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[175528_at]

Description AV183911_rc /REP_DB=TREMBL Accession /GB=AV183911 /CHR=1 /FEA=Genomic Cluster /DEF=Caenorhabditis elegans cDNA clone:yk657g12 : 3prime end, single read.
Cluster 6grp_highest_10_10 > 09      6grp_high1_10_10 > 91      6grp_highest_nonorm > 73      6grp_total > 93      4grp_total > 49      6grp_cgc > 99      6grp_high1_sub > 05      6grp_total_sub > Hat      4grp_rule_based > L3      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 965
1 2 3 4 range
A 265.8
(-3)
A 		969.5
(2.2)
P 		1082.2
(3)
P 		352
(-2.4)
A 		816
B 164.6
(-3)
M 		938.9
(2.3)
P 		1038.8
(3)
P 		335
(-1.8)
P 		874
C 154.8
(-3)
M 		933.8
(1.8)
P 		1119.5
(3)
P 		267.2
(-2.3)
P 		965
avr 195.1
(-3) 		947.4
(2.1) 		1080.2
(3) 		318.1
(-2.2) 		885

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 588
1 2 3 4 5 6 range
A 518.9
(-2)
P 		659.7
(-0.1)
P 		477.1
(-2.5)
P 		457.6
(-2.8)
P 		898.3
(3)
P 		442.9
(-3)
P 		455
B 346.6
(-2.4)
P 		540.5
(0.6)
P 		310.4
(-3)
P 		500.9
(0)
P 		690.9
(3)
P 		587.7
(1.4)
P 		381
C 340.6
(-3)
P 		523.5
(0)
P 		502.2
(-0.3)
P 		591.4
(1.2)
P 		702.5
(3)
P 		578.5
(0.9)
P 		362
avr 402
(-3) 		574.6
(-0.1) 		429.9
(-2.5) 		516.6
(-1.1) 		763.9
(3) 		536.4
(-0.8) 		362
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 345
1 2 3 4 range
A 96.8
(-1.8)
A 		210.5
(1.1)
P 		282.9
(3)
P 		51.5
(-3)
A 		231
B 52.5
(-3)
M 		231.9
(2.7)
P 		240.7
(3)
P 		71.4
(-2.4)
P 		188
C 51.2
(-2.9)
M 		268.5
(0.9)
P 		390.2
(3)
P 		45
(-3)
P 		345
avr 66.8
(-2.7) 		237
(1.4) 		304.6
(3) 		56
(-3) 		249

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 205
1 2 3 4 5 6 range
A 95.7
(-3)
P 		234.6
(1.8)
P 		103.9
(-2.7)
P 		116.1
(-2.3)
P 		271.1
(3)
P 		107.8
(-2.6)
P 		175
B 120.6
(-1.7)
P 		179.9
(0.1)
P 		75.4
(-3)
P 		132.7
(-1.3)
P 		280.7
(3)
P 		219.1
(1.2)
P 		205
C 126.2
(-2.6)
P 		159.7
(-0.7)
P 		127.8
(-2.5)
P 		118.9
(-3)
P 		227.3
(3)
P 		193.7
(1.1)
P 		108
avr 114.2
(-2.5) 		191.4
(0.4) 		102.4
(-3) 		122.6
(-2.2) 		259.7
(3) 		173.5
(-0.3) 		157
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 175528_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.20246
Sequence Type Exemplar sequence
Representative Public ID AV183911 NCBI
Target Description AV183911_rc /REP_DB=TREMBL Accession /GB=AV183911 /CHR=1 /FEA=Genomic Cluster /DEF=Caenorhabditis elegans cDNA clone:yk657g12 : 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_170859(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_170859 NCBI Caenorhabditis elegans SOX (mammalian SRY box) family member (sox-1) (sox-1) mRNA, complete cds. 11/11 None
C32E12.5.1 ENSEMBL cdna:known chromosome:CEL140:I:5204555:5208131:-1 gene:C32E12.5 11/11 None
C32E12.5.2 ENSEMBL cdna:known chromosome:CEL140:I:5204555:5215221:-1 gene:C32E12.5 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
chrI:5204620-5204956(-) 100.0 100.0
Public Domain and Genome References
Gene Title
Gene Symbol sox-1
Ensembl C32E12.5
Entrez Gene 172162 Entrez gene
SwissProt Q8T3B9 EMBL-EBI
WormBase CE30497 Wormbase
Functional Annotations
Gene Ontology
GO Biological Process (view graph)
ID Description Evidence Links
6355 regulation of transcription, DNA-dependent inferred from electronic annotation QuickGO AmiGO
GO Molecular Function (view graph)
ID Description Evidence Links
3677 DNA binding inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast AAM15556 Sox (mammalian sry box) family protein 1 [Caenorhabditis elegans] ref|NP_740846.1| SOX (mammalian SRY box) family member (sox-1) [Caenorhabditis elegans] 1.0E-175
blast T25591 hypothetical protein C32E12.3 - Caenorhabditis elegans 1.0E-165
blast CAE67368 Hypothetical protein CBG12839 [Caenorhabditis briggsae] 1.0E-117
Protein Domains
Database ID Description E-Value
Pfam IPR000910 EMBL-EBI HMG1/2 (high mobility group) box 6.4E-32
Sequence
Target Sequence 
>C. ELEGANS:175528_AT
tacaaaagtatcgtccccatttctttacccatttttatcctctcccagctttaccgagcc
agttttcattcgttctttcaactttcatcgattacccaattcgccgttgtacttgaaaaa
aaaaatttctgagatttcaagcacgaaattatgattgtatatgttgaacacttcccccca
tcccctgccctctacaatatgccaaatgtagctaccctttttcccaaacctgaagaaata
tttattctcttgttcatctctaaatatctcttatcctttt

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
TACAAAAGTATCGTCCCCATTTCTT 346 641 38 Antisense
CCAGCTTTACCGAGCCAGTTTTCAT 425 269 82 Antisense
ACCGAGCCAGTTTTCATTCGTTCTT 599 89 90 Antisense
TTTTCATTCGTTCTTTCAACTTTCA 482 675 100 Antisense
TCAACTTTCATCGATTACCCAATTC 33 631 115 Antisense
TTACCCAATTCGCCGTTGTACTTGA 282 683 129 Antisense
TGTATATGTTGAACACTTCCCCCCA 91 561 193 Antisense
TGCCAAATGTAGCTACCCTTTTTCC 20 585 237 Antisense
AATATTTATTCTCTTGTTCATCTCT 77 175 274 Antisense
TCTCTTGTTCATCTCTAAATATCTC 229 613 283 Antisense
ATCTCTAAATATCTCTTATCCTTTT 163 33 293 Antisense
Sequence Source Affymetrix Proprietary Database