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[188226_s_at]

Description T28H11.1 /REP_DB=WormBase Gene ID /WP=CE27451 /GEN=ssq-4 /TR=Q23062 /GB=AAB04604.2 /SUBMIT=ST.LOUIS /CHR=4 /FEA=Sanger Annotation
Cluster 6grp_total > 98      4grp_total > 17      6grp_cgc > 69      6grp_cgc_sub > Da      6grp_total_sub > Increase      6grp_rule_based > S6      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 12
1 2 3 4 range
A 2.1
(-3)
A 		5.1
(0.2)
A 		3.9
(-1.1)
A 		7.7
(3)
A 		6
B 2.5
(-3)
A 		6.7
(3)
A 		4.6
(-0)
A 		3.8
(-1.1)
A 		4
C 3
(-2.9)
A 		2.9
(-3)
A 		3.5
(-2.7)
A 		13.7
(3)
A 		11
avr 2.5
(-3) 		4.9
(-0.6) 		4
(-1.5) 		8.4
(3) 		6

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 262
1 2 3 4 5 6 range
A 2.1
(-3)
A 		6
(-2.9)
A 		3.5
(-3)
A 		4.8
(-2.9)
A 		123.2
(-0.2)
A 		264.4
(3)
P 		262
B 3.1
(-3)
A 		3.7
(-2.9)
A 		2
(-3)
A 		54.2
(-1)
A 		121.4
(1.6)
A 		158.4
(3)
A 		156
C 3.6
(-3)
A 		2.9
(-3)
A 		4.4
(-3)
A 		7.1
(-2.9)
A 		180.9
(2)
A 		216.3
(3)
A 		213
avr 2.9
(-3) 		4.2
(-3) 		3.3
(-3) 		22
(-2.5) 		141.8
(1) 		213
(3) 		210
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 2
1 2 3 4 range
A 0.8
(-3)
A 		1.1
(3)
A 		1
(1)
A 		1.1
(3)
A 		0
B 0.8
(-3)
A 		1.6
(3)
A 		1.1
(-0.8)
A 		0.8
(-3)
A 		1
C 1
(-2.2)
A 		0.8
(-3)
A 		1.2
(-1.4)
A 		2.3
(3)
A 		2
avr 0.9
(-3) 		1.2
(0.6) 		1.1
(-0.6) 		1.4
(3) 		0

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 72
1 2 3 4 5 6 range
A 0.4
(-3)
A 		2.1
(-2.8)
A 		0.8
(-3)
A 		1.2
(-2.9)
A 		37.2
(0.5)
A 		64.4
(3)
P 		64
B 1.1
(-2.9)
A 		1.2
(-2.9)
A 		0.5
(-3)
A 		14.4
(-1.6)
A 		49.3
(2)
A 		59.1
(3)
A 		59
C 1.3
(-3)
A 		0.9
(-3)
A 		1.1
(-3)
A 		1.4
(-3)
A 		58.5
(1.8)
A 		72.4
(3)
A 		72
avr 0.9
(-3) 		1.4
(-2.9) 		0.8
(-3) 		5.7
(-2.5) 		48.3
(1.4) 		65.3
(3) 		65
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 188226_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.10457
Sequence Type Exemplar sequence
Representative Public ID T28H11.1 NCBI
Target Description T28H11.1 /REP_DB=WormBase Gene ID /WP=CE27451 /GEN=ssq-4 /TR=Q23062 /GB=AAB04604.2 /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_068303(11), NM_068712(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_068303 NCBI Caenorhabditis elegans Sperm-Specific family, class Q family member (ssq-4) (ssq-4) mRNA, complete cds. 11/11 None
NM_068712 NCBI Caenorhabditis elegans Sperm-Specific family, class Q family member (ssq-3) (ssq-3) mRNA, complete cds. 11/11 A 
SNAP00000000752 ENSEMBL cdna:SNAP chromosome:CEL140:IV:5016499:5017714:1 11/11 None
GENEFINDER00000000757 ENSEMBL cdna:GeneFinder chromosome:CEL140:IV:5016499:5017714:1 11/11 None
SNAP00000039651 ENSEMBL cdna:SNAP chromosome:CEL140:IV:7111616:7112826:1 11/11 None
GENEFINDER00000039664 ENSEMBL cdna:GeneFinder chromosome:CEL140:IV:7111432:7112826:1 11/11 None
T28H11.1 ENSEMBL cdna:known chromosome:CEL140:IV:5016471:5017731:1 gene:T28H11.1 11/11 None
ZC477.1 ENSEMBL cdna:known chromosome:CEL140:IV:7111616:7112844:1 gene:ZC477.1 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
chrIV:5016504-5017720(+) 97.17 100.0
chrIV:7111621-7112832(+) 97.43 97.43
Public Domain and Genome References
Gene Title

Gene Symbol ssq-4
ssq-3
Ensembl T28H11.1
ZC477.1
Entrez Gene 177269 Entrez gene
191964 Entrez gene
SwissProt Q23062 EMBL-EBI
Q23347 EMBL-EBI
WormBase CE30698 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] 1.0E-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] 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
Sequence
Target Sequence 
>C. ELEGANS:188226_S_AT
tgggaggaggatcaacaatgactgccgttggaggagcgccatcaggagcttccaccatga
ctgctgttggcggagctccatccggagcatctaccatgaccgcaattggaggagccccac
gtggagcatcaacaatgacagctgtcggtggtgcaccaatgggagggtcatctacgatga
cagcggttggcggagcaccaattggtggatcttcgacaatgactgctgtgggaggagcac
cacgtggtgcctcgaccatgacagccgtcggaggtgctccaggaggagctagtaccatga
ctgcaa

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
TGGGAGGAGGATCAACAATGACTGC 434 543 560 Antisense
CCATGACCGCAATTGGAGGAGCCCC 407 271 653 Antisense
GAGCATCAACAATGACAGCTGTCGG 214 389 683 Antisense
AATGACAGCTGTCGGTGGTGCACCA 163 165 693 Antisense
GTGGTGCACCAATGGGAGGGTCATC 655 487 707 Antisense
CGGTTGGCGGAGCACCAATTGGTGG 625 1 743 Antisense
GGTGGATCTTCGACAATGACTGCTG 653 499 763 Antisense
GCTGTGGGAGGAGCACCACGTGGTG 709 293 784 Antisense
CTCGACCATGACAGCCGTCGGAGGT 317 233 810 Antisense
CATGACAGCCGTCGGAGGTGCTCCA 265 209 816 Antisense
GGAGGAGCTAGTACCATGACTGCAA 56 517 841 Antisense
Sequence Source Affymetrix Proprietary Database