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[176571_at]

Description F09G8.4 /REP_DB=WormBase Gene ID /WP=CE24891 /GEN=npc-2 /SUBMIT=ST.LOUIS /CHR=3 /FEA=Sanger Annotation
Cluster 6grp_total > 68      4grp_total > 12      6grp_cgc > 38      6grp_cgc_sub > Da      6grp_total_sub > Increase      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 111
1 2 3 4 range
A 73.3
(-0.2)
P 		24
(-3)
A 		48.3
(-1.6)
A 		129.6
(3)
A 		106
B 59.8
(-0.8)
A 		53.1
(-1.5)
A 		37.9
(-3)
A 		97.3
(3)
P 		59
C 63.1
(-0.2)
P 		85.6
(1.2)
M 		18.9
(-3)
A 		114.2
(3)
P 		95
avr 65.4
(-0.7) 		54.2
(-1.5) 		35
(-3) 		113.7
(3) 		79

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 64
1 2 3 4 5 6 range
A 41.9
(-2.7)
A 		39
(-3)
A 		62.4
(-0.8)
P 		43.9
(-2.5)
A 		81.3
(1.1)
M 		101.6
(3)
P 		63
B 100.8
(3)
P 		61.2
(-2.1)
A 		54.2
(-3)
P 		83.5
(0.8)
P 		55.7
(-2.8)
A 		91
(1.7)
P 		47
C 59.4
(-2.1)
P 		69.3
(-0.9)
A 		70.5
(-0.8)
P 		51.6
(-3)
A 		56.1
(-2.5)
P 		103.3
(3)
P 		52
avr 67.4
(-1.4) 		56.5
(-3) 		62.4
(-2.2) 		59.7
(-2.5) 		64.4
(-1.9) 		98.6
(3) 		42
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 22
1 2 3 4 range
A 26.7
(3)
P 		5.2
(-3)
A 		12.6
(-0.9)
A 		19
(0.9)
A 		22
B 19.1
(2.2)
A 		13.1
(-0.8)
A 		8.8
(-3)
A 		20.7
(3)
P 		12
C 20.9
(1.8)
P 		24.6
(3)
M 		6.6
(-3)
A 		19.3
(1.2)
P 		18
avr 22.2
(3) 		14.3
(-0.7) 		9.3
(-3) 		19.7
(1.8) 		13

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 27
1 2 3 4 5 6 range
A 7.7
(-3)
A 		13.9
(-0.8)
A 		13.6
(-0.9)
P 		11.1
(-1.8)
A 		24.5
(2.9)
M 		24.7
(3)
P 		17
B 35.1
(3)
P 		20.4
(-1)
A 		13.2
(-3)
P 		22.1
(-0.6)
P 		22.6
(-0.4)
A 		34
(2.7)
P 		22
C 22
(-0.1)
P 		21.1
(-0.3)
A 		17.9
(-1.1)
P 		10.4
(-3)
A 		18.2
(-1.1)
P 		34.6
(3)
P 		24
avr 21.6
(-0.4) 		18.5
(-1.6) 		14.9
(-2.9) 		14.5
(-3) 		21.8
(-0.4) 		31.1
(3) 		17
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 176571_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.6002
Sequence Type Exemplar sequence
Representative Public ID F09G8.4 NCBI
Target Description F09G8.4 /REP_DB=WormBase Gene ID /WP=CE24891 /GEN=npc-2 /SUBMIT=ST.LOUIS /CHR=3 /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_066412(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_066412 NCBI Caenorhabditis elegans NPC1 (human Niemann Pick C disease) Related family member (ncr-2) (ncr-2) mRNA, complete cds. 11/11 None
GENEFINDER00000034514 ENSEMBL cdna:GeneFinder chromosome:CEL140:III:8264098:8265604:1 11/11 None
SNAP00000034501 ENSEMBL cdna:SNAP chromosome:CEL140:III:8264238:8265604:1 11/11 None
F09G8.4 ENSEMBL cdna:known chromosome:CEL140:III:8258261:8265712:1 gene:F09G8.4 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
chrIII:8258256-8265600(+) 100.0 100.0
Public Domain and Genome References
Gene Title
Gene Symbol ncr-2
Ensembl F09G8.4
Entrez Gene 176165 Entrez gene
SwissProt P34389 EMBL-EBI
WormBase CE24891 Wormbase
Functional Annotations
Gene Ontology
GO Cellular Component (view graph)
ID Description Evidence Links
16020 membrane inferred from electronic annotation 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 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 0.0
blast CAE70180 Hypothetical protein CBG16653 [Caenorhabditis briggsae] 0.0
blast CAE68601 Hypothetical protein CBG14473 [Caenorhabditis briggsae] 1.0E-161
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-151
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-127
blast CAE70180 Hypothetical protein CBG16653 [Caenorhabditis briggsae] 1.0E-113
blast CAE70180 Hypothetical protein CBG16653 [Caenorhabditis briggsae] 1.0E-100
Protein Domains
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_498813.1 11 589-611,624-646,656-675,710-732,742-764,826-848,1079-1101,1106-1128,1138-1160,1172-1194,1204-1226
F09G8.4 11 589-611,624-646,656-675,710-732,742-764,826-848,1079-1101,1106-1128,1138-1160,1172-1194,1204-1226
GENEFINDER00000034514 5 121-143,147-166,173-195,227-246,259-281
SNAP00000034501 5 74-96,100-119,126-148,180-199,212-234
Sequence
Target Sequence 
>C. ELEGANS:176571_AT
tactcttgtagttctggttctttttgttgctttcgtcacgatttccctatttttacgcgt
taatttggctggaagtttagtcactgtatttgtactcctctcatcatatcttcacttgat
ggaatggatgtatctactcggaatcacagtgaatgtagtatcagttatcaatatggcaat
gtctcttggaatcgctgttgagttttttgggcaaatgctacatggattctataactcaaa
aaaaccgaaaagggaagaaagagcattcgctgcacttgtcagtaatggatctacgacatt
gtccggaatcttccctgctatcatgatcaccgctggatgtctttcatttgctgattctcg
tgtgctcatcacatacttctgcaatcaacttgttggaattggtcttgtttgtgcagttca
tggagttgtttacatgccaacacttttggcaattttcggatcggatttctatcagaatgt
gagcagtgaagaagaatcaaccgatgaagcagaactgcaggatactcctccatc

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
TACTCTTGTAGTTCTGGTTCTTTTT 121 647 3261 Antisense
TTCTTTTTGTTGCTTTCGTCACGAT 329 685 3278 Antisense
GTCACGATTTCCCTATTTTTACGCG 173 465 3295 Antisense
TCCTCTCATCATATCTTCACTTGAT 490 593 3356 Antisense
GGCAATGTCTCTTGGAATCGCTGTT 271 535 3435 Antisense
GAAAGAGCATTCGCTGCACTTGTCA 119 361 3517 Antisense
CTACGACATTGTCCGGAATCTTCCC 702 225 3551 Antisense
CACCGCTGGATGTCTTTCATTTGCT 254 201 3588 Antisense
TCATTTGCTGATTCTCGTGTGCTCA 21 621 3604 Antisense
GTGCTCATCACATACTTCTGCAATC 64 481 3622 Antisense
CAGAACTGCAGGATACTCCTCCATC 398 205 3770 Antisense
Sequence Source Affymetrix Proprietary Database