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[192230_at] low-density lipoprotein receptor

Description ZC101.1 /REP_DB=WormBase Gene ID /WP=CE16690 /TR=O18260 /GB=CAB07705.1 /SUBMIT=HINXTON /CHR=2 /FEA=Sanger Annotation /DEF=low-density lipoprotein receptor
Cluster 6grp_total > 14      4grp_total > 51      6grp_total_sub > Decrease      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 146
1 2 3 4 range
A 83.3
(-0.2)
A 		107.7
(3)
P 		68.3
(-2.1)
A 		61.6
(-3)
A 		46
B 122.5
(0.3)
P 		175.7
(3)
P 		147.2
(1.6)
A 		57.7
(-3)
A 		118
C 89.6
(2.2)
A 		90.6
(2.3)
A 		98.6
(3)
P 		29.7
(-3)
A 		69
avr 98.5
(0.9) 		124.7
(3) 		104.7
(1.4) 		49.7
(-3) 		75

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 87
1 2 3 4 5 6 range
A 61.4
(0.6)
A 		96.6
(3)
A 		49.5
(-0.2)
A 		73
(1.4)
A 		9.4
(-3)
A 		43.6
(-0.6)
A 		87
B 47.4
(0.8)
A 		66.6
(3)
A 		14.3
(-3)
A 		22.8
(-2)
A 		38.8
(-0.2)
A 		35.8
(-0.5)
A 		52
C 79.7
(3)
P 		17.1
(-3)
A 		40
(-0.8)
A 		62.2
(1.3)
A 		37.7
(-1)
A 		20.5
(-2.7)
A 		63
avr 62.8
(3) 		60.1
(2.5) 		34.6
(-1.9) 		52.7
(1.2) 		28.6
(-3) 		33.3
(-2.2) 		34
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 38
1 2 3 4 range
A 30.3
(3)
A 		23.4
(1.1)
P 		17.8
(-0.5)
A 		9
(-3)
A 		21
B 39.1
(2.2)
P 		43.4
(3)
P 		34.1
(1.2)
A 		12.3
(-3)
A 		31
C 29.6
(2)
A 		26.1
(1.3)
A 		34.4
(3)
P 		5
(-3)
A 		29
avr 33
(3) 		31
(2.5) 		28.8
(2) 		8.8
(-3) 		24

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 32
1 2 3 4 5 6 range
A 11.3
(-1.4)
A 		34.3
(3)
A 		10.8
(-1.5)
A 		18.5
(-0)
A 		2.8
(-3)
A 		10.6
(-1.5)
A 		32
B 16.5
(1.2)
A 		22.2
(3)
A 		3.5
(-3)
A 		6
(-2.2)
A 		15.8
(0.9)
A 		13.3
(0.1)
A 		19
C 29.6
(3)
P 		5.2
(-3)
A 		10.2
(-1.8)
A 		12.5
(-1.2)
A 		12.2
(-1.3)
A 		6.8
(-2.6)
A 		24
avr 19.1
(2.3) 		20.6
(3) 		8.2
(-3) 		12.3
(-1) 		10.3
(-2) 		10.2
(-2) 		12
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 192230_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.3724
Sequence Type Exemplar sequence
Representative Public ID ZC101.1 NCBI
Target Description ZC101.1 /REP_DB=WormBase Gene ID /WP=CE16690 /TR=O18260 /GB=CAB07705.1 /SUBMIT=HINXTON /CHR=2 /FEA=Sanger Annotation /DEF=low-density lipoprotein receptor
Cluster Evidence This cluster is supported by a 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_064647(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_064647 NCBI Caenorhabditis elegans ZC101.1 (ZC101.1) mRNA, complete cds. 11/11 None
SNAP00000013251 ENSEMBL cdna:SNAP chromosome:CEL140:II:14675243:14677678:-1 9/11 None
GENEFINDER00000013270 ENSEMBL cdna:GeneFinder chromosome:CEL140:II:14654105:14678428:-1 10/11 None
ZC101.1 ENSEMBL cdna:known chromosome:CEL140:II:14675154:14684187:-1 gene:ZC101.1 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
chrII:14675150-14684184(-) 93.93 100.0
Public Domain and Genome References
Gene Title low-density lipoprotein receptor
Ensembl ZC101.1
Entrez Gene 175127 Entrez gene
SwissProt O18260 EMBL-EBI
WormBase CE16690 Wormbase
Functional Annotations
Protein Similarities
Method ID Description E-Value
blast CAB07705 Hypothetical protein ZC101.1 [Caenorhabditis elegans] emb|CAB05541.1| Hypothetical protein ZC101.1 [Caenorhabditis elegans] ref|NP_497048.1| ZC101.1 [Caenorhabditis elegans] 0.0
blast CAE65898 Hypothetical protein CBG11065 [Caenorhabditis briggsae] 0.0
blast CAB07706 Hypothetical protein ZC101.2a [Caenorhabditis elegans] emb|CAB07567.1| Hypothetical protein ZC101.2a [Caenorhabditis elegans] ref|NP_497046.1| UNCoordinated family member (unc-52) [Caenorhabditis elegans] 0.0
blast CAB07708 Hypothetical protein ZC101.2e [Caenorhabditis elegans] emb|CAB07569.1| Hypothetical protein ZC101.2e [Caenorhabditis elegans] ref|NP_497044.3| UNCoordinated family member (unc-52) [Caenorhabditis elegans] sp|Q06561|UNC52_CAEEL Basement membrane proteoglycan precursor (Perlecan homolog) (Uncoordinated protein 52) pir||T19821 hypothetical protein ZC101.2e - Caenorhabditis elegans 0.0
blast AAA28156 basement membrane proteoglycan 0.0
blast CAB07705 Hypothetical protein ZC101.1 [Caenorhabditis elegans] emb|CAB05541.1| Hypothetical protein ZC101.1 [Caenorhabditis elegans] ref|NP_497048.1| ZC101.1 [Caenorhabditis elegans] 2.0E-81
blast CAE65898 Hypothetical protein CBG11065 [Caenorhabditis briggsae] 2.0E-68
blast CAB72286 EG:BACR25B3.1 [Drosophila melanogaster] 7.0E-27
Protein Domains
Database ID Description E-Value
Pfam IPR002172 EMBL-EBI Low density lipoprotein-receptor, class A 1.9E-15
Pfam IPR002172 EMBL-EBI Low density lipoprotein-receptor, class A 1.1E-9
Pfam IPR002172 EMBL-EBI Low density lipoprotein-receptor, class A 2.4E-9
Pfam IPR002172 EMBL-EBI Low density lipoprotein-receptor, class A 1.1E-14
Pfam IPR002172 EMBL-EBI Low density lipoprotein-receptor, class A 1.9E-15
Pfam IPR002172 EMBL-EBI Low density lipoprotein-receptor, class A 1.1E-9
Pfam IPR002172 EMBL-EBI Low density lipoprotein-receptor, class A 2.4E-9
Pfam IPR002172 EMBL-EBI Low density lipoprotein-receptor, class A 1.1E-14
Pfam IPR002172 EMBL-EBI Low density lipoprotein-receptor, class A 7.8E-18
Pfam IPR002172 EMBL-EBI Low density lipoprotein-receptor, class A 3.1E-20
Pfam IPR002172 EMBL-EBI Low density lipoprotein-receptor, class A 8.1E-20
Pfam IPR000034 EMBL-EBI Laminin B 9.3E-79
Pfam IPR000034 EMBL-EBI Laminin B 5.3E-73
Pfam IPR002049 EMBL-EBI Laminin-type EGF-like domain 7.8E-20
Pfam IPR007110 EMBL-EBI Immunoglobulin-like 2.7E-9
Pfam IPR007110 EMBL-EBI Immunoglobulin-like 1.5E-5
Pfam IPR007110 EMBL-EBI Immunoglobulin-like 0.41
Pfam IPR007110 EMBL-EBI Immunoglobulin-like 1.6E-5
Pfam IPR007110 EMBL-EBI Immunoglobulin-like 0.0010
Pfam IPR007110 EMBL-EBI Immunoglobulin-like 1.5E-5
Pfam IPR007110 EMBL-EBI Immunoglobulin-like 1.2E-6
Pfam IPR007110 EMBL-EBI Immunoglobulin-like 3.5E-6
Pfam IPR007110 EMBL-EBI Immunoglobulin-like 3.5E-6
Pfam IPR007110 EMBL-EBI Immunoglobulin-like 0.26
Pfam IPR007110 EMBL-EBI Immunoglobulin-like 0.0061
Pfam IPR007110 EMBL-EBI Immunoglobulin-like 2.5E-4
Pfam IPR007110 EMBL-EBI Immunoglobulin-like 0.0038
Pfam IPR007110 EMBL-EBI Immunoglobulin-like 0.0014
Pfam IPR007110 EMBL-EBI Immunoglobulin-like 3.8E-4
Pfam IPR002172 EMBL-EBI Low density lipoprotein-receptor, class A 2.7E-9
Pfam IPR002172 EMBL-EBI Low density lipoprotein-receptor, class A 1.3E-5
Pfam IPR002172 EMBL-EBI Low density lipoprotein-receptor, class A 3.3E-12
Pfam IPR002172 EMBL-EBI Low density lipoprotein-receptor, class A 1.9E-15
Pfam IPR002172 EMBL-EBI Low density lipoprotein-receptor, class A 1.1E-9
Pfam IPR002172 EMBL-EBI Low density lipoprotein-receptor, class A 2.4E-9
Pfam IPR002172 EMBL-EBI Low density lipoprotein-receptor, class A 1.1E-14
Sequence
Target Sequence 
>C. ELEGANS:192230_AT
cagctcaaccttcgcaagatcatcacgaggaacatcgtagacgtctcgaggagcatcgcc
gccgagaagaagaacaccatcgtcggcaagaggaggagtcgcgtgccagagctcttcagc
aatcactgctacatgctagccaggttgagagcaccgaagtgacattccaagatgagtatg
atggagatagtggagttgggtgcttggagcacgagttccagtgtgctattggagagtgta
ttgataaacgccgtgtgtgcgacactcgtcccgactgcctcgatgcctctgacgagcaaa
actgtgcggaccgggctccagctcctctaccgactcattcacagcaacatcatcatgttg
cgcaaccagcagcaccaccatcactcccatcagtgaacacttatccgggtcagttgcaaa
ttttcaagtggttagcacttaagttcaggttgttggcggaggatttgcgtgtgtatgtgt
ttggatgtatatatatatacttcgagctcattgtgccctcaaaatgtttgactctttttt
ttttgaaaaaaagaagtagtttgcactttatgttcattctttctgccg

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
CAGCTCAACCTTCGCAAGATCATCA 354 203 2111 Antisense
CGTAGACGTCTCGAGGAGCATCGCC 390 309 2146 Antisense
GAAGAACACCATCGTCGGCAAGAGG 114 339 2179 Antisense
CAAGAGGAGGAGTCGCGTGCCAGAG 467 185 2197 Antisense
CCAGAGCTCTTCAGCAATCACTGCT 56 273 2216 Antisense
GATAAACGCCGTGTGTGCGACACTC 331 423 2353 Antisense
TGCCTCGATGCCTCTGACGAGCAAA 440 585 2386 Antisense
TACCGACTCATTCACAGCAACATCA 688 649 2438 Antisense
GTGAACACTTATCCGGGTCAGTTGC 486 481 2503 Antisense
ATATACTTCGAGCTCATTGTGCCCT 172 19 2605 Antisense
CACTTTATGTTCATTCTTTCTGCCG 342 197 2674 Antisense
Sequence Source Affymetrix Proprietary Database