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[187960_at]

Description K07F5.11 /REP_DB=WormBase Gene ID /WP=CE06125 /GEN=ssq-1 /TR=Q21294 /GB=CAA94280.1 /SUBMIT=HINXTON /CHR=4 /FEA=Sanger Annotation
Cluster 6grp_total > 98      4grp_total > 42      6grp_cgc > 69      6grp_cgc_sub > Da      6grp_total_sub > Increase      6grp_rule_based > S6      4grp_rule_based > L2      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 164
1 2 3 4 range
A 117.2
(-3)
A 		261.5
(3)
P 		186.5
(-0.1)
A 		125.6
(-2.7)
A 		144
B 102.5
(-3)
A 		200.9
(3)
P 		158
(0.4)
P 		104.2
(-2.9)
A 		98
C 97.6
(-3)
A 		164.5
(3)
A 		122.2
(-0.8)
P 		148.8
(1.6)
A 		67
avr 105.8
(-3) 		209
(3) 		155.6
(-0.1) 		126.2
(-1.8) 		103

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 652
1 2 3 4 5 6 range
A 115.3
(-2.5)
A 		62.6
(-3)
A 		88.1
(-2.8)
A 		92.1
(-2.7)
A 		359.6
(-0.1)
P 		674.6
(3)
P 		612
B 22.4
(-3)
A 		35.7
(-2.8)
A 		96.6
(-2.1)
A 		117.9
(-1.8)
A 		407.5
(1.7)
P 		516.6
(3)
P 		494
C 75.9
(-2.3)
A 		29
(-3)
A 		74.3
(-2.3)
A 		106.6
(-1.9)
A 		445.7
(3)
P 		434.9
(2.8)
P 		417
avr 71.2
(-2.7) 		42.4
(-3) 		86.3
(-2.5) 		105.5
(-2.2) 		404.3
(1.3) 		542
(3) 		500
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 38
1 2 3 4 range
A 42.7
(0.8)
A 		56.8
(3)
P 		48.8
(1.8)
A 		18.4
(-3)
A 		38
B 32.7
(-0.7)
A 		49.6
(3)
P 		36.6
(0.2)
P 		22.2
(-3)
A 		27
C 32.3
(-1.1)
A 		47.3
(3)
A 		42.6
(1.7)
P 		25.1
(-3)
A 		22
avr 35.9
(-0.1) 		51.2
(3) 		42.7
(1.3) 		21.9
(-3) 		29

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 185
1 2 3 4 5 6 range
A 21.3
(-2.9)
A 		22.3
(-2.9)
A 		19.2
(-3)
A 		23.4
(-2.8)
A 		108.5
(0.7)
P 		164.2
(3)
P 		145
B 7.8
(-3)
A 		11.9
(-2.9)
A 		23.5
(-2.5)
A 		31.2
(-2.2)
A 		165.6
(2.1)
P 		192.6
(3)
P 		185
C 28.1
(-2.2)
A 		8.8
(-3)
A 		18.9
(-2.6)
A 		21.4
(-2.4)
A 		144.2
(2.9)
P 		145.6
(3)
P 		137
avr 19.1
(-2.8) 		14.3
(-3) 		20.5
(-2.8) 		25.3
(-2.6) 		139.4
(1.9) 		167.5
(3) 		153
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 187960_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.10091
Sequence Type Exemplar sequence
Representative Public ID K07F5.11 NCBI
Target Description K07F5.11 /REP_DB=WormBase Gene ID /WP=CE06125 /GEN=ssq-1 /TR=Q21294 /GB=CAA94280.1 /SUBMIT=HINXTON /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_069367(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_069367 NCBI Caenorhabditis elegans Sperm-Specific family, class Q family member (ssq-1) (ssq-1) mRNA, complete cds. 11/11 None
SNAP00000004253 ENSEMBL cdna:SNAP chromosome:CEL140:IV:9852562:9853531:1 11/11 None
GENEFINDER00000004262 ENSEMBL cdna:GeneFinder chromosome:CEL140:IV:9852562:9853531:1 11/11 None
K07F5.11 ENSEMBL cdna:known chromosome:CEL140:IV:9852542:9853531:1 gene:K07F5.11 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:9852567-9853537(+) 100.0 100.0
chrIV:4996172-4997492(+) 90.95 90.95
Public Domain and Genome References
Gene Title
Gene Symbol ssq-1
Ensembl K07F5.11
Entrez Gene 177835 Entrez gene
WormBase CE06125 Wormbase
Functional Annotations
Protein Similarities
Method ID Description E-Value
blast CAA94280 Hypothetical protein K07F5.11 [Caenorhabditis elegans] ref|NP_501768.1| Sperm-Specific family, class Q family member (ssq-1) [Caenorhabditis elegans] 1.0E-58
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] 6.0E-51
blast CAE64995 Hypothetical protein CBG09831 [Caenorhabditis briggsae] 1.0E-49
Sequence
Target Sequence 
>C. ELEGANS:187960_AT
ccaccagctggtggaggtgcctcgacaatgactgctcttggcggagcaccatctggcgca
tctactatgacagctgtcggaggagccccgagaggagcttccacgatgactgccgtcgga
ggagctccaactggtgcttccaccatgaccgctgtgggaggagctccgcgaggagcttca
accatgaccgctgtcggtggggcgccaactggagcttctacgatgacagctgttggagga
gccccaggtgaagcttccaccatgaccgctgttggcggagccccacgtggagcatctaca
atgactgctgttggagccccaggcggtggagcttctgctcttggagccgcgccaccagcc
ggatcaatgagcggaggaggcggtggtggtggagccacttctggatacttcggagtcgga
caaggcgttatgggaggtggtggagctgttggacaatctgcctacttcggagttggagga
ggtgctgctggaggtgccaagtctggaggcggtggtggaggtggaattcccggacaatct
a

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
CCACCAGCTGGTGGAGGTGCCTCGA 108 273 274 Antisense
ATCTGGCGCATCTACTATGACAGCT 27 35 324 Antisense
CCGAGAGGAGCTTCCACGATGACTG 299 263 361 Antisense
TGCCGTCGGAGGAGCTCCAACTGGT 380 579 384 Antisense
TCCAACTGGTGCTTCCACCATGACC 38 587 399 Antisense
CAACCATGACCGCTGTCGGTGGGGC 244 187 452 Antisense
GCTGTTGGAGGAGCCCCAGGTGAAG 511 295 502 Antisense
CAGGTGAAGCTTCCACCATGACCGC 73 207 518 Antisense
GCCACTTCTGGATACTTCGGAGTCG 625 277 667 Antisense
GTGGAGCTGTTGGACAATCTGCCTA 264 491 713 Antisense
GGAGGTGGAATTCCCGGACAATCTA 361 515 790 Antisense
Sequence Source Affymetrix Proprietary Database