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[173987_s_at] CUB domain (2 domains), Low-density lipoprotein receptor domain class A

Description CE8421 /REP_DB=TREMBL Accession /5_PRIME_EXT_ID=K05C4.11 /5_PRIME_EXT_DB=WormBase Gene ID /GB=T01842 /WB_GENE_ID=K05C4.11 /WP=CE19979 /CHR=1 /FEA=Genomic Cluster /DEF=CUB domain (2 domains), Low-density lipoprotein receptor domain class A; wEST02563 Early embryo, Stratagene (cat. no. 937007) Caenorhabditis elegans cDNA clone CEESW35, mRNA sequence.
Cluster 6grp_total > 91      4grp_total > 31      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 123
1 2 3 4 range
A 105.6
(3)
M 		19.7
(-3)
A 		19.5
(-3)
A 		83.7
(1.5)
A 		86
B 137.9
(3)
P 		15.7
(-3)
A 		29.3
(-2.3)
A 		62.7
(-0.7)
A 		122
C 93
(3)
M 		14.6
(-3)
A 		16.6
(-2.8)
A 		64.2
(0.8)
A 		78
avr 112.2
(3) 		16.7
(-3) 		21.8
(-2.7) 		70.2
(0.4) 		96

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 135
1 2 3 4 5 6 range
A 75.6
(-2.7)
A 		107.3
(0.3)
M 		77
(-2.6)
A 		137
(3)
M 		124.4
(1.8)
P 		72.2
(-3)
A 		65
B 126.6
(0.9)
A 		108.7
(-0.8)
P 		106.2
(-1.1)
P 		127.8
(1)
P 		149
(3)
P 		85.9
(-3)
P 		63
C 86.3
(-1.4)
A 		104.3
(-0.7)
A 		89.1
(-1.3)
A 		186.7
(3)
P 		98.3
(-0.9)
P 		51.3
(-3)
A 		135
avr 96.2
(-1) 		106.8
(-0.2) 		90.8
(-1.4) 		150.5
(3) 		123.9
(1) 		69.8
(-3) 		81
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 40
1 2 3 4 range
A 38.4
(3)
M 		4.3
(-3)
A 		5.1
(-2.9)
A 		12.2
(-1.6)
A 		34
B 44
(3)
P 		3.9
(-3)
A 		6.8
(-2.6)
A 		13.4
(-1.6)
A 		40
C 30.8
(3)
M 		4.2
(-3)
A 		5.8
(-2.6)
A 		10.8
(-1.5)
A 		27
avr 37.7
(3) 		4.1
(-3) 		5.9
(-2.7) 		12.1
(-1.6) 		34

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 47
1 2 3 4 5 6 range
A 13.9
(-3)
A 		38.2
(3)
M 		16.8
(-2.3)
A 		34.7
(2.1)
M 		37.5
(2.8)
P 		17.6
(-2.1)
A 		24
B 44.1
(0.2)
A 		36.2
(-1.2)
P 		25.8
(-3)
P 		33.9
(-1.6)
P 		60.5
(3)
P 		32
(-1.9)
P 		35
C 32
(1.4)
A 		31.8
(1.3)
A 		22.7
(-1.4)
A 		37.5
(3)
P 		31.8
(1.3)
P 		17.2
(-3)
A 		20
avr 30
(-0.7) 		35.4
(0.8) 		21.8
(-3) 		35.4
(0.8) 		43.3
(3) 		22.3
(-2.9) 		22
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 173987_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.23015
Sequence Type Exemplar sequence
Representative Public ID CE8421 NCBI
Target Description CE8421 /REP_DB=TREMBL Accession /5_PRIME_EXT_ID=K05C4.11 /5_PRIME_EXT_DB=WormBase Gene ID /GB=T01842 /WB_GENE_ID=K05C4.11 /WP=CE19979 /CHR=1 /FEA=Genomic Cluster /DEF=CUB domain (2 domains), Low-density lipoprotein receptor domain class A; wEST02563 Early embryo, Stratagene (cat. no. 937007) Caenorhabditis elegans cDNA clone CEESW35, mRNA sequence.
Cluster Evidence This cluster is supported by a Genomic Cluster.
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_061159(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_061159 NCBI Caenorhabditis elegans K05C4.11 (K05C4.11) mRNA, complete cds. 11/11 None
SNAP00000018535 ENSEMBL cdna:SNAP chromosome:CEL140:I:14728839:14732849:-1 10/11 None
GENEFINDER00000018546 ENSEMBL cdna:GeneFinder chromosome:CEL140:I:14728839:14732849:-1 10/11 None
K05C4.11 ENSEMBL cdna:known chromosome:CEL140:I:14729881:14732857:-1 gene:K05C4.11 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:14729878-14732781(-) 100.0 100.0
Public Domain and Genome References
Gene Title CUB domain (2 domains), Low-density lipoprotein receptor domain class A
Ensembl K05C4.11
Entrez Gene 173336 Entrez gene
SwissProt Q9XUU2 EMBL-EBI
WormBase CE19979 Wormbase
Functional Annotations
Protein Similarities
Method ID Description E-Value
blast CAB04576 Hypothetical protein K05C4.11 [Caenorhabditis elegans] ref|NP_493560.1| K05C4.11 [Caenorhabditis elegans] 0.0
blast CAE72559 Hypothetical protein CBG19743 [Caenorhabditis briggsae] 1.0E-152
blast CAB04568 Hypothetical protein K05C4.2 [Caenorhabditis elegans] ref|NP_493559.1| K05C4.2 [Caenorhabditis elegans] 1.0E-110
Protein Domains
Database ID Description E-Value
Pfam IPR002172 EMBL-EBI Low density lipoprotein-receptor, class A 3.1E-9
Pfam IPR000859 EMBL-EBI CUB 6.7E-11
Pfam IPR000859 EMBL-EBI CUB 1.1E-11
Pfam IPR009787 EMBL-EBI Protein of unknown function DUF1352 1.0E-126
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_493560.1 1 373-395
K05C4.11 1 373-395
SNAP00000018535 5 373-395,476-493,518-540,547-569,591-613
GENEFINDER00000018546 5 373-395,476-493,518-540,547-569,591-613
Sequence
Target Sequence 
>C. ELEGANS:173987_S_AT
ggaccaccgtcttcaatgattggggaagagaggattggatttaaagttgtatggactgca
gtggagggtctgattggagaaggtgatgagagtgttaatggaaattcttgtaaggatcaa
tttatgtgccatgggggacaagtttgtgttgaacagggtcatggaatttgcgcttcacgg
tcccgtctctgcattcacagctctctcgtttgtgacggaatccataattgtgttgaagga
gatttctccgacgagcaacacggttactcccgagagataataacatcggcggcactcgga
ttctcgttgattgtgctcacgatgctcgtcttggtgtgctgtgatcagttcaggaagcgg
cgacggcttcgggtgatgattcgggaacgaagagccgcgtcggagaatgggaaatgtaaa
aatatgaataataattcgattacaacacggatacagccgaaccggtg

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GGACCACCGTCTTCAATGATTGGGG 114 523 857 Antisense
GTCATGGAATTTGCGCTTCACGGTC 103 467 1014 Antisense
ACAGCTCTCTCGTTTGTGACGGAAT 169 109 1053 Antisense
AGGAGATTTCTCCGACGAGCAACAC 61 57 1093 Antisense
GATAATAACATCGGCGGCACTCGGA 202 423 1132 Antisense
GGCACTCGGATTCTCGTTGATTGTG 388 535 1147 Antisense
TTGATTGTGCTCACGATGCTCGTCT 147 705 1163 Antisense
TCGTCTTGGTGTGCTGTGATCAGTT 71 605 1182 Antisense
TCAGGAAGCGGCGACGGCTTCGGGT 671 593 1206 Antisense
TTCGGGAACGAAGAGCCGCGTCGGA 519 651 1236 Antisense
CAACACGGATACAGCCGAACCGGTG 606 187 1299 Antisense
Sequence Source Affymetrix Proprietary Database