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[176077_at]

Description Y41D4B.R /REP_DB=WormBase Gene ID /WP=CE26095 /CHR=4 /FEA=Sanger Annotation /DEF=(ST.LOUIS)
Cluster 6grp_total > 65      4grp_total > 0      4grp_rule_based > L4      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 163
1 2 3 4 range
A 116.5
(-3)
A 		162
(-1.2)
A 		154.7
(-1.5)
A 		271.4
(3)
P 		155
B 161.8
(-0.9)
A 		108.3
(-3)
A 		189.1
(0.2)
A 		260.2
(3)
P 		152
C 160.2
(-1.9)
P 		153
(-2.3)
A 		137.7
(-3)
A 		262.7
(3)
P 		125
avr 146.2
(-2.8) 		141.1
(-3) 		160.5
(-2.1) 		264.8
(3) 		124

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 139
1 2 3 4 5 6 range
A 122
(1.4)
A 		71.4
(-2.6)
A 		136.4
(2.6)
P 		97.7
(-0.5)
A 		66
(-3)
A 		141.7
(3)
A 		76
B 89.3
(-3)
M 		100.7
(-1.7)
A 		116.6
(0.1)
A 		137.3
(2.4)
A 		97
(-2.1)
A 		142.5
(3)
P 		53
C 87.1
(0.5)
A 		93.5
(0.8)
A 		118.8
(1.8)
A 		145.6
(3)
M 		6.3
(-3)
A 		145
(3)
P 		139
avr 99.5
(-0) 		88.5
(-0.8) 		123.9
(1.7) 		126.9
(1.9) 		56.4
(-3) 		143.1
(3) 		87
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 29
1 2 3 4 range
A 42.4
(3)
A 		35.2
(-3)
A 		40.4
(1.3)
A 		39.7
(0.8)
P 		7
B 51.6
(2.2)
A 		26.8
(-3)
A 		43.8
(0.6)
A 		55.5
(3)
P 		29
C 53
(3)
P 		44
(-3)
A 		48
(-0.3)
A 		44.3
(-2.8)
P 		9
avr 49
(3) 		35.3
(-3) 		44.1
(0.9) 		46.5
(1.9) 		14

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 51
1 2 3 4 5 6 range
A 22.5
(-1.9)
A 		25.4
(-0.7)
A 		29.7
(1)
P 		24.8
(-1)
A 		19.9
(-3)
A 		34.5
(3)
A 		15
B 31.1
(-2.3)
M 		33.5
(-1.7)
A 		28.3
(-3)
A 		36.4
(-1)
A 		39.4
(-0.3)
A 		53.1
(3)
P 		25
C 32.3
(0.9)
A 		28.5
(0.4)
A 		30.2
(0.6)
A 		29.3
(0.5)
M 		2
(-3)
A 		48.5
(3)
P 		47
avr 28.6
(-1) 		29.1
(-0.9) 		29.4
(-0.8) 		30.2
(-0.6) 		20.4
(-3) 		45.4
(3) 		25
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 176077_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.19247
Sequence Type Exemplar sequence
Representative Public ID Y41D4B.R NCBI
Target Description Y41D4B.R /REP_DB=WormBase Gene ID /WP=CE26095 /CHR=4 /FEA=Sanger Annotation /DEF=(ST.LOUIS)
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_067706(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_067706 NCBI Caenorhabditis elegans Y41D4B.11 (Y41D4B.11) mRNA, complete cds. 11/11 None
SNAP00000005512 ENSEMBL cdna:SNAP chromosome:CEL140:IV:1589786:1608814:1 11/11 None
GENEFINDER00000005549 ENSEMBL cdna:GeneFinder chromosome:CEL140:IV:1605710:1608814:1 11/11 None
Y41D4B.11 ENSEMBL cdna:known chromosome:CEL140:IV:1605710:1608890:1 gene:Y41D4B.11 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
chrIV:1605715-1608820(+) 84.1 100.0
Public Domain and Genome References
Gene Title
Ensembl Y41D4B.11
Entrez Gene 3565515 Entrez gene
SwissProt Q95Y11 EMBL-EBI
WormBase CE26095 Wormbase
Functional Annotations
Protein Similarities
Method ID Description E-Value
blast AAK68463 Cell death abnormality protein 2 [Caenorhabditis elegans] ref|NP_500105.1| CEll Death abnormality family member (ced-2) [Caenorhabditis elegans] gb|AAF33845.1| cell-corpse engulfment protein CED-2 [Caenorhabditis elegans] 1.0E-147
blast AAK68461 Hypothetical protein Y41D4B.11 [Caenorhabditis elegans] ref|NP_500107.1| Y41D4B.11 [Caenorhabditis elegans] 1.0E-130
blast CAE67964 Hypothetical protein CBG13568 [Caenorhabditis briggsae] 1.0E-122
blast AAK68461 Hypothetical protein Y41D4B.11 [Caenorhabditis elegans] ref|NP_500107.1| Y41D4B.11 [Caenorhabditis elegans] 1.0E-108
blast CAE67966 Hypothetical protein CBG13570 [Caenorhabditis briggsae] 1.0E-52
Protein Domains
Database ID Description E-Value
scop a.4.5.DNA-binding protein Mj223 All alpha proteins; DNA/RNA-binding 3-helical bundle; "Winged helix" DNA-binding domain; DNA-binding protein Mj223 3.5
Pfam IPR000980 EMBL-EBI SH2 motif 3.0E-20
Pfam IPR001452 EMBL-EBI SH3 1.5E-17
Pfam IPR001214 EMBL-EBI Nuclear protein SET 3.0E-13
Sequence
Target Sequence 
>C. ELEGANS:176077_AT
aacgagaacaggaagcccgacggctggaagaggtggagaagctgaaagagcagaaaaaag
ctgaaaaaaggaaaatgaaggaagcactggaaaaagaagaggaagaagagagctttgatg
aggatgaagtctctgaaaaacgggcaaaaattgagaaaagtactgaaaaaggaggcagtg
aaaaagcgacgacgaaactcagcaaaaaagaccgtagaaaggagacgttgaaagcgagaa
aatcggatgaacagaagcgacgtgccggcgaggcgttgattaattctagagaaataatcg
agtttggcgaacgaaacgacgcgccaccaacattcggcggagctcttaaaaagaaattcg
agccattgatggcaaaagccggccaaaagacgacgcttcttcttcattcaatgctccaaa
aaggcggcggccagaagacggaatatttgaataattcgacgaaaattcaagaggaacggc
agaaggtcatcgacgcgtacagagatatgaagaaacagaagagaattgctgccgctttt

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
AACGAGAACAGGAAGCCCGACGGCT 99 143 494 Antisense
AAGCCCGACGGCTGGAAGAGGTGGA 343 145 506 Antisense
ATGAACAGAAGCGACGTGCCGGCGA 382 43 740 Antisense
GCCGGCGAGGCGTTGATTAATTCTA 461 283 757 Antisense
TGGCGAACGAAACGACGCGCCACCA 650 543 798 Antisense
CACCAACATTCGGCGGAGCTCTTAA 350 203 818 Antisense
GCAAAAGCCGGCCAAAAGACGACGC 196 315 865 Antisense
AAAAGACGACGCTTCTTCTTCATTC 536 131 878 Antisense
AAGGCGGCGGCCAGAAGACGGAATA 527 149 914 Antisense
GGAACGGCAGAAGGTCATCGACGCG 62 531 966 Antisense
ACAGAAGAGAATTGCTGCCGCTTTT 282 109 1008 Antisense
Sequence Source Affymetrix Proprietary Database