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[188227_at]

Description T28H11.5 /REP_DB=WormBase Gene ID /WP=CE14377 /GEN=ssq-2 /TR=Q23057 /GB=AAB04598.1 /SUBMIT=ST.LOUIS /CHR=4 /FEA=Sanger Annotation
Cluster 6grp_total > 99      4grp_total > 08      6grp_cgc > 79      6grp_cgc_sub > Da      6grp_total_sub > Increase      6grp_rule_based > S5      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 87
1 2 3 4 range
A 4.1
(-3)
A 		16
(1.5)
A 		19.8
(3)
A 		18.7
(2.6)
A 		16
B 12.2
(3)
A 		12.2
(3)
A 		10
(0.8)
A 		6.2
(-3)
A 		6
C 7.6
(-2.9)
A 		5.8
(-3)
A 		16.5
(-2.2)
A 		90.9
(3)
A 		85
avr 8
(-3) 		11.3
(-2.4) 		15.4
(-1.5) 		38.6
(3) 		31

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 340
1 2 3 4 5 6 range
A 8.4
(-3)
A 		9.5
(-3)
A 		32.6
(-2.5)
A 		19.9
(-2.8)
A 		304
(3)
P 		288
(2.7)
P 		296
B 11.4
(-2.9)
A 		7.7
(-3)
A 		29.8
(-2.5)
A 		9.1
(-3)
A 		293.9
(3)
P 		233.2
(1.7)
P 		286
C 9.1
(-2.9)
A 		3.2
(-3)
A 		38.2
(-2.4)
A 		77.3
(-1.7)
A 		342.8
(3)
P 		224.3
(0.9)
P 		340
avr 9.6
(-2.9) 		6.8
(-3) 		33.5
(-2.5) 		35.4
(-2.4) 		313.6
(3) 		248.5
(1.7) 		307
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 14
1 2 3 4 range
A 1.5
(-3)
A 		3.5
(0.2)
A 		5.2
(3)
A 		2.7
(-1.1)
A 		4
B 3.9
(3)
A 		3
(0.9)
A 		2.3
(-0.7)
A 		1.3
(-3)
A 		3
C 2.5
(-2.6)
A 		1.7
(-3)
A 		5.7
(-1.2)
A 		15.3
(3)
A 		14
avr 2.6
(-3) 		2.7
(-2.8) 		4.4
(-0.2) 		6.4
(3) 		4

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 118
1 2 3 4 5 6 range
A 1.6
(-3)
A 		3.4
(-2.9)
A 		7.1
(-2.6)
A 		5.1
(-2.8)
A 		91.7
(3)
P 		70.1
(1.6)
P 		90
B 4
(-2.9)
A 		2.6
(-3)
A 		7.2
(-2.8)
A 		2.4
(-3)
A 		119.4
(3)
P 		86.9
(1.3)
P 		117
C 3.4
(-2.9)
A 		1
(-3)
A 		9.7
(-2.5)
A 		15.5
(-2.2)
A 		110.9
(3)
P 		75.1
(1)
P 		110
avr 3
(-3) 		2.3
(-3) 		8
(-2.7) 		7.7
(-2.7) 		107.3
(3) 		77.4
(1.3) 		105
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 188227_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.10855
Sequence Type Exemplar sequence
Representative Public ID T28H11.5 NCBI
Target Description T28H11.5 /REP_DB=WormBase Gene ID /WP=CE14377 /GEN=ssq-2 /TR=Q23057 /GB=AAB04598.1 /SUBMIT=ST.LOUIS /CHR=4 /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_068297(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_068297 NCBI Caenorhabditis elegans Sperm-Specific family, class Q family member (ssq-2) (ssq-2) mRNA, complete cds. 11/11 None
SNAP00000000746 ENSEMBL cdna:SNAP chromosome:CEL140:IV:4996167:4997486:1 11/11 None
GENEFINDER00000000759 ENSEMBL cdna:GeneFinder chromosome:CEL140:IV:4996167:4997486:1 11/11 None
T28H11.5 ENSEMBL cdna:known chromosome:CEL140:IV:4996132:4997524:1 gene:T28H11.5 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:4996172-4997492(+) 100.0 100.0
Public Domain and Genome References
Gene Title
Gene Symbol ssq-2
Ensembl T28H11.5
Entrez Gene 177265 Entrez gene
SwissProt Q23057 EMBL-EBI
WormBase CE14377 Wormbase
Functional Annotations
Protein Similarities
Method ID Description E-Value
blast AAB04598 Sperm-specific family, class q protein 2 [Caenorhabditis elegans] ref|NP_500698.1| Sperm-Specific family, class Q family member (ssq-2) [Caenorhabditis elegans] 1.0E-121
blast CAE64995 Hypothetical protein CBG09831 [Caenorhabditis briggsae] 1.0E-103
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-79
Sequence
Target Sequence 
>C. ELEGANS:188227_AT
gcgagcacaatgaccgctgttggtggagcaccaactggagcaagcaccatgaccgccgtc
ggaggagccccaaccggagcaagtacaatgaccgctgttggtggagtcccaactggagcg
tctacaatgactgctatcggaggagccccatctggtgcttccactatgaccgctgtggga
ggtgctccgagaggagcttcaaccatgactgctgtcggtggagcaccaactggagcttct
acgatgacagctgttggggcagccccaggcggagcttccaccatgactgctgtcggcgga
gccccccgtggagcatctacaatgaccgccgtcggagccccaggaggtggagcgtctgct
cttggagccgcaccaccagccggatcaatgagcggaggaggtggtggagccacgtctggg
tacttcggagttggacaaggagttatgggaggtggaggtgctgttggccaatctgcctac
ttcggagttggtggaggagctgctggaggtgccaagactggaggcggtggcggaggtgga
atccccggacaatcgatgtacat

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GCGAGCACAATGACCGCTGTTGGTG 74 291 604 Antisense
CAACTGGAGCAAGCACCATGACCGC 633 187 635 Antisense
TTGGTGGAGTCCCAACTGGAGCGTC 364 707 701 Antisense
GGAGCGTCTACAATGACTGCTATCG 518 521 718 Antisense
CAACCATGACTGCTGTCGGTGGAGC 98 187 803 Antisense
TCGGTGGAGCACCAACTGGAGCTTC 513 605 818 Antisense
CATCTACAATGACCGCCGTCGGAGC 588 211 917 Antisense
CAGGAGGTGGAGCGTCTGCTCTTGG 302 207 944 Antisense
CACGTCTGGGTACTTCGGAGTTGGA 341 155 1014 Antisense
GAGGTGGAGGTGCTGTTGGCCAATC 28 403 1052 Antisense
GAATCCCCGGACAATCGATGTACAT 469 327 1142 Antisense
Sequence Source Affymetrix Proprietary Database