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[193699_at] LDL receptor ligand-binding repeat bearing protein

Description B0393.7 /REP_DB=WormBase Gene ID /WP=CE00860 /TR=Q17496 /GB=CAA86060.1 /SUBMIT=HINXTON /CHR=3 /FEA=Sanger Annotation /DEF=LDL receptor ligand-binding repeat bearing protein
Cluster 6grp_total > 32      4grp_total > 21      6grp_total_sub > Hat      6grp_rule_based > S3      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 96
1 2 3 4 range
A 95.6
(1)
P 		76.4
(-0.2)
A 		30.7
(-3)
A 		127.1
(3)
A 		96
B 101
(3)
P 		73
(-0.8)
A 		56.2
(-3)
A 		75.8
(-0.4)
A 		45
C 73.8
(-0.8)
P 		50.5
(-2.7)
A 		46.6
(-3)
P 		120.6
(3)
P 		74
avr 90.1
(1.3) 		66.6
(-0.9) 		44.5
(-3) 		107.8
(3) 		63

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 102
1 2 3 4 5 6 range
A 82.8
(1.7)
A 		45.8
(-0.5)
M 		105.3
(3)
P 		39.4
(-0.9)
P 		44.2
(-0.6)
A 		4.4
(-3)
A 		101
B 65.6
(3)
A 		61.8
(2.6)
P 		55.4
(1.9)
A 		57.3
(2.1)
P 		29.3
(-0.9)
A 		9.6
(-3)
A 		56
C 39.1
(-0.5)
P 		82.2
(2.5)
P 		90
(3)
A 		62.7
(1.1)
A 		28.8
(-1.2)
A 		3
(-3)
A 		87
avr 62.5
(1.4) 		63.3
(1.4) 		83.6
(3) 		53.1
(0.7) 		34.1
(-0.8) 		5.7
(-3) 		78
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 27
1 2 3 4 range
A 34.8
(3)
P 		16.6
(-1.1)
A 		8
(-3)
A 		18.6
(-0.6)
A 		27
B 32.2
(3)
P 		18
(-1.4)
A 		13
(-3)
A 		16.1
(-2)
A 		19
C 24.4
(3)
P 		14.5
(-3)
A 		16.2
(-2)
P 		20.3
(0.5)
P 		10
avr 30.5
(3) 		16.4
(-1.7) 		12.4
(-3) 		18.3
(-1) 		18

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 24
1 2 3 4 5 6 range
A 15.3
(0.9)
A 		16.3
(1.2)
M 		22.9
(3)
P 		10
(-0.6)
P 		13.3
(0.4)
A 		1.1
(-3)
A 		22
B 22.8
(3)
A 		20.6
(2.3)
P 		13.5
(0.1)
A 		15.2
(0.6)
P 		11.9
(-0.4)
A 		3.6
(-3)
A 		19
C 14.5
(0.4)
P 		25.1
(3)
P 		22.9
(2.5)
A 		12.6
(-0.1)
A 		9.3
(-0.9)
A 		1
(-3)
A 		24
avr 17.5
(2) 		20.7
(3) 		19.8
(2.7) 		12.6
(0.4) 		11.5
(0.1) 		1.9
(-3) 		19
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 193699_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.8023
Sequence Type Exemplar sequence
Representative Public ID B0393.7 NCBI
Target Description B0393.7 /REP_DB=WormBase Gene ID /WP=CE00860 /TR=Q17496 /GB=CAA86060.1 /SUBMIT=HINXTON /CHR=3 /FEA=Sanger Annotation /DEF=LDL receptor ligand-binding repeat bearing protein
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_065582(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_065582 NCBI Caenorhabditis elegans B0393.7 (B0393.7) mRNA, complete cds. 11/11 None
SNAP00000037570 ENSEMBL cdna:SNAP chromosome:CEL140:III:4776295:4778018:-1 11/11 None
GENEFINDER00000037573 ENSEMBL cdna:GeneFinder chromosome:CEL140:III:4776295:4779971:-1 10/11 None
B0393.7 ENSEMBL cdna:known chromosome:CEL140:III:4776794:4779971:-1 gene:B0393.7 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:4776793-4779971(-) 100.0 100.0
Public Domain and Genome References
Gene Title LDL receptor ligand-binding repeat bearing protein
Ensembl B0393.7
Entrez Gene 181958 Entrez gene
SwissProt Q17496 EMBL-EBI
WormBase CE31767 Wormbase
Functional Annotations
Gene Ontology
GO Biological Process (view graph)
ID Description Evidence Links
6118 electron transport inferred from electronic annotation QuickGO AmiGO
GO Molecular Function (view graph)
ID Description Evidence Links
5489 electron transporter activity inferred from electronic annotation QuickGO AmiGO
20037 heme binding inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast NP_497983 B0393.7 [Caenorhabditis elegans] 0.0
blast CAE71133 Hypothetical protein CBG17987 [Caenorhabditis briggsae] 1.0E-131
blast CAE71133 Hypothetical protein CBG17987 [Caenorhabditis briggsae] 1.0E-125
blast CAA86060 Hypothetical protein B0393.7 [Caenorhabditis elegans] 1.0E-118
blast NP_497983 B0393.7 [Caenorhabditis elegans] 1.0E-118
blast CAJ34991 Hypothetical protein B0393.9 [Caenorhabditis elegans] 1.0E-109
Protein Domains
Database ID Description E-Value
Pfam IPR002172 EMBL-EBI Low density lipoprotein-receptor, class A 8.4E-8
Pfam IPR002172 EMBL-EBI Low density lipoprotein-receptor, class A 2.5E-11
Pfam IPR002172 EMBL-EBI Low density lipoprotein-receptor, class A 8.4E-8
Pfam IPR002172 EMBL-EBI Low density lipoprotein-receptor, class A 2.5E-11
Pfam IPR002172 EMBL-EBI Low density lipoprotein-receptor, class A 8.4E-8
Pfam IPR002172 EMBL-EBI Low density lipoprotein-receptor, class A 1.3E-8
Sequence
Target Sequence 
>C. ELEGANS:193699_AT
ggacaattaccagggccgaatgattatcctggaaaaataggcggacgttgtggactgttt
cagtttgattgtgatacaagagcacgaacaccactgtgcattccattggttgccgtgaga
gattgtacaccggattgtcctaatatgagtgatgaatggtgcggacaaggaacaatactt
tgcgacgctggagtcggtcaaaaacggtgtggaaaatgtgtgagacctcaagatatggca
aacttgtgtcttgacagaaaatggcaacatatttgtgcttatcaaggaacttacaaatgt
gcaaaaacaatgaattgcgtatttgcgaaatggcttatggatgggaaggatgattgtgga
gatggaagtgatgaggatgtgtgtgctcatggaatggtatcttgtacttccaatgagcct
acaccaactccaatactggacgctattacctctacggagaagccaaaggagcctaaaaag
aaaacagctttacaagtgtcgaaaagatgtgacctcggagaatttcgatgtctcgatggg
gaatgtcttga

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GGACAATTACCAGGGCCGAATGATT 427 523 1000 Antisense
TAGGCGGACGTTGTGGACTGTTTCA 128 653 1037 Antisense
CGAACACCACTGTGCATTCCATTGG 449 253 1084 Antisense
ATTCCATTGGTTGCCGTGAGAGATT 634 7 1099 Antisense
GAGATTGTACACCGGATTGTCCTAA 658 395 1118 Antisense
GGAACAATACTTTGCGACGCTGGAG 158 529 1168 Antisense
GAATGGTATCTTGTACTTCCAATGA 266 333 1391 Antisense
ACTTCCAATGAGCCTACACCAACTC 490 103 1405 Antisense
TACTGGACGCTATTACCTCTACGGA 359 645 1433 Antisense
GTGACCTCGGAGAATTTCGATGTCT 563 483 1508 Antisense
GATGTCTCGATGGGGAATGTCTTGA 446 409 1526 Antisense
Sequence Source Affymetrix Proprietary Database