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[174224_at]

Description C30996_rc /REP_DB=TREMBL Accession /GB=C30996 /CHR=4 /FEA=Genomic Cluster /DEF=C.elegans cDNA clone yk267a9 : 3prime end, single read.
Cluster 6grp_highest_10_10 > 40      6grp_high1_10_10 > 03      4grp_highest_8_8 > 24      4grp_high_8_8 > 51      6grp_highest_nonorm > 11      6grp_total > 15      4grp_total > 52      6grp_highest_sub > De      6grp_cgc > 21      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 1364
1 2 3 4 range
A 3221
(0.6)
P 		3666.1
(3)
P 		2932.9
(-1)
P 		2575.7
(-3)
P 		1090
B 3129.2
(-1.8)
P 		3355.7
(0.3)
P 		3639.9
(3)
P 		2998.1
(-3)
P 		642
C 3476.4
(3)
P 		3120.7
(1.2)
P 		3242.9
(1.8)
P 		2302.3
(-3)
P 		1174
avr 3275.5
(2.2) 		3380.8
(3) 		3271.9
(2.1) 		2625.4
(-3) 		755

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 2011
1 2 3 4 5 6 range
A 2745.8
(3)
P 		1913.1
(0.5)
P 		1283.9
(-1.4)
P 		763.7
(-3)
P 		976.6
(-2.4)
P 		816.2
(-2.8)
P 		1982
B 1767.9
(3)
P 		1702.6
(2.6)
P 		1643.2
(2.3)
P 		1025
(-1.3)
P 		735.3
(-3)
P 		831.7
(-2.4)
P 		1033
C 2262.5
(3)
P 		1378.8
(-0.6)
P 		1438.4
(-0.4)
P 		869.8
(-2.7)
P 		796.6
(-3)
P 		816.5
(-2.9)
P 		1466
avr 2258.7
(3) 		1664.8
(0.5) 		1455.2
(-0.4) 		886.2
(-2.7) 		836.2
(-2.9) 		821.5
(-3) 		1437
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 796
1 2 3 4 range
A 1172.8
(3)
P 		795.8
(0.2)
P 		766.7
(-0.1)
P 		377
(-3)
P 		796
B 997.9
(3)
P 		828.8
(0.2)
P 		843.4
(0.4)
P 		638.9
(-3)
P 		359
C 1150.8
(3)
P 		897.2
(1)
P 		1130.3
(2.8)
P 		388.2
(-3)
P 		763
avr 1107.2
(3) 		840.6
(0.5) 		913.5
(1.2) 		468
(-3) 		639

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 664
1 2 3 4 5 6 range
A 506.2
(0.9)
P 		680.4
(3)
P 		279.6
(-1.9)
P 		193.7
(-3)
P 		294.7
(-1.8)
P 		198.7
(-2.9)
P 		487
B 615.1
(3)
P 		566.7
(2.2)
P 		399
(-0.8)
P 		271.5
(-3)
P 		298.8
(-2.5)
P 		310.1
(-2.3)
P 		344
C 838.6
(3)
P 		420.7
(-0.8)
P 		366.1
(-1.3)
P 		174.9
(-3)
P 		257.8
(-2.3)
P 		273.3
(-2.1)
P 		664
avr 653.3
(3) 		555.9
(1.7) 		348.2
(-1.2) 		213.4
(-3) 		283.8
(-2) 		260.7
(-2.4) 		440
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 174224_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.21592
Sequence Type Exemplar sequence
Representative Public ID C30996 NCBI
Target Description C30996_rc /REP_DB=TREMBL Accession /GB=C30996 /CHR=4 /FEA=Genomic Cluster /DEF=C.elegans cDNA clone yk267a9 : 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_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
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.6.1 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 
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:6325432-6325711(+) 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
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-122
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:174224_AT
catcacctcaatcaccatctgaaatgcctccatcacagtcctcttcagaattcctgtttc
cttcctacctaatctttcaaaaaatgtccaaattgttttgtcctcacgcccagactcaat
caaaagcagttacaaatcgaccctaaatttctaacgcgcgtttttctttaattccttttt
tggcaatgacgatctgagatgtgttgttcccgaggttgaattttatatcgaaccagtttg
tt

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
CATCACCTCAATCACCATCTGAAAT 68 213 20 Antisense
CTCAATCACCATCTGAAATGCCTCC 660 227 26 Antisense
AGTCCTCTTCAGAATTCCTGTTTCC 376 61 56 Antisense
TTCCTACCTAATCTTTCAAAAAATG 445 695 81 Antisense
CTCACGCCCAGACTCAATCAAAAGC 474 227 122 Antisense
CAAAAGCAGTTACAAATCGACCCTA 3 185 140 Antisense
ATCGACCCTAAATTTCTAACGCGCG 629 1 155 Antisense
AATTCCTTTTTTGGCAATGACGATC 572 175 189 Antisense
ACGATCTGAGATGTGTTGTTCCCGA 30 93 208 Antisense
GATGTGTTGTTCCCGAGGTTGAATT 506 407 217 Antisense
GAATTTTATATCGAACCAGTTTGTT 255 323 237 Antisense
Sequence Source Affymetrix Proprietary Database