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[177225_at]

Description Y73B6BL.X /REP_DB=WormBase Gene ID /WP=CE26296 /CHR=4 /FEA=Sanger Annotation /DEF=(ST.LOUIS) protein_id:AAG23482.1
Cluster 6grp_highest_10_10 > 51      6grp_high1_10_10 > 16      4grp_highest_8_8 > 54      4grp_high_8_8 > 18      6grp_highest_nonorm > 20      6grp_total > 15      4grp_total > 22      6grp_highest_sub > De      6grp_cgc > 23      6grp_high1_sub > De      6grp_cgc_sub > De      6grp_total_sub > Decrease      6grp_rule_based > S1      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 597
1 2 3 4 range
A 2678.5
(1.6)
P 		2557.7
(0.3)
P 		2271.8
(-3)
P 		2798.7
(3)
P 		527
B 2726.2
(3)
P 		2201.4
(-3)
P 		2532
(0.8)
P 		2688.9
(2.6)
P 		525
C 2702.5
(1.7)
P 		2750.5
(3)
P 		2521.2
(-3)
P 		2530.4
(-2.8)
P 		229
avr 2702.4
(3) 		2503.2
(-1.6) 		2441.7
(-3) 		2672.7
(2.3) 		261

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 1185
1 2 3 4 5 6 range
A 1588.7
(3)
P 		1568
(2.8)
P 		817.2
(-2.7)
P 		932.2
(-1.8)
P 		771.9
(-3)
P 		1016.3
(-1.2)
P 		817
B 1415.1
(3)
P 		1285.9
(1.9)
P 		995.2
(-0.5)
P 		855.9
(-1.7)
P 		696.1
(-3)
P 		744.7
(-2.6)
P 		719
C 1841.1
(3)
P 		1244.4
(-0)
P 		1293.5
(0.2)
P 		842.9
(-2.1)
P 		819.3
(-2.2)
P 		656
(-3)
P 		1185
avr 1615
(3) 		1366.1
(1.2) 		1035.3
(-1.1) 		877
(-2.2) 		762.4
(-3) 		805.7
(-2.7) 		853
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 566
1 2 3 4 range
A 975.2
(3)
P 		555.2
(-1.5)
P 		593.9
(-1)
P 		409.7
(-3)
P 		566
B 869.4
(3)
P 		543.7
(-3)
P 		586.7
(-2.2)
P 		573
(-2.5)
P 		326
C 894.6
(3)
P 		790.8
(1.7)
P 		878.7
(2.8)
P 		426.7
(-3)
P 		468
avr 913.1
(3) 		629.9
(-0.8) 		686.4
(-0.1) 		469.8
(-3) 		443

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 513
1 2 3 4 5 6 range
A 292.9
(-1.2)
P 		557.7
(3)
P 		178
(-3)
P 		236.4
(-2.1)
P 		232.9
(-2.1)
P 		247.4
(-1.9)
P 		380
B 492.4
(3)
P 		428
(1.5)
P 		241.7
(-2.7)
P 		226.7
(-3)
P 		282.8
(-1.7)
P 		277.7
(-1.8)
P 		266
C 682.4
(3)
P 		379.7
(-0.5)
P 		329.2
(-1.1)
P 		169.5
(-3)
P 		265.1
(-1.9)
P 		219.6
(-2.4)
P 		513
avr 489.2
(3) 		455.1
(2.3) 		249.6
(-2.2) 		210.9
(-3) 		260.3
(-1.9) 		248.2
(-2.2) 		278
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 177225_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.19370
Sequence Type Exemplar sequence
Representative Public ID Y73B6BL.X NCBI
Target Description Y73B6BL.X /REP_DB=WormBase Gene ID /WP=CE26296 /CHR=4 /FEA=Sanger Annotation /DEF=(ST.LOUIS) protein_id:AAG23482.1
Cluster Evidence This cluster is supported by a 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_001028402(11), NM_001028403(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_001028402 NCBI Caenorhabditis elegans homologous to Drosophila SQD (squid) protein family member (sqd-1) (sqd-1) mRNA, complete cds. 11/11 None
NM_001028403 NCBI Caenorhabditis elegans homologous to Drosophila SQD (squid) protein family member (sqd-1) (sqd-1) mRNA, complete cds. 11/11 None
SNAP00000032034 ENSEMBL cdna:SNAP chromosome:CEL140:IV:6324329:6325419:1 11/11 None
GENEFINDER00000032105 ENSEMBL cdna:GeneFinder chromosome:CEL140:IV:6324329:6325419:1 11/11 None
Y73B6BL.6.7 ENSEMBL cdna:known chromosome:CEL140:IV:6324159:6326388:1 gene:Y73B6BL.6 11/11 A 
Y73B6BL.6.6 ENSEMBL cdna:known chromosome:CEL140:IV:6324163:6326388:1 gene:Y73B6BL.6 11/11 A 
Y73B6BL.6.3 ENSEMBL cdna:known chromosome:CEL140:IV:6324163:6326388:1 gene:Y73B6BL.6 11/11 A 
Y73B6BL.6.9 ENSEMBL cdna:known chromosome:CEL140:IV:6324165:6325419:1 gene:Y73B6BL.6 11/11 None
Y73B6BL.6.1 ENSEMBL cdna:known chromosome:CEL140:IV:6324165:6326388:1 gene:Y73B6BL.6 11/11 A 
Y73B6BL.6.4 ENSEMBL cdna:known chromosome:CEL140:IV:6324176:6326388:1 gene:Y73B6BL.6 11/11 A 
Y73B6BL.6.5 ENSEMBL cdna:known chromosome:CEL140:IV:6324184:6326388:1 gene:Y73B6BL.6 11/11 A 
Y73B6BL.6.2 ENSEMBL cdna:known chromosome:CEL140:IV:6324194:6326388:1 gene:Y73B6BL.6 11/11 A 
Y73B6BL.6.8 ENSEMBL cdna:known chromosome:CEL140:IV:6324200:6325419:1 gene:Y73B6BL.6 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:6322052-6325425(+) 100.0 100.0
Public Domain and Genome References
Ensembl Y73B6BL.6
Functional Annotations
Protein Similarities
Method ID Description E-Value
blast AAY43984 Homologous to drosophila sqd (squid) protein protein 1, isoform b [Caenorhabditis elegans] ref|NP_001023574.1| homologous to Drosophila SQD (squid) protein family member (sqd-1) [Caenorhabditis elegans] 1.0E-125
blast AAM44397 Homologous to drosophila sqd (squid) protein protein 1, isoform a [Caenorhabditis elegans] ref|NP_001023573.1| homologous to Drosophila SQD (squid) protein family member (sqd-1) [Caenorhabditis elegans] 1.0E-124
Protein Domains
Database ID Description E-Value
Pfam IPR000504 EMBL-EBI RNA-binding region RNP-1 (RNA recognition motif) 4.1E-21
Pfam IPR000504 EMBL-EBI RNA-binding region RNP-1 (RNA recognition motif) 4.3E-22
Sequence
Target Sequence 
>C. ELEGANS:177225_AT
ctcccatcggactacagcgagcaagatcttcgctctcatttcgaacaattcggcaaggtc
gacgacattgaatggccattcgataagcagaccaaggctcgtcgcaacttcgcttttatc
gtattcgaggaggaggagtccgcagacaaagcatcttcccagacaaaacagaccttcgga
actcgcgaatgtgacgtgaaaaaagcagttccacaaggaaaacggttcccaggcgcccaa
gggcgtatgccaggtggtcgcggaatgtatggtggacgtggtggaaataacaactcggga
tggtatgctggatggggacaaattggagctatgccatacggagctactggagcagcttgg
ggagactggtacggaaacggttattacggccaacaaggtgcagcacatcacaacaacagc
ggatcatcgcaaggttacggaagcggataccagagaaataacagtggattcgattaccaa
caagctcaaggagccagacagggcaacaatggccaaccacgct

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
CTCCCATCGGACTACAGCGAGCAAG 284 233 1216 Antisense
GAGCAAGATCTTCGCTCTCATTTCG 329 391 1234 Antisense
TAAGCAGACCAAGGCTCGTCGCAAC 106 637 1299 Antisense
TCGTCGCAACTTCGCTTTTATCGTA 332 605 1314 Antisense
GGAGTCCGCAGACAAAGCATCTTCC 458 517 1350 Antisense
GACAAAACAGACCTTCGGAACTCGC 22 367 1377 Antisense
TCCCAGGCGCCCAAGGGCGTATGCC 384 597 1442 Antisense
TATGCCAGGTGGTCGCGGAATGTAT 222 657 1461 Antisense
GGAGCTATGCCATACGGAGCTACTG 504 521 1540 Antisense
TACGGCCAACAAGGTGCAGCACATC 201 647 1600 Antisense
CAGGGCAACAATGGCCAACCACGCT 247 209 1714 Antisense
Sequence Source Affymetrix Proprietary Database