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[173120_s_at]

Description AV181429_rc /REP_DB=TREMBL Accession /FEA=EST Transcript /REVCOMP /GB=AV181429 /DEF=Caenorhabditis elegans cDNA clone:yk620c2 : 3prime end, single read.
Cluster 6grp_highest_10_10 > 74      6grp_high1_10_10 > 57      4grp_highest_8_8 > 40      4grp_high_8_8 > 43      6grp_highest_nonorm > 81      6grp_total > 58      4grp_total > 52      6grp_highest_sub > Cu      6grp_cgc > 27      6grp_high1_sub > Cu      6grp_cgc_sub > Cu      6grp_total_sub > Cup      4grp_rule_based > L2      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 239
1 2 3 4 range
A 350.6
(3)
P 		336.9
(2.5)
P 		280.6
(0.3)
P 		196.3
(-3)
P 		154
B 298.4
(0.8)
P 		368.9
(3)
P 		291.3
(0.5)
P 		179.5
(-3)
P 		189
C 418.3
(3)
P 		363.4
(1.5)
P 		304.6
(-0.1)
P 		201.1
(-3)
P 		217
avr 355.8
(3) 		356.4
(3) 		292.2
(0.7) 		192.3
(-3) 		164

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 222
1 2 3 4 5 6 range
A 287.7
(1.1)
P 		253.7
(-0.2)
P 		243.1
(-0.6)
P 		182.7
(-3)
P 		226.6
(-1.3)
P 		335.8
(3)
P 		153
B 358.8
(2.6)
P 		290.3
(0)
P 		368.1
(3)
P 		309.4
(0.8)
P 		210.4
(-3)
P 		365.7
(2.9)
P 		158
C 309.5
(0)
P 		270.5
(-1.2)
P 		213.9
(-3)
P 		272.5
(-1.2)
P 		289.7
(-0.6)
P 		404.5
(3)
P 		191
avr 318.7
(0.6) 		271.5
(-1.6) 		275
(-1.4) 		254.9
(-2.4) 		242.2
(-3) 		368.7
(3) 		127
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 110
1 2 3 4 range
A 127.7
(3)
P 		73.1
(-0.3)
P 		73.3
(-0.3)
P 		28.7
(-3)
P 		99
B 95.2
(3)
P 		91.1
(2.6)
P 		67.5
(0.1)
P 		38.3
(-3)
P 		57
C 138.5
(3)
P 		104.5
(1)
P 		106.2
(1.1)
P 		33.9
(-3)
P 		105
avr 120.5
(3) 		89.6
(0.9) 		82.3
(0.4) 		33.6
(-3) 		87

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 90
1 2 3 4 5 6 range
A 53
(-2.1)
P 		90.2
(3)
P 		52.9
(-2.1)
P 		46.3
(-3)
P 		68.4
(0)
P 		81.7
(1.8)
P 		44
B 124.8
(1.7)
P 		96.6
(-1.4)
P 		89.4
(-2.2)
P 		81.9
(-3)
P 		85.5
(-2.6)
P 		136.4
(3)
P 		55
C 114.7
(1.5)
P 		82.5
(-0.9)
P 		54.4
(-3)
P 		54.8
(-3)
P 		93.7
(-0.1)
P 		135.4
(3)
P 		81
avr 97.5
(0.9) 		89.8
(0) 		65.6
(-2.5) 		61
(-3) 		82.5
(-0.7) 		117.8
(3) 		57
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 173120_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.26732
Sequence Type Exemplar sequence
Representative Public ID AV181429 NCBI
Target Description AV181429_rc /REP_DB=TREMBL Accession /FEA=EST Transcript /REVCOMP /GB=AV181429 /DEF=Caenorhabditis elegans cDNA clone:yk620c2 : 3prime end, single read.
Cluster Evidence This cluster is supported by a EST Transcript.
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_064080(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_064080 NCBI Caenorhabditis elegans Nuclear Pore complex Protein family member (npp-5) (npp-5) mRNA, complete cds. 11/11 A 
SNAP00000044553 ENSEMBL cdna:SNAP chromosome:CEL140:II:11596828:11599708:-1 11/11 None
GENEFINDER00000044561 ENSEMBL cdna:GeneFinder chromosome:CEL140:II:11596828:11599708:-1 11/11 None
F07A11.3 ENSEMBL cdna:known chromosome:CEL140:II:11596682:11599712:-1 gene:F07A11.3 11/11 A 
Annotation Notes
Cross Hybridizing mRNA Matched Probes Nature of Assignment Related Probesets by Grade
NM_063377 1/11 Cross Hyb Matching Probes A 
SNAP00000010401 1/11 Cross Hyb Matching Probes None
GENEFINDER00000010411 1/11 Cross Hyb Matching Probes None
F22B5.2 1/11 Cross Hyb Matching Probes A 
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrII:11596779-11597030(-) 80.33 80.33
Public Domain and Genome References
Gene Title
Gene Symbol npp-5
Ensembl F07A11.3
Entrez Gene 174779 Entrez gene
SwissProt Q19131 EMBL-EBI
WormBase CE03145 Wormbase
Functional Annotations
Protein Similarities
Method ID Description E-Value
blast CAA91316 Hypothetical protein F07A11.3 [Caenorhabditis elegans] ref|NP_496481.1| Nuclear Pore complex Protein family member (npp-5) [Caenorhabditis elegans] 0.0
blast CAE59465 Hypothetical protein CBG02849 [Caenorhabditis briggsae] 0.0
Sequence
Target Sequence 
>C. ELEGANS:173120_S_AT
aggagattcggaatctcttcctcccgcaattcttcatccttcttgcacaagccgccgtga
gactcgacgataccacaaatttcaacgatttcttcacaagcttcaataatgacctcgggc
tcgatcaggaatggatggttttcatcaaagctttctacgcagaactcaatctcaaagtcg
aat

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
AGGAGATTCGGAATCTCTTCCTCCC 242 57 34 Antisense
CGCCGTGAGACTCGACGATACCACA 588 255 86 Antisense
GAGACTCGACGATACCACAAATTTC 289 393 92 Antisense
ACCACAAATTTCAACGATTTCTTCA 309 85 105 Antisense
ACGATTTCTTCACAAGCTTCAATAA 578 91 118 Antisense
AGCTTCAATAATGACCTCGGGCTCG 122 79 132 Antisense
AATGACCTCGGGCTCGATCAGGAAT 504 159 141 Antisense
GGGCTCGATCAGGAATGGATGGTTT 695 491 150 Antisense
GATGGTTTTCATCAAAGCTTTCTAC 57 409 167 Antisense
AGCTTTCTACGCAGAACTCAATCTC 94 79 182 Antisense
GCAGAACTCAATCTCAAAGTCGAAT 209 311 192 Antisense
Sequence Source Affymetrix Proprietary Database