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[188965_at] LDL receptor

Description F55H12.3 /REP_DB=WormBase Gene ID /WP=CE25008 /TR=P90891 /GB=CAB03143.2 /SUBMIT=HINXTON /CHR=1 /FEA=Sanger Annotation /DEF=LDL receptor
Cluster 6grp_highest_10_10 > 54      6grp_high1_10_10 > 45      4grp_highest_8_8 > 45      4grp_high_8_8 > 02      6grp_highest_nonorm > 71      6grp_total > 46      4grp_total > 14      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 267
1 2 3 4 range
A 387.9
(2.3)
P 		164
(-2.8)
P 		153.2
(-3)
P 		420.2
(3)
P 		267
B 303.7
(1.9)
P 		212.1
(-3)
P 		226.3
(-2.2)
P 		324.3
(3)
P 		112
C 377.2
(3)
P 		259.7
(-3)
P 		277.6
(-2.1)
P 		363.8
(2.3)
P 		118
avr 356.3
(2.5) 		211.9
(-3) 		219
(-2.7) 		369.4
(3) 		158

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 216
1 2 3 4 5 6 range
A 433.7
(3)
P 		411.3
(2.3)
P 		232
(-3)
P 		409.9
(2.3)
P 		262.9
(-2.1)
P 		371.9
(1.2)
P 		202
B 360.6
(3)
P 		275.8
(-0.6)
P 		349.7
(2.5)
P 		292.9
(0.2)
P 		217.6
(-3)
P 		304.2
(0.6)
P 		143
C 243.9
(-3)
P 		335.7
(0.6)
P 		345.3
(1)
P 		397.4
(3)
P 		250.2
(-2.8)
P 		340.1
(0.8)
P 		154
avr 346.1
(2) 		340.9
(1.7) 		309
(0.2) 		366.7
(3) 		243.6
(-3) 		338.7
(1.6) 		123
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 106
1 2 3 4 range
A 141.3
(3)
P 		35.6
(-3)
P 		40
(-2.8)
P 		61.5
(-1.5)
P 		106
B 96.8
(3)
P 		52.4
(-3)
P 		52.4
(-3)
P 		69.1
(-0.7)
P 		44
C 124.9
(3)
P 		74.7
(-1.7)
P 		96.8
(0.3)
P 		61.4
(-3)
P 		64
avr 121
(3) 		54.2
(-3) 		63.1
(-2.2) 		64
(-2.1) 		67

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 96
1 2 3 4 5 6 range
A 80
(-1.2)
P 		146.3
(3)
P 		50.5
(-3)
P 		104
(0.4)
P 		79.3
(-1.2)
P 		90.5
(-0.5)
P 		96
B 125.5
(3)
P 		91.8
(-1.2)
P 		84.9
(-2.1)
P 		77.6
(-3)
P 		88.4
(-1.6)
P 		113.4
(1.5)
P 		48
C 90.4
(-1.1)
P 		102.4
(1)
P 		87.9
(-1.6)
P 		79.9
(-3)
P 		80.9
(-2.8)
P 		113.8
(3)
P 		34
avr 98.6
(0.7) 		113.5
(3) 		74.4
(-3) 		87.2
(-1) 		82.9
(-1.7) 		105.9
(1.8) 		39
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 188965_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.406
Sequence Type Exemplar sequence
Representative Public ID F55H12.3 NCBI
Target Description F55H12.3 /REP_DB=WormBase Gene ID /WP=CE25008 /TR=P90891 /GB=CAB03143.2 /SUBMIT=HINXTON /CHR=1 /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_059996(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_059996 NCBI Caenorhabditis elegans F55H12.3 (F55H12.3) mRNA, complete cds. 11/11 None
GENEFINDER00000036160 ENSEMBL cdna:GeneFinder chromosome:CEL140:I:8880075:8901126:1 11/11 None
SNAP00000036155 ENSEMBL cdna:SNAP chromosome:CEL140:I:8888106:8901079:1 11/11 None
F55H12.3 ENSEMBL cdna:known chromosome:CEL140:I:8884209:8901175:1 gene:F55H12.3 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
chrI:8884139-8901010(+) 100.0 100.0
Public Domain and Genome References
Gene Title LDL receptor
Ensembl F55H12.3
Entrez Gene 172702 Entrez gene
SwissProt P90891 EMBL-EBI
WormBase CE25008 Wormbase
Functional Annotations
Gene Ontology
GO Molecular Function (view graph)
ID Description Evidence Links
5198 structural molecule activity inferred from electronic annotation QuickGO AmiGO
5509 calcium ion binding inferred from electronic annotation QuickGO AmiGO
5529 sugar binding inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast CAB03143 Hypothetical protein F55H12.3 [Caenorhabditis elegans] ref|NP_492397.1| F55H12.3 [Caenorhabditis elegans] 0.0
blast CAE66989 Hypothetical protein CBG12386 [Caenorhabditis briggsae] 0.0
blast CAB03142 Hypothetical protein F55H12.1 [Caenorhabditis elegans] ref|NP_492396.1| Sodium:Neurotransmitter symporter Family family member (snf-2) [Caenorhabditis elegans] 0.0
blast XP_396277 PREDICTED: similar to GA21569-PA [Apis mellifera] 6.0E-88
Protein Domains
Database ID Description E-Value
Pfam IPR002172 EMBL-EBI Low density lipoprotein-receptor, class A 2.5E-9
Pfam IPR006209 EMBL-EBI EGF-like domain 4.9E-6
Pfam IPR006209 EMBL-EBI EGF-like domain 1.5E-4
Pfam IPR006209 EMBL-EBI EGF-like domain 4.9E-4
Pfam IPR006209 EMBL-EBI EGF-like domain 9.8E-6
Pfam IPR006209 EMBL-EBI EGF-like domain 1.2E-6
Pfam IPR006209 EMBL-EBI EGF-like domain 4.6E-6
Pfam IPR006209 EMBL-EBI EGF-like domain 4.6E-5
Pfam IPR000175 EMBL-EBI Sodium:neurotransmitter symporter 1.8E-22
Pfam IPR000175 EMBL-EBI Sodium:neurotransmitter symporter 8.6E-65
Pfam IPR003410 EMBL-EBI Hyalin 1.8E-32
Pfam IPR000436 EMBL-EBI Sushi domain/SCR domain/CCP module 5.0E-6
Pfam IPR000436 EMBL-EBI Sushi domain/SCR domain/CCP module 8.5E-6
Pfam IPR006209 EMBL-EBI EGF-like domain 4.9E-6
Pfam IPR006209 EMBL-EBI EGF-like domain 1.5E-4
Pfam IPR006209 EMBL-EBI EGF-like domain 4.9E-4
Pfam IPR006209 EMBL-EBI EGF-like domain 9.8E-6
Pfam IPR006209 EMBL-EBI EGF-like domain 1.2E-6
Pfam IPR006209 EMBL-EBI EGF-like domain 4.6E-6
Pfam IPR006209 EMBL-EBI EGF-like domain 4.6E-5
Pfam IPR003410 EMBL-EBI Hyalin 1.8E-32
Pfam IPR000436 EMBL-EBI Sushi domain/SCR domain/CCP module 5.0E-6
Pfam IPR000436 EMBL-EBI Sushi domain/SCR domain/CCP module 8.5E-6
Pfam IPR002172 EMBL-EBI Low density lipoprotein-receptor, class A 2.5E-9
Pfam IPR006209 EMBL-EBI EGF-like domain 4.9E-6
Pfam IPR006209 EMBL-EBI EGF-like domain 1.5E-4
Pfam IPR006209 EMBL-EBI EGF-like domain 4.9E-4
Pfam IPR006209 EMBL-EBI EGF-like domain 9.8E-6
Pfam IPR006209 EMBL-EBI EGF-like domain 1.2E-6
Pfam IPR006209 EMBL-EBI EGF-like domain 4.6E-6
Pfam IPR006209 EMBL-EBI EGF-like domain 4.6E-5
Pfam IPR003410 EMBL-EBI Hyalin 1.8E-32
Pfam IPR000436 EMBL-EBI Sushi domain/SCR domain/CCP module 5.0E-6
Pfam IPR000436 EMBL-EBI Sushi domain/SCR domain/CCP module 8.5E-6
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_492397.1 2 63-85,2797-2819
F55H12.3 2 63-85,2797-2819
GENEFINDER00000036160 10 142-164,200-222,314-336,346-368,428-450,493-515,535-557,616-638,658-680,3483-3505
SNAP00000036155 1 2328-2350
Sequence
Target Sequence 
>C. ELEGANS:188965_AT
aactgtttgccggaagtgacacctgttccgggaaactcgaatgcaattaaaattgttctt
ggagttgtgtttggagttttacttcttataattattgtagtattggtatgcttcagaaaa
caaattatcgcatggttccggaaaactgacacaagtgacaatcaacacgtggcattatct
cattgggataatgcaacaaatagaaatgaggaagagaatcaaaaccccacttccacaaat
acttatccacgtataccacctcaagctccgattcctcatccgaatctgagaatagtgacg
tcacgggctgaaatggatcagcttccaccgcttccgactgcttcaacggcatcattccac
gtggattcagcatataaaagtgatgggtttggaagtggatttggaacgtcttctggaatg
agacatttgggaaccggaatatcaacagtacatccaacaattttttcatcaaatgacatt
gcctttgaagctaatggatcaccgataatccttcgatcaa

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
AACTGTTTGCCGGAAGTGACACCTG 559 121 8356 Antisense
GTGACACCTGTTCCGGGAAACTCGA 485 481 8371 Antisense
AACACGTGGCATTATCTCATTGGGA 494 135 8519 Antisense
AATACTTATCCACGTATACCACCTC 161 173 8593 Antisense
CTCCGATTCCTCATCCGAATCTGAG 50 235 8621 Antisense
GTGACGTCACGGGCTGAAATGGATC 202 483 8650 Antisense
TGAAATGGATCAGCTTCCACCGCTT 199 573 8664 Antisense
CTTCCGACTGCTTCAACGGCATCAT 401 219 8686 Antisense
CAACGGCATCATTCCACGTGGATTC 555 187 8699 Antisense
GTACATCCAACAATTTTTTCATCAA 247 461 8803 Antisense
GGATCACCGATAATCCTTCGATCAA 563 511 8851 Antisense
Sequence Source Affymetrix Proprietary Database