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[188898_at] LDL receptor

Description B0244.8 /REP_DB=WormBase Gene ID /WP=CE01755 /TR=Q09967 /GB=AAA68376.1 /SUBMIT=ST.LOUIS /CHR=3 /FEA=Sanger Annotation /DEF=LDL receptor
Cluster 6grp_total > 88      4grp_total > 34      6grp_cgc > 59      6grp_cgc_sub > Da      6grp_total_sub > Increase      6grp_rule_based > S6      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 91
1 2 3 4 range
A 93.3
(1.5)
A 		59.8
(-3)
A 		71.8
(-1.4)
M 		104.2
(3)
A 		44
B 64
(-3)
A 		95.1
(1.7)
A 		94.1
(1.5)
A 		104
(3)
P 		40
C 58.7
(-3)
A 		150.1
(3)
A 		76
(-1.9)
A 		76.4
(-1.8)
A 		91
avr 72
(-3) 		101.7
(3) 		80.6
(-1.3) 		94.9
(1.6) 		30

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 2118
1 2 3 4 5 6 range
A 66.6
(-3)
A 		53.8
(-3)
A 		109.7
(-2.8)
A 		171
(-2.7)
P 		1278.2
(0.5)
P 		2155.5
(3)
P 		2102
B 64.7
(-3)
A 		79.2
(-3)
A 		90.1
(-2.9)
A 		168.6
(-2.7)
P 		1180.2
(0.5)
P 		1989.1
(3)
P 		1924
C 37.6
(-3)
A 		68.8
(-2.9)
A 		82
(-2.9)
A 		117.6
(-2.7)
P 		1154.1
(0.5)
P 		1937.8
(3)
P 		1900
avr 56.3
(-3) 		67.3
(-3) 		93.9
(-2.9) 		152.4
(-2.7) 		1204.2
(0.5) 		2027.5
(3) 		1971
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 30
1 2 3 4 range
A 34
(3)
A 		13
(-3)
A 		18.8
(-1.3)
M 		15.2
(-2.4)
A 		21
B 20.4
(-3)
A 		23.5
(3)
A 		21.8
(-0.3)
A 		22.2
(0.5)
P 		3
C 19.4
(-1.7)
A 		43.2
(3)
A 		26.5
(-0.3)
A 		12.9
(-3)
A 		30
avr 24.6
(1.8) 		26.6
(3) 		22.4
(0.4) 		16.8
(-3) 		10

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 729
1 2 3 4 5 6 range
A 12.3
(-3)
A 		19.1
(-2.9)
A 		23.9
(-2.9)
A 		43.4
(-2.6)
P 		385.7
(1.4)
P 		524.8
(3)
P 		513
B 22.5
(-3)
A 		26.4
(-3)
A 		21.9
(-3)
A 		44.7
(-2.8)
P 		479.5
(0.8)
P 		741.7
(3)
P 		720
C 13.9
(-3)
A 		21
(-2.9)
A 		20.9
(-2.9)
A 		23.7
(-2.9)
P 		373.4
(0.4)
P 		648.7
(3)
P 		635
avr 16.2
(-3) 		22.2
(-2.9) 		22.2
(-2.9) 		37.3
(-2.8) 		412.9
(0.8) 		638.4
(3) 		622
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 188898_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.7264
Sequence Type Exemplar sequence
Representative Public ID B0244.8 NCBI
Target Description B0244.8 /REP_DB=WormBase Gene ID /WP=CE01755 /TR=Q09967 /GB=AAA68376.1 /SUBMIT=ST.LOUIS /CHR=3 /FEA=Sanger Annotation /DEF=LDL 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_065836(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_065836 NCBI Caenorhabditis elegans EGG sterile (unfertilizable) family member (egg-1) (egg-1) mRNA, complete cds. 11/11 None
SNAP00000015988 ENSEMBL cdna:SNAP chromosome:CEL140:III:5728131:5729971:1 11/11 None
GENEFINDER00000016001 ENSEMBL cdna:GeneFinder chromosome:CEL140:III:5728131:5729971:1 11/11 None
B0244.8 ENSEMBL cdna:known chromosome:CEL140:III:5728128:5730081:1 gene:B0244.8 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:5727558-5729970(+) 100.0 100.0
Public Domain and Genome References
Gene Title LDL receptor
Gene Symbol egg-1
Ensembl B0244.8
Entrez Gene 175804 Entrez gene
SwissProt Q09967 EMBL-EBI
WormBase CE32094 Wormbase
Functional Annotations
Protein Similarities
Method ID Description E-Value
blast AAA68376 Egg sterile (unfertilizable) protein 1 [Caenorhabditis elegans] ref|NP_498237.2| EGG sterile (unfertilizable) family member (egg-1) [Caenorhabditis elegans] 0.0
blast CAE63952 Hypothetical protein CBG08534 [Caenorhabditis briggsae] 0.0
blast NP_498537 EGG sterile (unfertilizable) family member (egg-2) [Caenorhabditis elegans] gb|AAA50645.1| Egg sterile (unfertilizable) protein 2 [Caenorhabditis elegans] 0.0
Protein Domains
Database ID Description E-Value
Pfam IPR002172 EMBL-EBI Low density lipoprotein-receptor, class A 4.3E-12
Pfam IPR002172 EMBL-EBI Low density lipoprotein-receptor, class A 5.4E-10
Pfam IPR002172 EMBL-EBI Low density lipoprotein-receptor, class A 4.5E-6
Pfam IPR002172 EMBL-EBI Low density lipoprotein-receptor, class A 2.9E-8
Pfam IPR002172 EMBL-EBI Low density lipoprotein-receptor, class A 2.2E-12
Pfam IPR002172 EMBL-EBI Low density lipoprotein-receptor, class A 1.4E-6
Pfam IPR002172 EMBL-EBI Low density lipoprotein-receptor, class A 1.8E-7
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_498237.2 1 47-69
B0244.8 1 47-69
SNAP00000015988 1 47-69
GENEFINDER00000016001 1 47-69
Sequence
Target Sequence 
>C. ELEGANS:188898_AT
gaagctgaagcgtgttctggttcgtttgaaagttgcgatcacgattgcccaaattccaaa
tgccatccgaagctcgctttcacatgcccagcaagtaaagaagcacgaaaaatgtgcatc
agccgacgtaaagtctgcgatggaacacctgactgtgacgatggagccgatgaaatcaac
tgcacgccgatcaaggaatgtggcattgccaaaaatactcagttcaaatgtgatcacaaa
tgcctggattcaagccgtcgatgcgatggagtttgggattgtgaagacaaatcagatgag
aagggatgtgataaatgcccatctggtactatcaaatgtgctgctgataagaagtgtctt
ccagccttcacccgttgcaatggagttgctgactgttcagatggaagcgatgaacttaag
tgctcctgccaagaatgcctgggcgtccattccaacacctacatgtgcaacgaatcgaac
agatgcctgaaacgcgacgaagtgtgctctccgtattcaatgtgccccaatgccacatac
accgacaaagcgttttgcgctgcactgttc

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GAAGCTGAAGCGTGTTCTGGTTCGT 97 341 1138 Antisense
GAAAGTTGCGATCACGATTGCCCAA 580 359 1165 Antisense
GATTGCCCAAATTCCAAATGCCATC 395 433 1180 Antisense
GCATCAGCCGACGTAAAGTCTGCGA 703 307 1253 Antisense
GTCTGCGATGGAACACCTGACTGTG 48 471 1270 Antisense
AAATCAACTGCACGCCGATCAAGGA 1 117 1310 Antisense
CACAAATGCCTGGATTCAAGCCGTC 564 193 1372 Antisense
TAAGAAGTGTCTTCCAGCCTTCACC 176 637 1485 Antisense
TAAGTGCTCCTGCCAAGAATGCCTG 280 635 1554 Antisense
TCCATTCCAACACCTACATGTGCAA 597 591 1583 Antisense
CAAAGCGTTTTGCGCTGCACTGTTC 584 191 1683 Antisense
Sequence Source Affymetrix Proprietary Database