0.3)
P 		58.8
(-3)
P 		62
avr 121.4
(3) 		71.2
(-2.5) 		80
(-1.6) 		67
(-3) 		54

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 133
1 2 3 4 5 6 range
A 85.6
(-2.2)
P 		189.1
(3)
P 		69.9
(-3)
P 		85.4
(-2.2)
P 		97.7
(-1.6)
P 		133.4
(0.2)
P 		119
B 153.8
(0.9)
P 		133.4
(0)
P 		66.2
(-3)
P 		97.9
(-1.6)
P 		139.7
(0.3)
P 		199.3
(3)
P 		133
C 138.8
(1.1)
P 		125.3
(0.3)
P 		74.6
(-2.8)
P 		71
(-3)
P 		116.6
(-0.2)
P 		169.5
(3)
P 		99
avr 126.1
(0.5) 		149.3
(1.9) 		70.2
(-3) 		84.8
(-2.1) 		118
(-0) 		167.4
(3) 		97
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 188174_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.5035
Sequence Type Exemplar sequence
Representative Public ID Y49F6B.4 NCBI
Target Description Y49F6B.4 /REP_DB=WormBase Gene ID /WP=CE25338 /GEN=smu-2 /TR=Q9N4U5 /GB=AAF60731.1 /SUBMIT=ST.LOUIS /CHR=2 /FEA=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_062158(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_062158 NCBI Caenorhabditis elegans Suppressor of Mec and Unc defects family member (smu-2) (smu-2) mRNA, complete cds. 11/11 A 
SNAP00000021093 ENSEMBL cdna:SNAP chromosome:CEL140:II:3474049:3490072:1 11/11 None
GENEFINDER00000021111 ENSEMBL cdna:GeneFinder chromosome:CEL140:II:3482480:3490072:1 11/11 None
Y49F6B.4 ENSEMBL cdna:known chromosome:CEL140:II:3482443:3490134:1 gene:Y49F6B.4 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
chrII:3482506-3490071(+) 98.18 100.0
Public Domain and Genome References
Gene Title
Gene Symbol smu-2
Ensembl Y49F6B.4
Entrez Gene 173693 Entrez gene
SwissProt Q9N4U5 EMBL-EBI
WormBase CE25338 Wormbase
Functional Annotations
Ortholog
ID Title Organism
ATH1-121501:245054_AT RED family protein at
CANINE:1600282_AT similar to RED protein cfa
CANINE:1596323_AT similar to RED protein cfa
CANINE:1585800_AT similar to RED protein cfa
CANINE_2:CFA.10903.1.A1_AT similar to RED protein cfa
CANINE_2:CFA.10903.1.A1_S_AT similar to RED protein cfa
CANINE_2:CFA.18968.1.S1_S_AT similar to RED protein cfa
DROSOPHILA_2:1630176_AT dm
DROSGENOME1:154006_AT dm
CHICKEN:GGA.9691.1.S1_S_AT IK cytokine, down-regulator of HLA II gga
CHICKEN:GGAAFFX.20814.1.S1_S_AT IK cytokine, down-regulator of HLA II gga
PLASMODIUM_ANOPHELES:200066_AT IK cytokine, down-regulator of HLA II hs
HG-U133B:200066_AT IK cytokine, down-regulator of HLA II hs
HG-U133A:200066_AT IK cytokine, down-regulator of HLA II hs
HG-U133_PLUS_2:200066_AT IK cytokine, down-regulator of HLA II hs
HG-FOCUS:200066_AT IK cytokine, down-regulator of HLA II hs
HG-U133A_2:200066_AT IK cytokine, down-regulator of HLA II hs
U133_X3P:200066_AT IK cytokine, down-regulator of HLA II hs
HG-U95AV2:218_AT IK cytokine, down-regulator of HLA II hs
HC-G110:218_AT IK cytokine, down-regulator of HLA II hs
HUGENEFL:S74221_AT IK cytokine, down-regulator of HLA II hs
HG-U95AV2:38046_AT IK cytokine, down-regulator of HLA II hs
U133_X3P:G5901877_3P_AT IK cytokine, down-regulator of HLA II hs
HG-U95AV2:32377_AT IK cytokine, down-regulator of HLA II hs
HG-U95E:87819_AT IK cytokine, down-regulator of HLA II hs
MOE430A:1435988_X_AT IK cytokine mm
MOUSE430A_2:1435988_X_AT IK cytokine mm
MOUSE430_2:1435988_X_AT IK cytokine mm
MOUSE430A_2:1439271_X_AT IK cytokine mm
MOE430A:1439271_X_AT IK cytokine mm
MOUSE430_2:1439271_X_AT IK cytokine mm
MU11KSUBA:AA259592_S_AT IK cytokine mm
MG-U74AV2:160397_AT IK cytokine mm
MOE430A:1423791_AT IK cytokine mm
MOUSE430A_2:1423791_AT IK cytokine mm
MOUSE430_2:1423791_AT IK cytokine mm
MOE430A:1451113_A_AT IK cytokine mm
MOUSE430A_2:1451113_A_AT IK cytokine mm
MOUSE430_2:1451113_A_AT IK cytokine mm
RG-U34B:RC_AI070067_AT RED protein rn
RG-U34B:RC_AA996993_S_AT RED protein rn
RAE230A:1389062_AT RED protein rn
RAT230_2:1389062_AT RED protein rn
RAE230B:1385123_AT RED protein rn
RAT230_2:1385123_AT RED protein rn
Protein Similarities
Method ID Description E-Value
blast NP_494559 Suppressor of Mec and Unc defects family member (smu-2) [Caenorhabditis elegans] gb|AAF60731.1| Suppressor of mec and unc defects protein 2 [Caenorhabditis elegans] 0.0
blast CAE70949 Hypothetical protein CBG17759 [Caenorhabditis briggsae] 1.0E-171
blast CAE70949 Hypothetical protein CBG17759 [Caenorhabditis briggsae] 1.0E-170
blast CAE70949 Hypothetical protein CBG17759 [Caenorhabditis briggsae] 1.0E-162
blast NP_494559 Suppressor of Mec and Unc defects family member (smu-2) [Caenorhabditis elegans] gb|AAF60731.1| Suppressor of mec and unc defects protein 2 [Caenorhabditis elegans] 1.0E-137
blast NP_494556 Y49F6B.5 [Caenorhabditis elegans] gb|AAF60732.1| Hypothetical protein Y49F6B.5 [Caenorhabditis elegans] 1.0E-102
blast XP_394867 PREDICTED: similar to ENSANGP00000017679 [Apis mellifera] 3.0E-38
Sequence
Target Sequence 
>C. ELEGANS:188174_S_AT
ctgccaactctcgtcgcgaggaagaacaaaaccgccgtgagcagcaacgtgaacgtgaac
gagccgaacaagaacgccgccgtgaacgtgaaaaagaacgtgaacaggaaaaagccaagg
aacgagagaaaaagcgaaaagaattggaagaatcatcaggctacgatgaatgttatccag
gcggcctagtagagatgggcggtgcatgggattcagatgaagaagccgactattcgaaaa
tggatgcagggcctaagaagaatcaagctgttaatcgatgggattttgatacggaggagg
agtatgcctcttatatggaaggacgtgaagctctgccaaaagccgcctatcaatacggag
tcaaaaatggagaaggtggccgaaagaacaagaaacagtcggcagtgtcggatgcgaagc
ggctcgatcgggagctcaatgag

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
CTGCCAACTCTCGTCGCGAGGAAGA 196 237 1133 Antisense
AACCGCCGTGAGCAGCAACGTGAAC 148 145 1162 Antisense
GAACGAGCCGAACAAGAACGCCGCC 298 345 1189 Antisense
CAAGAACGCCGCCGTGAACGTGAAA 573 185 1201 Antisense
ATGAATGTTATCCAGGCGGCCTAGT 84 43 1298 Antisense
GATGGGCGGTGCATGGGATTCAGAT 1 407 1326 Antisense
GGAAGGACGTGAAGCTCTGCCAAAA 541 531 1449 Antisense
TCTGCCAAAAGCCGCCTATCAATAC 323 609 1464 Antisense
GAAACAGTCGGCAGTGTCGGATGCG 99 357 1524 Antisense
TGTCGGATGCGAAGCGGCTCGATCG 244 557 1538 Antisense
GCGGCTCGATCGGGAGCTCAATGAG 562 293 1551 Antisense
Sequence Source Affymetrix Proprietary Database