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[192216_at] low-density lipoprotein receptor

Description F58H1.7 /REP_DB=WormBase Gene ID /WP=CE20895 /TR=Q18790 /GB=CAB00110.1 /SUBMIT=HINXTON /CHR=5 /FEA=Sanger Annotation /DEF=low-density lipoprotein receptor
Cluster 6grp_highest_10_10 > 06      6grp_high1_10_10 > 50      4grp_highest_8_8 > 47      4grp_high_8_8 > 11      6grp_highest_nonorm > 23      6grp_total > 40      4grp_total > 13      6grp_highest_sub > 04      6grp_high1_sub > 03_04      6grp_total_sub > Hat      6grp_rule_based > S4      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 3237
1 2 3 4 range
A 3064.7
(0.5)
P 		1612.4
(-2.2)
P 		1200.8
(-3)
P 		4437.8
(3)
P 		3237
B 3204.9
(0.8)
P 		1703.8
(-2.1)
P 		1218.9
(-3)
P 		4353.1
(3)
P 		3134
C 3118.2
(1.5)
P 		1715.5
(-1.9)
P 		1263.5
(-3)
P 		3729.2
(3)
P 		2466
avr 3129.3
(0.9) 		1677.2
(-2.1) 		1227.7
(-3) 		4173.4
(3) 		2946

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 1492
1 2 3 4 5 6 range
A 2514.2
(3)
P 		1980.4
(0.4)
P 		2302.5
(2)
P 		2066.2
(0.8)
P 		1713.3
(-0.9)
P 		1281.9
(-3)
P 		1232
B 1869.6
(-0.9)
P 		2391.2
(1.4)
P 		2315.6
(1.1)
P 		2749.6
(3)
P 		1475.3
(-2.6)
P 		1387.5
(-3)
P 		1362
C 1813.4
(-0.5)
P 		2317.6
(1.8)
P 		2035.5
(0.5)
P 		2575.7
(3)
P 		1257.7
(-3)
P 		1576.1
(-1.6)
P 		1318
avr 2065.7
(0.7) 		2229.7
(1.7) 		2217.9
(1.6) 		2463.8
(3) 		1482.1
(-2.6) 		1415.2
(-3) 		1049
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 834
1 2 3 4 range
A 1115.9
(3)
P 		350
(-2.7)
P 		313.9
(-3)
P 		649.6
(-0.5)
P 		802
B 1022
(3)
P 		420.8
(-1.9)
P 		282.4
(-3)
P 		927.6
(2.2)
P 		740
C 1032.2
(3)
P 		493.2
(-2.5)
P 		440.4
(-3)
P 		628.8
(-1.1)
P 		592
avr 1056.7
(3) 		421.3
(-2.4) 		345.6
(-3) 		735.3
(0.3) 		711

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 484
1 2 3 4 5 6 range
A 463.5
(-0.7)
P 		704.3
(3)
P 		501.4
(-0.1)
P 		524
(0.2)
P 		517
(0.1)
P 		312.1
(-3)
P 		392
B 650.5
(-0.1)
P 		795.9
(3)
P 		562.3
(-2)
P 		728.3
(1.5)
P 		599.4
(-1.2)
P 		517.4
(-3)
P 		279
C 672.2
(2.3)
P 		707.2
(3)
P 		518.1
(-0.8)
P 		518
(-0.8)
P 		407
(-3)
P 		527.6
(-0.6)
P 		300
avr 595.4
(0) 		735.8
(3) 		527.3
(-1.4) 		590.1
(-0.1) 		507.8
(-1.8) 		452.4
(-3) 		283
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 192216_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.12742
Sequence Type Exemplar sequence
Representative Public ID F58H1.7 NCBI
Target Description F58H1.7 /REP_DB=WormBase Gene ID /WP=CE20895 /TR=Q18790 /GB=CAB00110.1 /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_073600(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_073600 NCBI Caenorhabditis elegans F58H1.7 (F58H1.7) mRNA, complete cds. 11/11 None
F58H1.7 ENSEMBL cdna:known chromosome:CEL140:V:11965634:11967396:-1 gene:F58H1.7 11/11 None
Annotation Notes
Cross Hybridizing mRNA Matched Probes Nature of Assignment Related Probesets by Grade
SNAP00000006513 3/11 Cross Hyb Matching Probes None
GENEFINDER00000006514 3/11 Cross Hyb Matching Probes None
SNAP00000019782 7/11 Cross Hyb Matching Probes None
GENEFINDER00000019796 7/11 Cross Hyb Matching Probes None
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrV:11965891-11967396(-) 100.0 100.0
Public Domain and Genome References
Gene Title low-density lipoprotein receptor
Ensembl F58H1.7
Entrez Gene 179636 Entrez gene
SwissProt Q18790 EMBL-EBI
WormBase CE20895 Wormbase
Functional Annotations
Ortholog
ID Title Organism
DROSOPHILA_2:1625462_S_AT dm
DROSGENOME1:151057_AT dm
DROSGENOME1:150198_AT dm
Protein Similarities
Method ID Description E-Value
blast CAB01419 Hypothetical protein F58H1.7 [Caenorhabditis elegans] emb|CAB00110.1| Hypothetical protein F58H1.7 [Caenorhabditis elegans] ref|NP_506001.1| F58H1.7 [Caenorhabditis elegans] 1.0E-105
blast CAE75358 Hypothetical protein CBG23341 [Caenorhabditis briggsae] 2.0E-99
blast EAL29185 GA16102-PA [Drosophila pseudoobscura] 8.0E-37
Protein Domains
Database ID Description E-Value
Pfam IPR002172 EMBL-EBI Low density lipoprotein-receptor, class A 4.9E-12
Sequence
Target Sequence 
>C. ELEGANS:192216_AT
caccgcttgttcctttagtatccgggacattatcaacgggaaacggggagctgatgctgc
aattccagccccctgtcctacatggcatccgtttgcatgtccatcgggtgaatgcgtgcc
aatcaagtacctgtgcgacggatcacctgactgttcagacgagtatgacgagaacaagag
catgtgcacagcagccacacgaccgcccgttgaggagactcaggcgtttttgaaggctct
catgtccgcccatggaaaagattttctcgtcaaggtatttggtccaaaagcgaaagcaga
actgtctggaatgggtggagttgacaaagttgcagttgctctttctcaaactccgacagc
agacctgtttgcatctgaaatgaaattggacgatggagaaacacagcatatgttggaagt
tatggagggaattttgaatggatcaactgatgaacttacatccaacgaggctgctgattt
ccg

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
CACCGCTTGTTCCTTTAGTATCCGG 386 199 48 Antisense
ACGGGGAGCTGATGCTGCAATTCCA 38 97 90 Antisense
TGTCCTACATGGCATCCGTTTGCAT 423 557 121 Antisense
TGTCCATCGGGTGAATGCGTGCCAA 649 555 145 Antisense
CGTGCCAATCAAGTACCTGTGCGAC 1 247 162 Antisense
GACGGATCACCTGACTGTTCAGACG 127 377 184 Antisense
AAGAGCATGTGCACAGCAGCCACAC 583 153 223 Antisense
TTTTTGAAGGCTCTCATGTCCGCCC 309 675 274 Antisense
AGTTGCAGTTGCTCTTTCTCAAACT 17 65 375 Antisense
AACTCCGACAGCAGACCTGTTTGCA 13 139 396 Antisense
CATCCAACGAGGCTGCTGATTTCCG 203 209 506 Antisense
Sequence Source Affymetrix Proprietary Database