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[173612_s_at]

Description C49347 /REP_DB=TREMBL Accession /5_PRIME_EXT_ID=Y77E11A.13B /5_PRIME_EXT_DB=WormBase Gene ID /GB=C49347 /WB_GENE_ID=Y77E11A.13B /WP=CE25615 /CHR=4 /FEA=Genomic Cluster /DEF=C.elegans cDNA clone yk469c3 : 5prime end, single read.
Cluster 6grp_highest_10_10 > 07      6grp_high1_10_10 > 70      4grp_highest_8_8 > 19      4grp_high_8_8 > 63      6grp_highest_nonorm > 73      6grp_total > 80      4grp_total > 48      6grp_highest_sub > 04      6grp_cgc > 95      6grp_high1_sub > 04      6grp_cgc_sub > 04      6grp_total_sub > Hat      4grp_rule_based > L3      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 487
1 2 3 4 range
A 493.1
(-2.5)
P 		473.2
(-2.8)
P 		859.1
(3)
P 		461.6
(-3)
P 		398
B 471.5
(-0.2)
P 		464.6
(-0.4)
P 		582.9
(3)
P 		372.5
(-3)
P 		210
C 476.2
(-0.4)
P 		489.1
(0)
P 		584.4
(3)
P 		391
(-3)
P 		193
avr 480.3
(-1.4) 		475.6
(-1.5) 		675.5
(3) 		408.4
(-3) 		267

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 439
1 2 3 4 5 6 range
A 450.6
(-1.4)
P 		484.8
(-0.5)
P 		508.3
(0.2)
P 		610.9
(3)
P 		554.6
(1.5)
P 		392
(-3)
P 		219
B 547.6
(1.1)
P 		603.2
(3)
P 		572.2
(2)
P 		595.9
(2.8)
P 		518.4
(0.1)
P 		425.6
(-3)
P 		178
C 648.9
(-0.1)
P 		526.5
(-2.1)
P 		537.1
(-2)
P 		830.7
(3)
P 		540.7
(-1.9)
P 		475
(-3)
P 		356
avr 549
(-0.1) 		538.2
(-0.4) 		539.2
(-0.4) 		679.2
(3) 		537.9
(-0.4) 		430.9
(-3) 		248
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 159
1 2 3 4 range
A 179.5
(1.3)
P 		102.7
(-1.7)
P 		224.6
(3)
P 		67.6
(-3)
P 		157
B 150.4
(3)
P 		114.7
(-0)
P 		135.1
(1.7)
P 		79.4
(-3)
P 		71
C 157.6
(1)
P 		140.6
(0.3)
P 		203.7
(3)
P 		65.9
(-3)
P 		138
avr 162.5
(1.7) 		119.3
(-0.5) 		187.8
(3) 		71
(-3) 		117

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 157
1 2 3 4 5 6 range
A 83.1
(-3)
P 		172.4
(3)
P 		110.7
(-1.1)
P 		154.9
(1.8)
P 		167.4
(2.7)
P 		95.4
(-2.2)
P 		89
B 190.5
(1.3)
P 		200.8
(2.2)
P 		138.9
(-3)
P 		157.8
(-1.4)
P 		210.6
(3)
P 		158.7
(-1.3)
P 		72
C 240.5
(3)
P 		160.7
(-1.6)
P 		136.7
(-3)
P 		167.1
(-1.2)
P 		175
(-0.8)
P 		159
(-1.7)
P 		104
avr 171.4
(1.6) 		178
(2.3) 		128.8
(-3) 		159.9
(0.4) 		184.3
(3) 		137.7
(-2) 		56
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 173612_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.24977
Sequence Type Exemplar sequence
Representative Public ID C49347 NCBI
Target Description C49347 /REP_DB=TREMBL Accession /5_PRIME_EXT_ID=Y77E11A.13B /5_PRIME_EXT_DB=WormBase Gene ID /GB=C49347 /WB_GENE_ID=Y77E11A.13B /WP=CE25615 /CHR=4 /FEA=Genomic Cluster /DEF=C.elegans cDNA clone yk469c3 : 5prime 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_067685(11), NM_067686(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_067685 NCBI Caenorhabditis elegans Nuclear Pore complex Protein family member (npp-20) (npp-20) mRNA, complete cds. 11/11 A 
NM_067686 NCBI Caenorhabditis elegans Nuclear Pore complex Protein family member (npp-20) (npp-20) mRNA, complete cds. 11/11 None
GENEFINDER00000027321 ENSEMBL cdna:GeneFinder chromosome:CEL140:IV:1490759:1496006:-1 11/11 None
Y77E11A.13a ENSEMBL cdna:known chromosome:CEL140:IV:1490723:1496006:-1 gene:Y77E11A.13 11/11 A 
Y77E11A.13b ENSEMBL cdna:known chromosome:CEL140:IV:1490726:1496019:-1 gene:Y77E11A.13 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:1490878-1496013(-) 100.0 100.0
Public Domain and Genome References
Ensembl Y77E11A.13
Functional Annotations
Protein Similarities
Method ID Description E-Value
blast AAF36082 Nuclear pore complex protein protein 20, isoform a [Caenorhabditis elegans] ref|NP_500086.1| Nuclear Pore complex Protein family member (npp-20) [Caenorhabditis elegans] 0.0
blast AAF36083 Nuclear pore complex protein protein 20, isoform b [Caenorhabditis elegans] ref|NP_500087.1| Nuclear Pore complex Protein family member (npp-20) [Caenorhabditis elegans] 1.0E-123
blast AAF36082 Nuclear pore complex protein protein 20, isoform a [Caenorhabditis elegans] ref|NP_500086.1| Nuclear Pore complex Protein family member (npp-20) [Caenorhabditis elegans] 1.0E-108
blast AAF36083 Nuclear pore complex protein protein 20, isoform b [Caenorhabditis elegans] ref|NP_500087.1| Nuclear Pore complex Protein family member (npp-20) [Caenorhabditis elegans] 1.0E-108
blast AAF36083 Nuclear pore complex protein protein 20, isoform b [Caenorhabditis elegans] ref|NP_500087.1| Nuclear Pore complex Protein family member (npp-20) [Caenorhabditis elegans] 1.0E-107
blast AAF36082 Nuclear pore complex protein protein 20, isoform a [Caenorhabditis elegans] ref|NP_500086.1| Nuclear Pore complex Protein family member (npp-20) [Caenorhabditis elegans] 1.0E-107
Protein Domains
Database ID Description E-Value
Pfam IPR001680 EMBL-EBI G-protein beta WD-40 repeat 0.0030
Pfam IPR001680 EMBL-EBI G-protein beta WD-40 repeat 5.2E-11
Pfam IPR001680 EMBL-EBI G-protein beta WD-40 repeat 3.3E-6
Pfam IPR001680 EMBL-EBI G-protein beta WD-40 repeat 6.7E-8
Pfam IPR001680 EMBL-EBI G-protein beta WD-40 repeat 1.4E-4
Pfam IPR001680 EMBL-EBI G-protein beta WD-40 repeat 0.031
Pfam IPR001680 EMBL-EBI G-protein beta WD-40 repeat 1.4E-4
Pfam IPR001680 EMBL-EBI G-protein beta WD-40 repeat 0.031
Sequence
Target Sequence 
>C. ELEGANS:173612_S_AT
cacggtccgccagagaatcgatacacaacatcgtgacgcaatgcacgacgctcagctcaa
catctacggaagccgactcgccacgtgtggatctgaccgtcttgtgaagatttttgaggt
tcgcccaaatggccagtcatatccgatggcggagcttgtcggacacagtggtcccgtttg
gaaagtctcatgggctcatccgaaatatggaggacttcttgcctccgcttcctatgatag
aaaagtgataatctggaacgaacaacaaggccgctggcaaaaagcctacgaatgggccgc
tcatgaggccagtacgacttgtgtggcctttgcaccacaccaatatggcctaatgttggc
ttctgcctctgctgacggtgatatcggtattcttcgatacgacaattcgagcaacgaatg
gatttcgtcgaaaattcagaaatgtcatgaacaaggagttaattcagtgtgttgggcacc
tggaagtgctgatccggc

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
CACGGTCCGCCAGAGAATCGATACA 114 199 19 Antisense
CAACATCTACGGAAGCCGACTCGCC 174 189 76 Antisense
CGACTCGCCACGTGTGGATCTGACC 522 249 92 Antisense
TGAGGTTCGCCCAAATGGCCAGTCA 649 565 133 Antisense
GTCGGACACAGTGGTCCCGTTTGGA 207 473 176 Antisense
AAAGTCTCATGGGCTCATCCGAAAT 152 123 200 Antisense
AGCCTACGAATGGGCCGCTCATGAG 421 83 301 Antisense
CGCTCATGAGGCCAGTACGACTTGT 651 251 316 Antisense
ATGGCCTAATGTTGGCTTCTGCCTC 676 53 363 Antisense
TGCCTCTGCTGACGGTGATATCGGT 385 585 382 Antisense
GGGCACCTGGAAGTGCTGATCCGGC 286 493 492 Antisense
Sequence Source Affymetrix Proprietary Database