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[173819_s_at]

Description AV190008 /REP_DB=TREMBL Accession /5_PRIME_EXT_ID=H20J18.1 /5_PRIME_EXT_DB=WormBase Gene ID /GB=AV190008 /WB_GENE_ID=H20J18.1 /WP=CE18818 /CHR=X /FEA=Genomic Cluster /GEN=scd-1 /DEF=Caenorhabditis elegans cDNA clone:yk565f7 : 5prime end, single read.
Cluster 6grp_highest_10_10 > 61      6grp_high1_10_10 > 27      4grp_highest_8_8 > 47      4grp_high_8_8 > 11      6grp_highest_nonorm > 20      6grp_total > 27      4grp_total > 13      6grp_highest_sub > De      6grp_cgc > 04      6grp_high1_sub > Cu      6grp_cgc_sub > Cu      6grp_total_sub > Decrease      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 1883
1 2 3 4 range
A 1719
(0.2)
P 		1006.7
(-2.6)
P 		903.7
(-3)
P 		2422.4
(3)
P 		1519
B 1896.1
(1)
P 		1164.7
(-1.3)
P 		626.4
(-3)
P 		2509.7
(3)
P 		1883
C 1752.1
(2.1)
P 		913.5
(-2.6)
P 		845
(-3)
P 		1918.5
(3)
P 		1074
avr 1789.1
(1) 		1028.3
(-2) 		791.7
(-3) 		2283.5
(3) 		1492

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 1181
1 2 3 4 5 6 range
A 1626.9
(3)
P 		1462.8
(2)
P 		657.1
(-3)
P 		710.5
(-2.7)
P 		813.1
(-2)
P 		1269.1
(0.8)
P 		970
B 1697.6
(3)
P 		1324.8
(0.8)
P 		845.8
(-2.1)
P 		843.6
(-2.1)
P 		695.6
(-3)
P 		895.8
(-1.8)
P 		1002
C 1772.5
(3)
P 		1327.3
(0.7)
P 		869.7
(-1.6)
P 		591.4
(-3)
P 		1040.8
(-0.7)
P 		830.5
(-1.8)
P 		1181
avr 1699
(3) 		1371.6
(1) 		790.9
(-2.5) 		715.2
(-3) 		849.8
(-2.2) 		998.5
(-1.3) 		984
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 481
1 2 3 4 range
A 625.9
(3)
P 		218.5
(-3)
P 		236.2
(-2.7)
P 		354.6
(-1)
P 		407
B 604.6
(3)
P 		287.7
(-1.1)
P 		145.2
(-3)
P 		534.8
(2.1)
P 		459
C 580
(3)
P 		262.6
(-3)
P 		294.5
(-2.4)
P 		323.5
(-1.8)
P 		317
avr 603.5
(3) 		256.3
(-2.5) 		225.3
(-3) 		404.3
(-0.2) 		378

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 538
1 2 3 4 5 6 range
A 299.9
(-0.5)
P 		520.2
(3)
P 		143.1
(-3)
P 		180.2
(-2.4)
P 		245.4
(-1.4)
P 		309
(-0.4)
P 		377
B 590.7
(3)
P 		441
(0.7)
P 		205.4
(-3)
P 		223.4
(-2.7)
P 		282.6
(-1.8)
P 		334
(-1)
P 		385
C 657
(3)
P 		405
(0.2)
P 		221.4
(-1.9)
P 		118.9
(-3)
P 		336.8
(-0.6)
P 		278
(-1.2)
P 		538
avr 515.9
(3) 		455.4
(1.9) 		190
(-2.7) 		174.2
(-3) 		288.3
(-1) 		307
(-0.7) 		342
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 173819_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.25907
Sequence Type Exemplar sequence
Representative Public ID AV190008 NCBI
Target Description AV190008 /REP_DB=TREMBL Accession /5_PRIME_EXT_ID=H20J18.1 /5_PRIME_EXT_DB=WormBase Gene ID /GB=AV190008 /WB_GENE_ID=H20J18.1 /WP=CE18818 /CHR=X /FEA=Genomic Cluster /GEN=scd-1 /DEF=Caenorhabditis elegans cDNA clone:yk565f7 : 5prime 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_171974(11), NM_171785(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_171974 NCBI Caenorhabditis elegans Suppressor of Constitutive Dauer formation family member (scd-1) (scd-1) mRNA, complete cds. 11/11 None
NM_171785 NCBI Caenorhabditis elegans Suppressor of Constitutive Dauer formation family member (scd-1) (scd-1) mRNA, complete cds. 11/11 None
SNAP00000025288 ENSEMBL cdna:SNAP chromosome:CEL140:X:12504540:12509137:-1 11/11 None
GENEFINDER00000025290 ENSEMBL cdna:GeneFinder chromosome:CEL140:X:12504540:12509137:-1 11/11 None
H20J18.1a ENSEMBL cdna:known chromosome:CEL140:X:12503807:12513968:-1 gene:H20J18.1 11/11 A 
H20J18.1b ENSEMBL cdna:known chromosome:CEL140:X:12504540:12509137:-1 gene:H20J18.1 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
chrX:12504361-12509138(-) 87.0 100.0
Public Domain and Genome References
Ensembl H20J18.1
Functional Annotations
Protein Similarities
Method ID Description E-Value
blast CAA18898 Hypothetical protein H20J18.1a [Caenorhabditis elegans] ref|NP_741912.1| Suppressor of Constitutive Dauer formation family member (scd-1) [Caenorhabditis elegans] 0.0
blast CAD44137 Hypothetical protein H20J18.1b [Caenorhabditis elegans] ref|NP_741911.1| Suppressor of Constitutive Dauer formation family member (scd-1) [Caenorhabditis elegans] 0.0
Sequence
Target Sequence 
>C. ELEGANS:173819_S_AT
gacagcgaacgggcatcaagtgggcgttgatgacgatggtcaagtggttgactttgccgc
gcgtccaattgatcccattttcaaggatgctcgcgaggatatgaaggcaaaagacgtccg
cacattggagcatgctgtgaaaaggcccttctccaacaacatggcaactcatgctaaaaa
tgtgaaggaaagcccatcaccacaaagacatgctggacaatccccacatcaaattccatc
tccaatgcgtcagggagctcataatccactgggaatcaatagatcgatcccggatgccgc
tccaccaaagatcgaagctgatagctccagatcgcccagcgaagacttggaagaagacgg
tggaggaaaacgtctccgtattgcaactgatg

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GACAGCGAACGGGCATCAAGTGGGC 181 333 2458 Antisense
AGACGTCCGCACATTGGAGCATGCT 274 71 2569 Antisense
AGCATGCTGTGAAAAGGCCCTTCTC 543 77 2586 Antisense
GCCCTTCTCCAACAACATGGCAACT 8 287 2602 Antisense
GAAGGAAAGCCCATCACCACAAAGA 73 333 2641 Antisense
TGGACAATCCCCACATCAAATTCCA 705 547 2671 Antisense
AATTCCATCTCCAATGCGTCAGGGA 657 177 2689 Antisense
GCGTCAGGGAGCTCATAATCCACTG 660 289 2704 Antisense
CAATAGATCGATCCCGGATGCCGCT 206 181 2734 Antisense
CGAAGCTGATAGCTCCAGATCGCCC 426 253 2770 Antisense
AAACGTCTCCGTATTGCAACTGATG 93 123 2825 Antisense
Sequence Source Affymetrix Proprietary Database