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[187969_s_at]

Description F02E8.6 /REP_DB=WormBase Gene ID /WP=CE07021 /GEN=npc-1 /TR=Q19127 /GB=AAA96211.1 /SUBMIT=ST.LOUIS /CHR=X /FEA=Sanger Annotation
Cluster 6grp_highest_10_10 > 60      6grp_high1_10_10 > 27      4grp_highest_8_8 > 46      4grp_high_8_8 > 10      6grp_highest_nonorm > 40      6grp_total > 07      4grp_total > 21      6grp_highest_sub > De      6grp_cgc > 13      6grp_high1_sub > Cu      6grp_cgc_sub > De      6grp_total_sub > Decrease      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 275
1 2 3 4 range
A 693.5
(0.8)
P 		564
(-3)
P 		582.9
(-2.4)
P 		767.6
(3)
P 		204
B 657.1
(0.6)
P 		587.2
(-0.9)
P 		492.9
(-3)
P 		765.5
(3)
P 		273
C 719.1
(3)
P 		590.8
(-1.3)
P 		540.1
(-3)
P 		641.6
(0.4)
P 		179
avr 689.9
(1.9) 		580.7
(-1.6) 		538.6
(-3) 		724.9
(3) 		186

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 522
1 2 3 4 5 6 range
A 965.6
(3)
P 		694.9
(-0.5)
P 		501.4
(-3)
P 		536.7
(-2.5)
P 		510.4
(-2.9)
P 		617.1
(-1.5)
P 		464
B 778
(3)
P 		689.4
(1.4)
P 		545.8
(-1.2)
P 		627.2
(0.3)
P 		443.5
(-3)
P 		573.4
(-0.7)
P 		335
C 739.7
(3)
P 		578.3
(-1.4)
P 		620.3
(-0.3)
P 		649.7
(0.5)
P 		521.1
(-3)
P 		546.7
(-2.3)
P 		219
avr 827.8
(3) 		654.2
(-0.1) 		555.8
(-1.9) 		604.5
(-1) 		491.7
(-3) 		579.1
(-1.4) 		336
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 144
1 2 3 4 range
A 252.5
(3)
P 		122.4
(-2.6)
P 		152.4
(-1.3)
P 		112.4
(-3)
P 		140
B 209.5
(3)
P 		145
(-1.1)
P 		114.2
(-3)
P 		163.1
(0.1)
P 		95
C 238
(3)
P 		169.9
(-0.1)
P 		188.2
(0.7)
P 		108.2
(-3)
P 		130
avr 233.3
(3) 		145.8
(-2) 		151.6
(-1.7) 		127.9
(-3) 		105

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 165
1 2 3 4 5 6 range
A 178
(-0)
P 		247.1
(3)
P 		109.2
(-3)
P 		136.1
(-1.8)
P 		154
(-1.1)
P 		150.2
(-1.2)
P 		138
B 270.7
(3)
P 		229.5
(1.2)
P 		132.5
(-3)
P 		166.1
(-1.5)
P 		180.2
(-0.9)
P 		213.8
(0.5)
P 		138
C 274.2
(3)
P 		176.5
(-1.1)
P 		157.9
(-1.9)
P 		130.7
(-3)
P 		168.6
(-1.4)
P 		183
(-0.8)
P 		144
avr 241
(3) 		217.7
(1.7) 		133.2
(-3) 		144.3
(-2.4) 		167.6
(-1.1) 		182.3
(-0.3) 		108
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 187969_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.16728
Sequence Type Exemplar sequence
Representative Public ID F02E8.6 NCBI
Target Description F02E8.6 /REP_DB=WormBase Gene ID /WP=CE07021 /GEN=npc-1 /TR=Q19127 /GB=AAA96211.1 /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_076370(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_076370 NCBI Caenorhabditis elegans NPC1 (human Niemann Pick C disease) Related family member (ncr-1) (ncr-1) mRNA, complete cds. 11/11 None
F02E8.6 ENSEMBL cdna:known chromosome:CEL140:X:4472257:4480049:-1 gene:F02E8.6 11/11 None
Annotation Notes
Cross Hybridizing mRNA Matched Probes Nature of Assignment Related Probesets by Grade
SNAP00000018051 8/11 Cross Hyb Matching Probes None
GENEFINDER00000018055 8/11 Cross Hyb Matching Probes None
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrX:4472499-4480050(-) 100.0 100.0
Public Domain and Genome References
Gene Title
Gene Symbol ncr-1
Ensembl F02E8.6
Entrez Gene 180719 Entrez gene
SwissProt Q19127 EMBL-EBI
WormBase CE29251 Wormbase
Functional Annotations
Ortholog
ID Title Organism
HG-U133_PLUS_2:220106_AT NPC1 (Niemann-Pick disease, type C1, gene)-like 1 hs
HG-U133A:220106_AT NPC1 (Niemann-Pick disease, type C1, gene)-like 1 hs
HG-FOCUS:220106_AT NPC1 (Niemann-Pick disease, type C1, gene)-like 1 hs
HG-U133A_2:220106_AT NPC1 (Niemann-Pick disease, type C1, gene)-like 1 hs
HG-U133_PLUS_2:224306_AT NPC1 (Niemann-Pick disease, type C1, gene)-like 1 hs
HG-U133B:224306_AT NPC1 (Niemann-Pick disease, type C1, gene)-like 1 hs
HG-U133_PLUS_2:224305_S_AT NPC1 (Niemann-Pick disease, type C1, gene)-like 1 hs
HG-U133B:224305_S_AT NPC1 (Niemann-Pick disease, type C1, gene)-like 1 hs
HU35KSUBC:RC_N53757_AT NPC1 (Niemann-Pick disease, type C1, gene)-like 1 hs
U133_X3P:G7019468_3P_AT NPC1 (Niemann-Pick disease, type C1, gene)-like 1 hs
U133_X3P:G6643037_3P_X_AT NPC1 (Niemann-Pick disease, type C1, gene)-like 1 hs
U133_X3P:G6643037_3P_AT NPC1 (Niemann-Pick disease, type C1, gene)-like 1 hs
U133_X3P:G6643037_3P_A_AT NPC1 (Niemann-Pick disease, type C1, gene)-like 1 hs
HG-U95B:54375_AT NPC1 (Niemann-Pick disease, type C1, gene)-like 1 hs
MOE430B:1438514_AT NPC1-like 1 mm
MOUSE430_2:1438514_AT NPC1-like 1 mm
Gene Ontology
GO Cellular Component (view graph)
ID Description Evidence Links
16020 membrane inferred from electronic annotation QuickGO AmiGO
5770 late endosome inferred from sequence similarity QuickGO AmiGO
5764 lysosome inferred from sequence similarity QuickGO AmiGO
GO Molecular Function (view graph)
ID Description Evidence Links
8158 hedgehog receptor activity inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast AAA96211 Npc1 (human niemann pick c disease) related protein 1 [Caenorhabditis elegans] ref|NP_508771.1| NPC1 (human Niemann Pick C disease) Related family member (ncr-1) [Caenorhabditis elegans] sp|Q19127|NPC1_CAEEL Niemann-Pick C1 protein homolog 1 precursor 0.0
blast CAE68601 Hypothetical protein CBG14473 [Caenorhabditis briggsae] 0.0
blast NP_498813 NPC1 (human Niemann Pick C disease) Related family member (ncr-2) [Caenorhabditis elegans] gb|AAK84521.1| Npc1 (human niemann pick c disease) related protein 2 [Caenorhabditis elegans] sp|P34389|NPC2_CAEEL Niemann-Pick C1 protein homolog 2 precursor 1.0E-168
Protein Domains
Database ID Description E-Value
Pfam IPR003392 EMBL-EBI Patched family 6.4E-5
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_508771.1 13 283-305,356-373,630-652,665-687,697-719,740-762,777-799,856-878,1129-1151,1164-1184,1189-1211,1223-1245,1260-1282
F02E8.6 13 283-305,356-373,630-652,665-687,697-719,740-762,777-799,856-878,1129-1151,1164-1184,1189-1211,1223-1245,1260-1282
Sequence
Target Sequence 
>C. ELEGANS:187969_S_AT
attgttcctcatcactattgtcagcagtgctgtccatgctctcatcatattgcctatttt
gcttgccttcggaggatcgagaggccatggaagttcagagactagcacgaatgacaatga
cgagcaacatgacgcgtgcgttttgtcgccaaccgcggaaagtcatatttcaaacgtgga
agaaggaatccttaaccgtccttctttactggacgccagccacattctcgatccgcttct
taaagcggaaggtgggattgataaagcaattggtagggatttcaaatatcataacaatcg
atcgctcttacccatctacgccatcttcactgccatgtacctcccgaatgccaagagctc
atatagaaccggatctccgatctttgtagataccgatttactcttcacttattctattcc
atacattcactttgttatttccgtgtcatttatcaaatgccatgtattgtacatttatgc
ggcaacaataggtactcttgttgttttttgtcacttctcatacacttctcatccactcat
taaaact

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
ATTGTTCCTCATCACTATTGTCAGC 544 5 3789 Antisense
TCCATGCTCTCATCATATTGCCTAT 98 591 3821 Antisense
CATATTGCCTATTTTGCTTGCCTTC 147 215 3834 Antisense
GACGAGCAACATGACGCGTGCGTTT 389 379 3907 Antisense
ACCGTCCTTCTTTACTGGACGCCAG 314 89 3983 Antisense
TCATAACAATCGATCGCTCTTACCC 531 619 4077 Antisense
TACCTCCCGAATGCCAAGAGCTCAT 267 651 4126 Antisense
AGAACCGGATCTCCGATCTTTGTAG 694 73 4153 Antisense
TTTACTCTTCACTTATTCTATTCCA 642 673 4185 Antisense
GGTACTCTTGTTGTTTTTTGTCACT 279 505 4279 Antisense
CACTTCTCATCCACTCATTAAAACT 100 197 4311 Antisense
Sequence Source Affymetrix Proprietary Database