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[172752_x_at]

Description ZC477.8_rc /REP_DB=WormBase Gene ID /WP=CE05064 /CHR=4 /FEA=Sanger Annotation /REVCOMP /DEF=(ST.LOUIS) TR:Q23348 protein_id:AAA81511.1
Cluster 6grp_total > 98      4grp_total > 50      6grp_cgc > 79      6grp_cgc_sub > Da      6grp_total_sub > Increase      6grp_rule_based > S6      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 44
1 2 3 4 range
A 10.3
(-2.1)
A 		47.6
(3)
A 		11.7
(-1.9)
A 		3.5
(-3)
A 		44
B 4.4
(-3)
A 		39.7
(3)
A 		8.4
(-2.3)
A 		6.7
(-2.6)
A 		35
C 8.5
(-2.4)
A 		11.6
(-1.9)
A 		38.8
(3)
A 		5.2
(-3)
A 		34
avr 7.7
(-2.4) 		33
(3) 		19.6
(0.1) 		5.1
(-3) 		28

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 552
1 2 3 4 5 6 range
A 46.9
(-2.6)
A 		6.4
(-3)
A 		58.9
(-2.4)
A 		93.1
(-2.1)
A 		323
(0.5)
A 		555.4
(3)
P 		549
B 9.3
(-3)
A 		8.6
(-3)
A 		7.4
(-3)
A 		51.6
(-2.2)
A 		284.7
(2)
A 		340.5
(3)
A 		333
C 5.9
(-3)
A 		3.4
(-3)
A 		10.2
(-2.9)
A 		3.1
(-3)
A 		421
(3)
P 		335.3
(1.8)
A 		418
avr 20.7
(-2.8) 		6.1
(-3) 		25.5
(-2.7) 		49.3
(-2.4) 		342.9
(2) 		410.4
(3) 		404
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 13
1 2 3 4 range
A 3.7
(-1)
A 		10.3
(3)
A 		3.1
(-1.4)
A 		0.5
(-3)
A 		10
B 1.4
(-3)
A 		9.8
(3)
A 		1.9
(-2.6)
A 		1.4
(-3)
A 		8
C 2.8
(-2.1)
A 		3.3
(-1.9)
A 		13.5
(3)
A 		0.9
(-3)
A 		13
avr 2.6
(-1.5) 		7.8
(3) 		6.2
(1.6) 		0.9
(-3) 		7

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 136
1 2 3 4 5 6 range
A 8.6
(-2.7)
A 		2.3
(-3)
A 		12.8
(-2.5)
A 		23.6
(-2)
A 		97.5
(1.3)
A 		135.2
(3)
P 		133
B 3.2
(-2.9)
A 		2.9
(-2.9)
A 		1.8
(-3)
A 		13.7
(-2.4)
A 		115.7
(2.5)
A 		127
(3)
A 		125
C 2.2
(-2.9)
A 		1
(-3)
A 		2.6
(-2.9)
A 		0.6
(-3)
A 		136.2
(3)
P 		112.2
(1.9)
A 		136
avr 4.7
(-2.9) 		2.1
(-3) 		5.7
(-2.8) 		12.6
(-2.5) 		116.5
(2.6) 		124.8
(3) 		123
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 172752_x_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.28138
Sequence Type Exemplar sequence
Representative Public ID ZC477.8 NCBI
Target Description ZC477.8_rc /REP_DB=WormBase Gene ID /WP=CE05064 /CHR=4 /FEA=Sanger Annotation /REVCOMP /DEF=(ST.LOUIS) TR:Q23348 protein_id:AAA81511.1
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_068712(9)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_068712 NCBI Caenorhabditis elegans Sperm-Specific family, class Q family member (ssq-3) (ssq-3) mRNA, complete cds. 9/11 A 
SNAP00000039651 ENSEMBL cdna:SNAP chromosome:CEL140:IV:7111616:7112826:1 9/11 None
GENEFINDER00000039664 ENSEMBL cdna:GeneFinder chromosome:CEL140:IV:7111432:7112826:1 9/11 None
ZC477.1 ENSEMBL cdna:known chromosome:CEL140:IV:7111616:7112844:1 gene:ZC477.1 9/11 A 
Annotation Notes
Cross Hybridizing mRNA Matched Probes Nature of Assignment Related Probesets by Grade
NM_068297 1/11 Cross Hyb Matching Probes None
NM_068303 5/11 Cross Hyb Matching Probes A 
SNAP00000000752 5/11 Cross Hyb Matching Probes None
GENEFINDER00000000757 5/11 Cross Hyb Matching Probes None
T28H11.5 1/11 Cross Hyb Matching Probes R A 
T28H11.1 5/11 Cross Hyb Matching Probes R A 
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrIV:7111912-7112946(+) 100.0 100.0
chrIV:5016796-5017831(+) 93.79 96.89
Public Domain and Genome References
Gene Title
Gene Symbol ssq-3
Ensembl ZC477.1
Entrez Gene 191964 Entrez gene
SwissProt Q23347 EMBL-EBI
WormBase CE28161 Wormbase
Functional Annotations
Ortholog
ID Title Organism
DROSOPHILA_2:1635073_AT dm
DROSGENOME1:146184_AT dm
Protein Similarities
Method ID Description E-Value
blast AAB04604 Sperm-specific family, class q protein 4 [Caenorhabditis elegans] ref|NP_500704.2| Sperm-Specific family, class Q family member (ssq-4) [Caenorhabditis elegans] 4.0E-93
blast AAB04604 Sperm-specific family, class q protein 4 [Caenorhabditis elegans] ref|NP_500704.2| Sperm-Specific family, class Q family member (ssq-4) [Caenorhabditis elegans] 3.0E-85
blast T27609 hypothetical protein ZC477.1 - Caenorhabditis elegans 3.0E-84
blast AAK19014 Sperm-specific family, class q protein 3 [Caenorhabditis elegans] ref|NP_501113.1| Sperm-Specific family, class Q family member (ssq-3) [Caenorhabditis elegans] 1.0E-78
blast T27609 hypothetical protein ZC477.1 - Caenorhabditis elegans 1.0E-78
blast AAK19014 Sperm-specific family, class q protein 3 [Caenorhabditis elegans] ref|NP_501113.1| Sperm-Specific family, class Q family member (ssq-3) [Caenorhabditis elegans] 2.0E-78
blast T27609 hypothetical protein ZC477.1 - Caenorhabditis elegans 2.0E-78
Sequence
Target Sequence 
>C. ELEGANS:172752_X_AT
ttccaccatgactgctgttggcggagctccatccggagcgtctaccatgaccgcaattgg
aggagccccacgtggagcatcaacaatgacagctgtcggtggtgcaccaatgggagggtc
atccacgatgactgcggttggcggagcaccaattggtggatcttcgacaatgactgctgt
gggaggagcaccacgtggtgtctcgaccatgacagccgtcggaggtgctccaggaggagc
tagtaccatgactgcaatgggaggtggaccatcagcttttggaggagcaccaccacctcc
atctagcctttttaaggaggcggtggaggtatccccggacagtcggtttacatgggagcc
ggtggcggcggcggtggtggaggcggagctacttctgcttactttgctccaagataattg
cactaaaataatggatgatttataaatgatgattttgaatttattgttgttttttgttct
tacatgcatc

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
TTCCACCATGACTGCTGTTGGCGGA 305 699 319 Antisense
GCGTCTACCATGACCGCAATTGGAG 278 291 356 Antisense
AATGACAGCTGTCGGTGGTGCACCA 162 165 403 Antisense
CATCCACGATGACTGCGGTTGGCGG 106 211 438 Antisense
GGTGGATCTTCGACAATGACTGCTG 652 499 473 Antisense
GAGGAGCACCACGTGGTGTCTCGAC 430 403 501 Antisense
CATGACAGCCGTCGGAGGTGCTCCA 264 209 526 Antisense
CACCTCCATCTAGCCTTTTTAAGGA 439 193 612 Antisense
GTATCCCCGGACAGTCGGTTTACAT 511 1 647 Antisense
GAGCTACTTCTGCTTACTTTGCTCC 444 375 704 Antisense
GTTGTTTTTTGTTCTTACATGCATC 384 437 784 Antisense
Sequence Source Affymetrix Proprietary Database