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[184890_at]

Description Y42G9A.2 /REP_DB=WormBase Gene ID /WP=CE24275 /TR=Q9N4Z4 /GB=AAF60557.1 /SUBMIT=ST.LOUIS /CHR=3 /FEA=Sanger Annotation
Cluster 6grp_highest_10_10 > 12      6grp_high1_10_10 > 20      4grp_highest_8_8 > 56      4grp_high_8_8 > 34      6grp_highest_nonorm > 22      6grp_total > 40      4grp_total > 45      6grp_total_sub > Hat      4grp_rule_based > L1      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 1252
1 2 3 4 range
A 2020.3
(3)
P 		1890.6
(2.1)
P 		1430.3
(-1.1)
P 		1163.4
(-3)
P 		857
B 2415.7
(3)
P 		1814.7
(-0.8)
P 		1468.3
(-3)
P 		1586.6
(-2.3)
P 		947
C 2092
(3)
P 		1861.2
(1.3)
P 		1264
(-3)
P 		1368.6
(-2.2)
P 		828
avr 2176
(3) 		1855.5
(0.6) 		1387.5
(-2.9) 		1372.9
(-3) 		803

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 800
1 2 3 4 5 6 range
A 1589.6
(0.7)
P 		1479.1
(-0.3)
P 		1653
(1.2)
P 		1858.3
(3)
P 		1169.2
(-3)
P 		1600
(0.8)
P 		689
B 1927.5
(3)
P 		1798.4
(1.9)
P 		1929
(3)
P 		1421.2
(-1.3)
P 		1228.5
(-3)
P 		1269.8
(-2.6)
P 		701
C 1832.6
(1.8)
P 		1858.6
(2.1)
P 		1799.1
(1.5)
P 		1969
(3)
P 		1269.3
(-3)
P 		1465.2
(-1.3)
P 		700
avr 1783.2
(2.9) 		1712
(2.1) 		1793.7
(3) 		1749.5
(2.5) 		1222.3
(-3) 		1445
(-0.7) 		571
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 600
1 2 3 4 range
A 735.6
(3)
P 		410.4
(-0.5)
P 		373.9
(-0.8)
P 		170.3
(-3)
P 		565
B 770.4
(3)
P 		448.2
(-1.5)
P 		340.2
(-3)
P 		338.1
(-3)
P 		432
C 692.5
(3)
P 		535.1
(1)
P 		440.5
(-0.3)
P 		230.8
(-3)
P 		462
avr 732.8
(3) 		464.6
(-0.3) 		384.9
(-1.3) 		246.4
(-3) 		486

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 386
1 2 3 4 5 6 range
A 293
(-3)
P 		526
(3)
P 		360
(-1.3)
P 		471.3
(1.6)
P 		352.8
(-1.5)
P 		389.5
(-0.5)
P 		233
B 670.7
(3)
P 		598.6
(1.5)
P 		468.4
(-1.1)
P 		376.4
(-3)
P 		499.1
(-0.5)
P 		473.5
(-1)
P 		294
C 679.3
(3)
P 		567.1
(0.6)
P 		457.9
(-1.7)
P 		396
(-3)
P 		410.7
(-2.7)
P 		490.5
(-1)
P 		283
avr 547.7
(2.3) 		563.9
(3) 		428.8
(-2.4) 		414.6
(-3) 		420.9
(-2.7) 		451.2
(-1.5) 		149
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 184890_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.6875
Sequence Type Exemplar sequence
Representative Public ID Y42G9A.2 NCBI
Target Description Y42G9A.2 /REP_DB=WormBase Gene ID /WP=CE24275 /TR=Q9N4Z4 /GB=AAF60557.1 /SUBMIT=ST.LOUIS /CHR=3 /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_065930(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_065930 NCBI Caenorhabditis elegans Y42G9A.2 (Y42G9A.2) mRNA, complete cds. 11/11 None
GENEFINDER00000011134 ENSEMBL cdna:GeneFinder chromosome:CEL140:III:6146237:6148950:1 9/11 None
SNAP00000011129 ENSEMBL cdna:SNAP chromosome:CEL140:III:6148138:6148950:1 11/11 None
Y42G9A.2 ENSEMBL cdna:known chromosome:CEL140:III:6148126:6148984:1 gene:Y42G9A.2 11/11 None
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:6148136-6148949(+) 100.0 100.0
Public Domain and Genome References
Gene Title
Ensembl Y42G9A.2
Entrez Gene 175866 Entrez gene
SwissProt Q9N4Z4 EMBL-EBI
WormBase CE24275 Wormbase
Functional Annotations
Protein Similarities
Method ID Description E-Value
blast NP_001022864 Y42G9A.3a [Caenorhabditis elegans] gb|AAF60555.1| Hypothetical protein Y42G9A.3a [Caenorhabditis elegans] 0.0
blast CAE73621 Hypothetical protein CBG21115 [Caenorhabditis briggsae] 1.0E-164
blast NP_001022865 Y42G9A.3b [Caenorhabditis elegans] gb|AAP31426.1| Hypothetical protein Y42G9A.3b [Caenorhabditis elegans] 1.0E-148
blast NP_498331 Y42G9A.2 [Caenorhabditis elegans] gb|AAF60557.1| Hypothetical protein Y42G9A.2 [Caenorhabditis elegans] 9.0E-64
blast CAE73622 Hypothetical protein CBG21116 [Caenorhabditis briggsae] 1.0E-39
Protein Domains
Database ID Description E-Value
Pfam IPR001611 EMBL-EBI Leucine-rich repeat 0.0095
Pfam IPR001611 EMBL-EBI Leucine-rich repeat 0.31
Pfam IPR001611 EMBL-EBI Leucine-rich repeat 2.4E-4
Pfam IPR001611 EMBL-EBI Leucine-rich repeat 0.065
Pfam IPR001611 EMBL-EBI Leucine-rich repeat 0.0077
Pfam IPR001611 EMBL-EBI Leucine-rich repeat 0.0029
Pfam IPR001611 EMBL-EBI Leucine-rich repeat 0.11
Sequence
Target Sequence 
>C. ELEGANS:184890_AT
gtgattttgactgtattccatgtggaatgtgcaacaagagcaccaaaactttcgaaacac
acaaagaaaacagtcaacaagttggtcaactgtctgactcccgtggacaccgttttggcc
gccaagacagccgattgtgaagacagtatctgtgtgtcaagtgctaaacaatatgcacag
agacgatatccaacacagtatcatagtacagtagtcccatgtctctcatcaacaactaca
ttggctcctgtcactgagaa

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GTGATTTTGACTGTATTCCATGTGG 697 483 46 Antisense
GAGCACCAAAACTTTCGAAACACAC 636 389 83 Antisense
CAAGTTGGTCAACTGTCTGACTCCC 336 185 123 Antisense
ACACCGTTTTGGCCGCCAAGACAGC 411 71 152 Antisense
GCCGCCAAGACAGCCGATTGTGAAG 645 285 163 Antisense
AGTATCTGTGTGTCAAGTGCTAAAC 367 63 190 Antisense
GCACAGAGACGATATCCAACACAGT 481 317 220 Antisense
TAGTACAGTAGTCCCATGTCTCTCA 465 653 249 Antisense
TCCCATGTCTCTCATCAACAACTAC 392 595 260 Antisense
TCAACAACTACATTGGCTCCTGTCA 622 629 274 Antisense
CTACATTGGCTCCTGTCACTGAGAA 297 227 281 Antisense
Sequence Source Affymetrix Proprietary Database