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[174313_s_at]

Description C29267_rc /REP_DB=TREMBL Accession /GB=C29267 /CHR=X /FEA=Genomic Cluster /DEF=C.elegans cDNA clone yk199g8 : 3prime end, single read.
Cluster 6grp_highest_10_10 > 70      6grp_high1_10_10 > 18      4grp_highest_8_8 > 51      4grp_high_8_8 > 25      6grp_highest_nonorm > 50      6grp_total > 07      4grp_total > 47      6grp_highest_sub > De      6grp_cgc > 12      6grp_cgc_sub > De      6grp_total_sub > Decrease      6grp_rule_based > S1      4grp_rule_based > L1      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 989
1 2 3 4 range
A 1250.9
(3)
P 		307.8
(-2.8)
P 		277.2
(-3)
P 		364.4
(-2.5)
P 		974
B 1265.9
(3)
P 		411.4
(-2.4)
P 		308.5
(-3)
P 		497.8
(-1.8)
P 		957
C 1119.9
(3)
P 		506.5
(-1.7)
P 		335.4
(-3)
P 		504.1
(-1.7)
P 		785
avr 1212.2
(3) 		408.6
(-2.3) 		307
(-3) 		455.4
(-2) 		905

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 944
1 2 3 4 5 6 range
A 1155.1
(3)
P 		572.9
(-1)
P 		280.5
(-3)
P 		315.7
(-2.8)
P 		433.9
(-1.9)
P 		359.5
(-2.5)
P 		875
B 962.4
(3)
P 		488.9
(-0.8)
P 		211.4
(-3)
P 		495.7
(-0.7)
P 		336.8
(-2)
P 		314.6
(-2.2)
P 		751
C 874.3
(3)
P 		621.9
(0.3)
P 		430.5
(-1.8)
P 		328.6
(-2.9)
P 		345.3
(-2.7)
P 		320.1
(-3)
P 		554
avr 997.3
(3) 		561.2
(-0.8) 		307.5
(-3) 		380
(-2.4) 		372
(-2.4) 		331.4
(-2.8) 		690
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 402
1 2 3 4 range
A 455.4
(3)
P 		66.8
(-2.8)
P 		72.5
(-2.7)
P 		53.3
(-3)
P 		402
B 403.7
(3)
P 		101.6
(-2.5)
P 		71.5
(-3)
P 		106.1
(-2.4)
P 		332
C 370.7
(3)
P 		145.6
(-1.7)
P 		116.9
(-2.3)
P 		85
(-3)
P 		286
avr 409.9
(3) 		104.7
(-2.6) 		87
(-2.9) 		81.5
(-3) 		328

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 284
1 2 3 4 5 6 range
A 212.9
(3)
P 		203.7
(2.6)
P 		61.1
(-3)
P 		80.1
(-2.2)
P 		130.9
(-0.2)
P 		87.5
(-2)
P 		152
B 334.9
(3)
P 		162.7
(-0.6)
P 		51.3
(-3)
P 		131.3
(-1.3)
P 		136.8
(-1.2)
P 		117.3
(-1.6)
P 		284
C 324.1
(3)
P 		189.8
(-0.1)
P 		109.6
(-2)
P 		66.1
(-3)
P 		111.7
(-1.9)
P 		107.2
(-2)
P 		258
avr 290.6
(3) 		185.4
(0.1) 		74
(-3) 		92.5
(-2.5) 		126.5
(-1.5) 		104
(-2.2) 		217
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 174313_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.22203
Sequence Type Exemplar sequence
Representative Public ID C29267 NCBI
Target Description C29267_rc /REP_DB=TREMBL Accession /GB=C29267 /CHR=X /FEA=Genomic Cluster /DEF=C.elegans cDNA clone yk199g8 : 3prime end, single read.
Cluster Evidence This cluster is supported by a Genomic Cluster.
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_171725(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_171725 NCBI Caenorhabditis elegans SOX (mammalian SRY box) family member (sox-2) (sox-2) mRNA, complete cds. 11/11 None
K08A8.2a.1 ENSEMBL cdna:known chromosome:CEL140:X:7458238:7463681:-1 gene:K08A8.2 11/11 A 
K08A8.2a.2 ENSEMBL cdna:known chromosome:CEL140:X:7458238:7460493:-1 gene:K08A8.2 11/11 A 
Annotation Notes
There are no noteworthy cross hybridizing mRNAs found for this probe set.
Splice Variants
Entrez Total Refseq Isoforms Total Detected By This Probeset Refseq Probesets
181002 2 1 NM_171725 174313_s_at (11)
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrX:7458301-7458590(-) 100.0 100.0
Public Domain and Genome References
Ensembl K08A8.2
Functional Annotations
Protein Similarities
Method ID Description E-Value
blast AAA79747 Sox (mammalian sry box) family protein 2, isoform a [Caenorhabditis elegans] ref|NP_741836.1| SOX (mammalian SRY box) family member (sox-2) [Caenorhabditis elegans] 1.0E-159
blast CAE70216 Hypothetical protein CBG16696 [Caenorhabditis briggsae] 1.0E-134
blast AAN72421 Sox (mammalian sry box) family protein 2, isoform b [Caenorhabditis elegans] ref|NP_741837.1| SOX (mammalian SRY box) family member (sox-2) [Caenorhabditis elegans] 1.0E-106
Protein Domains
Database ID Description E-Value
Pfam IPR000910 EMBL-EBI HMG1/2 (high mobility group) box 1.7E-32
Sequence
Target Sequence 
>C. ELEGANS:174313_S_AT
ttttctccgtcctgattcttgataattctcactgttcttcgatttttgtttgctctctta
cccattatttgatgccacttgtgtcagccgtcattttccacgtttccccagttttttaat
ccatgcaaccaatttattgctcctaactctcatcaccttcagttttattgtatatt

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
TTTTCTCCGTCCTGATTCTTGATAA 330 675 20 Antisense
TCCGTCCTGATTCTTGATAATTCTC 417 595 25 Antisense
GATTCTTGATAATTCTCACTGTTCT 649 431 33 Antisense
TTCTCACTGTTCTTCGATTTTTGTT 573 691 45 Antisense
GTTCTTCGATTTTTGTTTGCTCTCT 374 443 53 Antisense
TTTGCTCTCTTACCCATTATTTGAT 321 669 68 Antisense
TACCCATTATTTGATGCCACTTGTG 487 649 78 Antisense
AACCAATTTATTGCTCCTAACTCTC 90 143 146 Antisense
CTAACTCTCATCACCTTCAGTTTTA 376 227 162 Antisense
CTCTCATCACCTTCAGTTTTATTGT 89 231 166 Antisense
ATCACCTTCAGTTTTATTGTATATT 276 29 171 Antisense
Sequence Source Affymetrix Proprietary Database