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[193409_at] low-density lipoprotein receptor

Description T04H1.6 /REP_DB=WormBase Gene ID /WP=CE13177 /GEN=lrx-1 /TR=Q22179 /GB=CAB01583.1 /SUBMIT=HINXTON /CHR=5 /FEA=Sanger Annotation /DEF=low-density lipoprotein receptor
Cluster 6grp_total > 83      4grp_total > 48      6grp_cgc > 86      6grp_cgc_sub > 04      6grp_total_sub > Hat      4grp_rule_based > L3      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 235
1 2 3 4 range
A 5.1
(-3)
A 		166.7
(2.8)
P 		171.9
(3)
P 		50.2
(-1.4)
A 		167
B 10.6
(-3)
A 		177.5
(1.4)
P 		238.1
(3)
P 		19.7
(-2.8)
A 		228
C 3.2
(-3)
A 		145.3
(1.2)
P 		208.3
(3)
P 		44.3
(-1.8)
A 		205
avr 6.3
(-3) 		163.2
(1.7) 		206.1
(3) 		38.1
(-2) 		200

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 225
1 2 3 4 5 6 range
A 101.4
(-3)
A 		206.2
(0.3)
P 		164
(-1)
P 		290.8
(3)
P 		179
(-0.5)
P 		155.6
(-1.3)
P 		189
B 65.4
(-3)
A 		164.4
(1.3)
P 		139.1
(0.2)
P 		193.3
(2.6)
P 		203.1
(3)
P 		192
(2.5)
P 		138
C 67.3
(-3)
A 		133.3
(-0.8)
P 		157.3
(-0.1)
P 		250.9
(3)
P 		217.7
(1.9)
P 		144.8
(-0.5)
P 		184
avr 78
(-3) 		168
(0.2) 		153.5
(-0.3) 		245
(3) 		199.9
(1.4) 		164.1
(0.1) 		167
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 72
1 2 3 4 range
A 1.9
(-3)
A 		36.2
(1.8)
P 		44.9
(3)
P 		7.4
(-2.2)
A 		43
B 3.4
(-3)
A 		43.8
(1.7)
P 		55.2
(3)
P 		4.2
(-2.9)
A 		52
C 1.1
(-3)
A 		41.8
(0.4)
P 		72.6
(3)
P 		7.5
(-2.5)
A 		72
avr 2.1
(-3) 		40.6
(1.2) 		57.6
(3) 		6.4
(-2.5) 		56

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 64
1 2 3 4 5 6 range
A 18.7
(-3)
A 		73.3
(2.9)
P 		35.7
(-1.1)
P 		73.8
(3)
P 		54
(0.8)
P 		37.9
(-0.9)
P 		55
B 22.8
(-3)
A 		54.7
(0.2)
P 		33.8
(-1.9)
P 		51.2
(-0.1)
P 		82.5
(3)
P 		71.6
(1.9)
P 		60
C 24.9
(-3)
A 		40.7
(-0.9)
P 		40
(-1)
P 		50.5
(0.4)
P 		70.5
(3)
P 		48.5
(0.1)
P 		46
avr 22.1
(-3) 		56.2
(1.4) 		36.5
(-1.2) 		58.5
(1.7) 		69
(3) 		52.7
(0.9) 		47
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 193409_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.13386
Sequence Type Exemplar sequence
Representative Public ID T04H1.6 NCBI
Target Description T04H1.6 /REP_DB=WormBase Gene ID /WP=CE13177 /GEN=lrx-1 /TR=Q22179 /GB=CAB01583.1 /SUBMIT=HINXTON /CHR=5 /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_073671(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_073671 NCBI Caenorhabditis elegans LRP X(cross)-hybridizing family member (lrx-1) (lrx-1) mRNA, complete cds. 11/11 None
SNAP00000026403 ENSEMBL cdna:SNAP chromosome:CEL140:V:12255366:12257982:1 11/11 None
GENEFINDER00000026408 ENSEMBL cdna:GeneFinder chromosome:CEL140:V:12255366:12257982:1 11/11 None
T04H1.6 ENSEMBL cdna:known chromosome:CEL140:V:12256637:12257982:1 gene:T04H1.6 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
chrV:12256636-12257982(+) 100.0 100.0
Public Domain and Genome References
Gene Title low-density lipoprotein receptor
Gene Symbol lrx-1
Ensembl T04H1.6
Entrez Gene 192091 Entrez gene
SwissProt Q22179 EMBL-EBI
WormBase CE38413 Wormbase
Functional Annotations
Protein Similarities
Method ID Description E-Value
blast CAB01583 Hypothetical protein T04H1.6 [Caenorhabditis elegans] ref|NP_506072.2| LRP X(cross)-hybridizing family member (lrx-1) [Caenorhabditis elegans] 0.0
blast CAB01583 Hypothetical protein T04H1.6 [Caenorhabditis elegans] ref|NP_506072.2| LRP X(cross)-hybridizing family member (lrx-1) [Caenorhabditis elegans] 1.0E-125
blast CAE75429 Hypothetical protein CBG23422 [Caenorhabditis briggsae] 1.0E-121
blast XP_422146 PREDICTED: similar to Low-density lipoprotein receptor-related protein 1B precursor (Low-density lipoprotein receptor-related protein-deleted in tumor) (LRP-DIT) [Gallus gallus] 9.0E-27
blast XP_422146 PREDICTED: similar to Low-density lipoprotein receptor-related protein 1B precursor (Low-density lipoprotein receptor-related protein-deleted in tumor) (LRP-DIT) [Gallus gallus] 2.0E-26
Protein Domains
Database ID Description E-Value
Pfam IPR002172 EMBL-EBI Low density lipoprotein-receptor, class A 4.1E-13
Pfam IPR002172 EMBL-EBI Low density lipoprotein-receptor, class A 9.4E-6
Pfam IPR002172 EMBL-EBI Low density lipoprotein-receptor, class A 5.6E-10
Pfam IPR002172 EMBL-EBI Low density lipoprotein-receptor, class A 1.3E-6
Pfam IPR002172 EMBL-EBI Low density lipoprotein-receptor, class A 4.1E-13
Pfam IPR002172 EMBL-EBI Low density lipoprotein-receptor, class A 9.4E-6
Pfam IPR002172 EMBL-EBI Low density lipoprotein-receptor, class A 5.6E-10
Pfam IPR002172 EMBL-EBI Low density lipoprotein-receptor, class A 1.3E-6
Sequence
Target Sequence 
>C. ELEGANS:193409_AT
ttctgtccagaatacgatcatgtcatgcactgtacaatcaaagacacctgtactgaaaat
gagtttgcttgttgtgcaatgcctcaatcctgtatccatgtgagcaaacgttgtgatggt
cacccagactgtgccgatggggaagatgagaacaattgtccatcgtgtgcacgtgatgag
tttgcatgtgtgaagagtgaacattgtattcctgcaaacaaaagatgtgacggtgtggct
gatgattgtgaagatggatcgaatcttgatgaaattggatgcagtaaaaatacaacttgt
attggaaagttcgtctgtggaacatcgcgtggaggtgtttcatgtgtggatttagatatg
cattgtgatggaaagaaagattgtttaaatggagaagatgaaatgaattgtaaacaagaa
ggacgccaaaaatatttgctctgcgagaatcaaaaacaatcagtgacacgtctacaatgg
tg

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
TTCTGTCCAGAATACGATCATGTCA 203 693 76 Antisense
GATCATGTCATGCACTGTACAATCA 186 419 91 Antisense
GCTTGTTGTGCAATGCCTCAATCCT 344 307 142 Antisense
GCCTCAATCCTGTATCCATGTGAGC 96 279 156 Antisense
GCAAACGTTGTGATGGTCACCCAGA 373 317 179 Antisense
GTCACCCAGACTGTGCCGATGGGGA 73 467 194 Antisense
GAACAATTGTCCATCGTGTGCACGT 384 353 225 Antisense
GTGACGGTGTGGCTGATGATTGTGA 356 483 302 Antisense
TTCGTCTGTGGAACATCGCGTGGAG 581 691 385 Antisense
ATCGCGTGGAGGTGTTTCATGTGTG 387 35 399 Antisense
AATCAGTGACACGTCTACAATGGTG 309 171 533 Antisense
Sequence Source Affymetrix Proprietary Database