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[171992_x_at]

Description AV199678_rc /REP_DB=TREMBL Accession /GB=AV199678 /FEA=Transcript Cluster /DEF=Caenorhabditis elegans cDNA clone:yk550a11 : 3prime end, single read.
Cluster 6grp_total > 58      4grp_total > 21      6grp_total_sub > Cup      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 89
1 2 3 4 range
A 45.6
(-0.7)
A 		17.2
(-2.6)
A 		11.4
(-3)
A 		100.8
(3)
M 		89
B 65.2
(3)
A 		29.1
(-1)
A 		11.5
(-3)
A 		56.4
(2)
P 		54
C 55.6
(3)
A 		41.7
(-1.1)
A 		35.5
(-3)
P 		52.2
(2)
A 		20
avr 55.5
(1.3) 		29.3
(-1.8) 		19.5
(-3) 		69.8
(3) 		50

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 117
1 2 3 4 5 6 range
A 39
(-1.6)
A 		55.2
(-0.7)
P 		52.3
(-0.9)
A 		14.5
(-3)
A 		42.6
(-1.4)
A 		120.5
(3)
P 		106
B 37.2
(2.1)
A 		38.4
(2.4)
A 		19.9
(-3)
A 		25.2
(-1.4)
A 		34.8
(1.4)
M 		40.3
(3)
A 		20
C 72.2
(3)
P 		3.4
(-3)
A 		44.3
(0.6)
A 		6.9
(-2.7)
A 		40.1
(0.2)
A 		48.9
(1)
P 		69
avr 49.5
(0.8) 		32.3
(-1.1) 		38.8
(-0.4) 		15.5
(-3) 		39.2
(-0.4) 		69.9
(3) 		54
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 18
1 2 3 4 range
A 16.6
(3)
A 		3.7
(-2.7)
A 		3
(-3)
A 		14.8
(2.2)
M 		14
B 20.8
(3)
A 		7.2
(-1.5)
A 		2.7
(-3)
A 		12
(0.1)
P 		18
C 18.4
(3)
A 		12
(-1)
A 		12.4
(-0.8)
P 		8.8
(-3)
A 		10
avr 18.6
(3) 		7.6
(-2.2) 		6
(-3) 		11.9
(-0.2) 		13

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 28
1 2 3 4 5 6 range
A 7.2
(-2.2)
A 		19.6
(0.7)
P 		11.4
(-1.2)
A 		3.7
(-3)
A 		12.8
(-0.9)
A 		29.3
(3)
P 		26
B 12.9
(1.8)
A 		12.8
(1.7)
A 		4.8
(-3)
A 		6.7
(-1.9)
A 		14.1
(2.5)
M 		15
(3)
A 		10
C 26.8
(3)
P 		1
(-3)
A 		11.3
(-0.6)
A 		1.4
(-2.9)
A 		13
(-0.2)
A 		16.4
(0.6)
P 		26
avr 15.6
(1.3) 		11.1
(-0.3) 		9.2
(-1) 		3.9
(-3) 		13.3
(0.5) 		20.2
(3) 		16
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 171992_x_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.27766
Sequence Type Exemplar sequence
Representative Public ID AV199678 NCBI
Target Description AV199678_rc /REP_DB=TREMBL Accession /GB=AV199678 /FEA=Transcript Cluster /DEF=Caenorhabditis elegans cDNA clone:yk550a11 : 3prime end, single read.
Cluster Evidence This cluster is supported by a Transcript Cluster.
Annotation Method Description
Annotation Description This probe set was annotated using the Genome Target Overlap based pipeline to a RefSeq identifier using 1 transcript(s).
Annotation Grade This is a grade B annotation.
Annotation Transcript Cluster (# of Matching Probes) NM_001027257, NM_001027258
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_001027258 NCBI Caenorhabditis elegans Y38E10A.6b (Y38E10A.6) mRNA, complete cds. None
NM_001027257 NCBI Caenorhabditis elegans Y38E10A.6a (Y38E10A.6) mRNA, complete cds. None
Y38E10A.6b ENSEMBL cdna:known chromosome:CEL140:II:12582110:12603581:-1 gene:Y38E10A.6 A 
SNAP00000017429 ENSEMBL cdna:SNAP chromosome:CEL140:II:12582277:12603581:-1 None
Y38E10A.6a ENSEMBL cdna:known chromosome:CEL140:II:12582277:12603581:-1 gene:Y38E10A.6 A 
GENEFINDER00000017474 ENSEMBL cdna:GeneFinder chromosome:CEL140:II:12582277:12603581:-1 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
chrII:12582140-12582343(-) 65.57 65.57
Public Domain and Genome References
Ensembl Y38E10A.6
Functional Annotations
Protein Similarities
Method ID Description E-Value
blast CAE46683 Hypothetical protein Y38E10A.6b [Caenorhabditis elegans] ref|NP_001022429.1| Y38E10A.6b [Caenorhabditis elegans] 0.0
blast CAB60334 Hypothetical protein Y38E10A.6a [Caenorhabditis elegans] ref|NP_001022428.1| Y38E10A.6a [Caenorhabditis elegans] 0.0
blast T26656 hypothetical protein Y38E10A.f - Caenorhabditis elegans 0.0
Protein Domains
Database ID Description E-Value
scop a.4.1.Homeodomain All alpha proteins; DNA/RNA-binding 3-helical bundle; Homeodomain-like; Homeodomain 1.70000004768372
scop a.4.1.Homeodomain All alpha proteins; DNA/RNA-binding 3-helical bundle; Homeodomain-like; Homeodomain 1.60000002384186
scop a.4.1.Homeodomain All alpha proteins; DNA/RNA-binding 3-helical bundle; Homeodomain-like; Homeodomain 1.20000004768372
scop a.4.1.Homeodomain All alpha proteins; DNA/RNA-binding 3-helical bundle; Homeodomain-like; Homeodomain 2.29999995231628
scop a.4.1.Homeodomain All alpha proteins; DNA/RNA-binding 3-helical bundle; Homeodomain-like; Homeodomain 0.28999999165535
scop a.4.1.Homeodomain All alpha proteins; DNA/RNA-binding 3-helical bundle; Homeodomain-like; Homeodomain 0.280000001192093
scop a.4.1.Homeodomain All alpha proteins; DNA/RNA-binding 3-helical bundle; Homeodomain-like; Homeodomain 1.89999997615814
scop a.4.1.Homeodomain All alpha proteins; DNA/RNA-binding 3-helical bundle; Homeodomain-like; Homeodomain 0.00899999961256981
scop a.4.1.Homeodomain All alpha proteins; DNA/RNA-binding 3-helical bundle; Homeodomain-like; Homeodomain 0.00800000037997961
scop a.4.1.Homeodomain All alpha proteins; DNA/RNA-binding 3-helical bundle; Homeodomain-like; Homeodomain 0.0230000000447035
scop a.4.1.Homeodomain All alpha proteins; DNA/RNA-binding 3-helical bundle; Homeodomain-like; Homeodomain 0.25
scop a.4.1.Homeodomain All alpha proteins; DNA/RNA-binding 3-helical bundle; Homeodomain-like; Homeodomain 0.270000010728836
scop a.4.1.Homeodomain All alpha proteins; DNA/RNA-binding 3-helical bundle; Homeodomain-like; Homeodomain 0.00100000004749745
Pfam IPR001356 EMBL-EBI Homeobox 1.6E-4
Pfam IPR001356 EMBL-EBI Homeobox 5.1E-4
Pfam IPR001356 EMBL-EBI Homeobox 16.0
Pfam IPR001356 EMBL-EBI Homeobox 0.58
Pfam IPR001356 EMBL-EBI Homeobox 23.0
Pfam IPR001356 EMBL-EBI Homeobox 0.51
Pfam IPR001356 EMBL-EBI Homeobox 20.0
Pfam IPR001356 EMBL-EBI Homeobox 0.095
Pfam IPR001356 EMBL-EBI Homeobox 28.0
Pfam IPR001356 EMBL-EBI Homeobox 5.1E-4
Pfam IPR001356 EMBL-EBI Homeobox 16.0
Pfam IPR001356 EMBL-EBI Homeobox 0.58
Pfam IPR001356 EMBL-EBI Homeobox 23.0
Pfam IPR001356 EMBL-EBI Homeobox 0.51
Pfam IPR001356 EMBL-EBI Homeobox 1.6E-4
Pfam IPR001356 EMBL-EBI Homeobox 5.1E-4
Pfam IPR001356 EMBL-EBI Homeobox 16.0
Pfam IPR001356 EMBL-EBI Homeobox 0.58
Pfam IPR001356 EMBL-EBI Homeobox 23.0
Pfam IPR001356 EMBL-EBI Homeobox 0.51
Pfam IPR001356 EMBL-EBI Homeobox 20.0
Sequence
Target Sequence 
>C. ELEGANS:171992_X_AT
acagccaaaggtgagatttccaagaccagaattctngaggaagcatacgccaattttatg
aaagacggaaaactgacggcccatgagatngccacannnnncgccanccgcaacaacaac
accgaaattgaccagaagccgagaatcca

BLASTn GenBank NR
Note: "n"'s represent regions that are not probed by the probe sequences.
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
ACAGCCAAAGGTGAGATTTCCAAGA 631 107 13 Antisense
GTGAGATTTCCAAGACCAGAATTCT 79 483 23 Antisense
GAGGAAGCATACGCCAATTTTATGA 355 405 49 Antisense
GAAGCATACGCCAATTTTATGAAAG 304 341 52 Antisense
ATACGCCAATTTTATGAAAGACGGA 277 19 57 Antisense
GAAAGACGGAAAACTGACGGCCCAT 41 361 72 Antisense
AGACGGAAAACTGACGGCCCATGAG 265 65 75 Antisense
ACGGAAAACTGACGGCCCATGAGAT 593 95 77 Antisense
CCGCAACAACAACACCGAAATTGAC 104 249 120 Antisense
AACACCGAAATTGACCAGAAGCCGA 286 111 130 Antisense
AAATTGACCAGAAGCCGAGAATCCA 614 113 137 Antisense
Sequence Source Affymetrix Proprietary Database