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[180237_s_at]

Description Y54E5A.4 /REP_DB=WormBase Gene ID /WP=CE20315 /TR=Q9XWK3 /GB=CAA21657.1 /SUBMIT=HINXTON /CHR=1 /FEA=Sanger Annotation
Cluster 6grp_highest_10_10 > 82      6grp_high1_10_10 > 38      4grp_highest_8_8 > 32      4grp_high_8_8 > 51      6grp_highest_nonorm > 40      6grp_total > 28      4grp_total > 52      6grp_highest_sub > Cu      6grp_cgc > 05      6grp_high1_sub > Cu      6grp_cgc_sub > Cu      6grp_total_sub > Cup      4grp_rule_based > L1      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 475
1 2 3 4 range
A 792.6
(2.1)
P 		789.5
(2)
P 		834.5
(3)
P 		552.6
(-3)
P 		282
B 876.6
(2.3)
P 		931.5
(3)
P 		680.8
(-0.2)
P 		456.2
(-3)
P 		475
C 729.2
(2.9)
P 		671.7
(0.3)
P 		732
(3)
P 		598.6
(-3)
P 		133
avr 799.5
(3) 		797.6
(3) 		749.1
(1.9) 		535.8
(-3) 		264

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 577
1 2 3 4 5 6 range
A 1029.5
(3)
P 		641.4
(-1)
P 		549.4
(-2)
P 		452.3
(-3)
P 		705.1
(-0.4)
P 		664.9
(-0.8)
P 		577
B 980.5
(3)
P 		712.1
(-0.1)
P 		494.1
(-2.6)
P 		530.5
(-2.2)
P 		463.8
(-3)
P 		817.2
(1.1)
P 		517
C 743.9
(3)
P 		671.7
(1.2)
P 		500.3
(-3)
P 		499.3
(-3)
P 		588.9
(-0.8)
P 		623.4
(0)
P 		245
avr 918
(3) 		675.1
(-0.4) 		514.6
(-2.7) 		494
(-3) 		585.9
(-1.7) 		701.8
(-0.1) 		424
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 208
1 2 3 4 range
A 288.6
(3)
P 		171.4
(-0.4)
P 		218.1
(1)
P 		80.9
(-3)
P 		208
B 279.5
(3)
P 		230.1
(1.4)
P 		157.8
(-1)
P 		97.2
(-3)
P 		182
C 241.4
(2.5)
P 		193.1
(0.6)
P 		255.1
(3)
P 		100.9
(-3)
P 		154
avr 269.8
(3) 		198.2
(0.6) 		210.3
(1) 		93
(-3) 		177

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 241
1 2 3 4 5 6 range
A 189.8
(1)
P 		228.1
(3)
P 		119.6
(-2.7)
P 		114.7
(-3)
P 		212.8
(2.2)
P 		161.9
(-0.5)
P 		113
B 341.2
(3)
P 		237
(0.2)
P 		120
(-3)
P 		140.5
(-2.4)
P 		188.4
(-1.1)
P 		304.7
(2)
P 		221
C 275.7
(3)
P 		204.9
(0.6)
P 		127.3
(-2.1)
P 		100.4
(-3)
P 		190.5
(0.1)
P 		208.7
(0.7)
P 		175
avr 268.9
(3) 		223.3
(1.2) 		122.3
(-2.8) 		118.5
(-3) 		197.2
(0.1) 		225.1
(1.3) 		150
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 180237_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.1132
Sequence Type Exemplar sequence
Representative Public ID Y54E5A.4 NCBI
Target Description Y54E5A.4 /REP_DB=WormBase Gene ID /WP=CE20315 /TR=Q9XWK3 /GB=CAA21657.1 /SUBMIT=HINXTON /CHR=1 /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_061151(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_061151 NCBI Caenorhabditis elegans Nuclear Pore complex Protein family member (npp-4) (npp-4) mRNA, complete cds. 11/11 None
GENEFINDER00000041555 ENSEMBL cdna:GeneFinder chromosome:CEL140:I:14709385:14714638:-1 11/11 None
Y54E5A.4.1 ENSEMBL cdna:known chromosome:CEL140:I:14709253:14714640:-1 gene:Y54E5A.4 11/11 None
Y54E5A.4.2 ENSEMBL cdna:known chromosome:CEL140:I:14709253:14714644:-1 gene:Y54E5A.4 11/11 None
Annotation Notes
Cross Hybridizing mRNA Matched Probes Nature of Assignment Related Probesets by Grade
SNAP00000041548 5/11 Cross Hyb Matching Probes None
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrI:14709358-14714569(-) 99.63 100.0
Public Domain and Genome References
Gene Title
Gene Symbol npp-4
Ensembl Y54E5A.4
Entrez Gene 173329 Entrez gene
SwissProt Q9XWK3 EMBL-EBI
WormBase CE20315 Wormbase
Functional Annotations
Protein Similarities
Method ID Description E-Value
blast CAA21657 Hypothetical protein Y54E5A.4 [Caenorhabditis elegans] ref|NP_493552.1| Nuclear Pore complex Protein family member (npp-4) [Caenorhabditis elegans] 0.0
blast CAA21657 Hypothetical protein Y54E5A.4 [Caenorhabditis elegans] ref|NP_493552.1| Nuclear Pore complex Protein family member (npp-4) [Caenorhabditis elegans] 1.0E-170
blast CAE72567 Hypothetical protein CBG19751 [Caenorhabditis briggsae] 5.0E-91
blast CAE72567 Hypothetical protein CBG19751 [Caenorhabditis briggsae] 6.0E-81
blast AAB52432 Nuclear pore complex protein protein 11 [Caenorhabditis elegans] ref|NP_491232.1| Nuclear Pore complex Protein family member (npp-11) [Caenorhabditis elegans] 4.0E-9
Sequence
Target Sequence 
>C. ELEGANS:180237_S_AT
cacatcatcatgtcactgagctcggaaaagaaattgaagaaattcgagattttctaattg
aacaaggatatactcaattgagaaaatggtcgactacagctgcttcagcagcagcaccaa
tagcttcgaattctgaaatgattgttagagaaggagccgagttcttcccatcacaatcta
gtctggcaatcattggaagctcgttgagagcaccggctgctccggctccagctgttggag
ggcttggattgggcactggaaccagtctttttggaaatactggaacaacttctcttttcg
gatcaacggccacaaaaccagctttctctggaggatctctattcggtgcaacaacttcta
ctgcaacatcctcagctgctgccaccaccacaactccgactacatcactcttcggatcaa
ccaaaccagccaccacaactacaccatttgcatcgactgtt

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
CACATCATCATGTCACTGAGCTCGG 15 197 1127 Antisense
TCTTCCCATCACAATCTAGTCTGGC 613 617 1289 Antisense
GAAGCTCGTTGAGAGCACCGGCTGC 247 343 1322 Antisense
TCCGGCTCCAGCTGTTGGAGGGCTT 98 593 1347 Antisense
AGGGCTTGGATTGGGCACTGGAACC 632 57 1365 Antisense
TTCTCTTTTCGGATCAACGGCCACA 92 689 1416 Antisense
GAGGATCTCTATTCGGTGCAACAAC 522 403 1457 Antisense
CAACTTCTACTGCAACATCCTCAGC 149 189 1478 Antisense
AACTCCGACTACATCACTCTTCGGA 173 141 1518 Antisense
TCTTCGGATCAACCAAACCAGCCAC 593 615 1535 Antisense
AACTACACCATTTGCATCGACTGTT 221 139 1563 Antisense
Sequence Source Affymetrix Proprietary Database