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[187500_at]

Description C53C9.2 /REP_DB=WormBase Gene ID /WP=CE27882 /TR=SW:Q09936 /GB=AAB52603.2 /SUBMIT=ST.LOUIS /CHR=X /FEA=Sanger Annotation
Cluster 6grp_highest_10_10 > 40      6grp_high1_10_10 > 05      4grp_highest_8_8 > 58      4grp_high_8_8 > 33      6grp_highest_nonorm > 03      6grp_total > 15      4grp_total > 38      6grp_highest_sub > De      6grp_high1_sub > De      6grp_total_sub > Decrease      6grp_rule_based > S1      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 4239
1 2 3 4 range
A 6880
(3)
P 		4208.7
(-1.6)
P 		3388.1
(-3)
P 		4299.8
(-1.4)
P 		3492
B 7626.7
(3)
P 		4540.2
(-1.4)
P 		3428.4
(-3)
P 		4496
(-1.5)
P 		4198
C 7046.9
(3)
P 		4778.3
(-0.9)
P 		3533.4
(-3)
P 		3801.1
(-2.5)
P 		3514
avr 7184.5
(3) 		4509.1
(-1.3) 		3450
(-3) 		4199
(-1.8) 		3735

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 5938
1 2 3 4 5 6 range
A 5107.7
(1.4)
P 		6353.2
(3)
P 		1929.1
(-2.8)
P 		2740.7
(-1.7)
P 		1779.7
(-2.9)
P 		1737.3
(-3)
P 		4616
B 4757.3
(3)
P 		3644.1
(1.2)
P 		2158.7
(-1.2)
P 		2027.6
(-1.4)
P 		1779.4
(-1.8)
P 		1059.4
(-3)
P 		3698
C 6851.9
(3)
P 		3378.9
(-0.5)
P 		4550.5
(0.7)
P 		1670.5
(-2.2)
P 		2693.6
(-1.2)
P 		913.9
(-3)
P 		5938
avr 5572.3
(3) 		4458.7
(1.5) 		2879.4
(-0.7) 		2146.3
(-1.7) 		2084.2
(-1.8) 		1236.9
(-3) 		4335
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 1876
1 2 3 4 range
A 2505
(3)
P 		913.6
(-2.1)
P 		885.7
(-2.2)
P 		629.4
(-3)
P 		1876
B 2432.1
(3)
P 		1121.3
(-1.8)
P 		794.4
(-3)
P 		958.1
(-2.4)
P 		1638
C 2332.7
(3)
P 		1373.8
(-0.4)
P 		1231.5
(-0.9)
P 		640.9
(-3)
P 		1692
avr 2423.3
(3) 		1136.2
(-1.6) 		970.5
(-2.2) 		742.8
(-3) 		1681

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 2234
1 2 3 4 5 6 range
A 941.6
(-1.3)
P 		2259.5
(3)
P 		420.1
(-3)
P 		695.1
(-2.1)
P 		537
(-2.6)
P 		423
(-3)
P 		1839
B 1655.3
(3)
P 		1213
(0.9)
P 		524.2
(-2.4)
P 		537
(-2.3)
P 		722.9
(-1.4)
P 		395.1
(-3)
P 		1260
C 2539.7
(3)
P 		1031
(-1.1)
P 		1158.2
(-0.7)
P 		335.9
(-2.9)
P 		871.6
(-1.5)
P 		305.9
(-3)
P 		2234
avr 1712.2
(3) 		1501.2
(2.1) 		700.8
(-1.5) 		522.7
(-2.3) 		710.5
(-1.5) 		374.7
(-3) 		1338
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 187500_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.16364
Sequence Type Exemplar sequence
Representative Public ID C53C9.2 NCBI
Target Description C53C9.2 /REP_DB=WormBase Gene ID /WP=CE27882 /TR=SW:Q09936 /GB=AAB52603.2 /SUBMIT=ST.LOUIS /CHR=X /FEA=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_076898(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_076898 NCBI Caenorhabditis elegans C53C9.2 (C53C9.2) mRNA, complete cds. 11/11 None
GENEFINDER00000002526 ENSEMBL cdna:GeneFinder chromosome:CEL140:X:7686836:7696662:-1 11/11 None
SNAP00000002523 ENSEMBL cdna:SNAP chromosome:CEL140:X:7686879:7688790:-1 11/11 None
C53C9.2 ENSEMBL cdna:known chromosome:CEL140:X:7686585:7689158:-1 gene:C53C9.2 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
chrX:7686877-7688789(-) 88.23 95.7
Public Domain and Genome References
Gene Title
Ensembl C53C9.2
Entrez Gene 181031 Entrez gene
SwissProt Q09936 EMBL-EBI
WormBase CE27882 Wormbase
Functional Annotations
Protein Similarities
Method ID Description E-Value
blast AAB52603 Hypothetical protein C53C9.2 [Caenorhabditis elegans] ref|NP_509299.1| C53C9.2 [Caenorhabditis elegans] sp|Q09936|YSE2_CAEEL Hypothetical protein C53C9.2 in chromosome X 0.0
blast T15827 hypothetical protein C53C9.2 - Caenorhabditis elegans 0.0
blast CAE70260 Hypothetical protein CBG16761 [Caenorhabditis briggsae] 0.0
blast AAR25654 K (potassium) voltage-gated sensory channel subunit protein 1, isoform b [Caenorhabditis elegans] ref|NP_001024490.1| K (potassium) Voltage-gated Sensory channel subunit family member (kvs-1) [Caenorhabditis elegans] 0.0
blast CAE70261 Hypothetical protein CBG16762 [Caenorhabditis briggsae] 0.0
blast AAR30209 K (potassium) voltage-gated sensory channel subunit protein 1, isoform c [Caenorhabditis elegans] ref|NP_001024491.1| K (potassium) Voltage-gated Sensory channel subunit family member (kvs-1) [Caenorhabditis elegans] 0.0
Protein Domains
Database ID Description E-Value
Pfam IPR000557 EMBL-EBI Calponin repeat 1.5E-6
Pfam IPR000557 EMBL-EBI Calponin repeat 0.0037
Pfam IPR000557 EMBL-EBI Calponin repeat 2.1
Pfam IPR000557 EMBL-EBI Calponin repeat 8.9E-4
Pfam IPR000557 EMBL-EBI Calponin repeat 0.46
Pfam IPR000557 EMBL-EBI Calponin repeat 1.7E-9
Pfam IPR005821 EMBL-EBI Ion transport protein 1.8E-17
Pfam IPR005821 EMBL-EBI Ion transport protein 1.1E-22
Pfam IPR003131 EMBL-EBI K+ channel tetramerisation 2.9E-20
Pfam IPR000557 EMBL-EBI Calponin repeat 1.5E-6
Pfam IPR000557 EMBL-EBI Calponin repeat 0.0037
Pfam IPR000557 EMBL-EBI Calponin repeat 2.1
Pfam IPR000557 EMBL-EBI Calponin repeat 8.9E-4
Pfam IPR000557 EMBL-EBI Calponin repeat 0.46
Pfam IPR000557 EMBL-EBI Calponin repeat 1.7E-9
Trans Membrane
ID Number Of Domains Domain Boundaries
GENEFINDER00000002526 6 235-257,302-324,334-356,440-462,472-494,501-523
Sequence
Target Sequence 
>C. ELEGANS:187500_AT
gaagacattctccgacgaggaaccgaattcacaccatggtactctggacaaaacaaattc
gccacccaagctggatctggaggtttccttaaggttcgtgacgttctaccacacaccgtt
ggaggaaaagacatcgaagaggagctcaagcaaaagtccgagggaattgttccacttcaa
tctggaaccaacaagttggcttctcaacgtggaatgactggattcggaacaccaagaaac
acccaacttagggctggatggaagaaggaatggattgaggattacgaggctgctctcaaa
gaatgggaagagaccaagccaccaggcagtgcttcttctgttgacccatttggtcactac
aagaagaagttcgaggagcgtgagtcatcccgccaatcggaaattg

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GAAGACATTCTCCGACGAGGAACCG 658 339 670 Antisense
TTCACACCATGGTACTCTGGACAAA 710 685 697 Antisense
CAAAACAAATTCGCCACCCAAGCTG 451 191 718 Antisense
GCCACCCAAGCTGGATCTGGAGGTT 479 277 730 Antisense
TAAGGTTCGTGACGTTCTACCACAC 571 611 759 Antisense
GTTCTACCACACACCGTTGGAGGAA 252 439 772 Antisense
GAAACACCCAACTTAGGGCTGGATG 420 355 905 Antisense
GAGGATTACGAGGCTGCTCTCAAAG 609 403 946 Antisense
TGGGAAGAGACCAAGCCACCAGGCA 419 545 973 Antisense
GTTCGAGGAGCGTGAGTCATCCCGC 52 443 1038 Antisense
GAGTCATCCCGCCAATCGGAAATTG 21 401 1051 Antisense
Sequence Source Affymetrix Proprietary Database