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[191883_at] LDL-like receptor

Description T11F8.3 /REP_DB=WormBase Gene ID /WP=CE25992 /GEN=rme-2 /TR=O44191 /GB=AAB88554.2 /SUBMIT=ST.LOUIS /CHR=4 /FEA=Sanger Annotation /DEF=LDL-like receptor
Cluster 6grp_total > 88      4grp_total > 16      6grp_cgc > 59      6grp_cgc_sub > Da      6grp_total_sub > Increase      6grp_rule_based > S6      4grp_rule_based > L4      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 130
1 2 3 4 range
A 75.9
(-2.3)
A 		61.2
(-3)
A 		116.8
(-0.4)
A 		190.9
(3)
P 		130
B 73
(-3)
A 		127.4
(0.6)
A 		121.2
(0.2)
A 		163
(3)
A 		90
C 102
(-2.4)
A 		120.2
(-1)
A 		94.7
(-3)
A 		171
(3)
M 		76
avr 83.6
(-3) 		102.9
(-1.7) 		110.9
(-1.2) 		175
(3) 		91

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 3449
1 2 3 4 5 6 range
A 67.6
(-3)
A 		87.5
(-3)
A 		70.1
(-3)
A 		306.1
(-2.6)
P 		1532.8
(-0.4)
P 		3492.8
(3)
P 		3425
B 43.7
(-3)
A 		88.1
(-2.9)
A 		113.8
(-2.8)
A 		280.6
(-2.5)
P 		1536.5
(0.3)
P 		2733.4
(3)
P 		2690
C 65.4
(-3)
A 		136.6
(-2.9)
P 		130.8
(-2.9)
P 		261
(-2.6)
P 		1805.3
(0.6)
P 		2929.6
(3)
P 		2864
avr 58.9
(-3) 		104.1
(-2.9) 		104.9
(-2.9) 		282.6
(-2.6) 		1624.9
(0.1) 		3051.9
(3) 		2993
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 21
1 2 3 4 range
A 27.6
(2)
A 		13.3
(-3)
A 		30.5
(3)
A 		27.9
(2.1)
P 		17
B 23.3
(-3)
A 		31.5
(1.3)
A 		28.1
(-0.5)
A 		34.7
(3)
A 		11
C 33.8
(2.3)
A 		34.5
(3)
A 		33
(1.4)
A 		28.8
(-3)
M 		6
avr 28.2
(-0.4) 		26.4
(-3) 		30.5
(3) 		30.5
(3) 		4

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 1007
1 2 3 4 5 6 range
A 12.5
(-3)
A 		31.1
(-2.9)
A 		15.3
(-3)
A 		77.6
(-2.5)
P 		462.5
(0.2)
P 		850.4
(3)
P 		838
B 15.2
(-3)
A 		29.3
(-2.9)
A 		27.6
(-2.9)
A 		74.3
(-2.6)
P 		624.2
(0.6)
P 		1019.3
(3)
P 		1004
C 24.2
(-3)
A 		41.7
(-2.9)
P 		33.3
(-2.9)
P 		52.5
(-2.8)
P 		584.2
(0.5)
P 		980.7
(3)
P 		957
avr 17.3
(-3) 		34
(-2.9) 		25.4
(-2.9) 		68.1
(-2.7) 		557
(0.5) 		950.1
(3) 		933
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 191883_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.10540
Sequence Type Exemplar sequence
Representative Public ID T11F8.3 NCBI
Target Description T11F8.3 /REP_DB=WormBase Gene ID /WP=CE25992 /GEN=rme-2 /TR=O44191 /GB=AAB88554.2 /SUBMIT=ST.LOUIS /CHR=4 /FEA=Sanger Annotation /DEF=LDL-like 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_068414(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_068414 NCBI Caenorhabditis elegans Receptor Mediated Endocytosis family member (rme-2) (rme-2) mRNA, complete cds. 11/11 None
SNAP00000002003 ENSEMBL cdna:SNAP chromosome:CEL140:IV:5470016:5473075:1 11/11 None
GENEFINDER00000002009 ENSEMBL cdna:GeneFinder chromosome:CEL140:IV:5470016:5473075:1 11/11 None
T11F8.3.2 ENSEMBL cdna:known chromosome:CEL140:IV:5469982:5473159:1 gene:T11F8.3 11/11 None
T11F8.3.1 ENSEMBL cdna:known chromosome:CEL140:IV:5469996:5473158:1 gene:T11F8.3 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
chrIV:5470030-5473081(+) 100.0 100.0
Public Domain and Genome References
Gene Title LDL-like receptor
Gene Symbol rme-2
Ensembl T11F8.3
Entrez Gene 177329 Entrez gene
SwissProt O44191 EMBL-EBI
WormBase CE22368 Wormbase
Functional Annotations
Gene Ontology
GO Cellular Component (view graph)
ID Description Evidence Links
16020 membrane inferred from electronic annotation QuickGO AmiGO
GO Molecular Function (view graph)
ID Description Evidence Links
5509 calcium ion binding inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast NP_500815 Receptor Mediated Endocytosis family member (rme-2) [Caenorhabditis elegans] gb|AAB88554.3| Receptor mediated endocytosis protein 2 [Caenorhabditis elegans] 0.0
blast AAD56241 yolk receptor RME-2 [Caenorhabditis elegans] 0.0
blast AAD09364 similar to low density lipoprotein receptor [Caenorhabditis elegans] 0.0
Protein Domains
Database ID Description E-Value
Pfam IPR006209 EMBL-EBI EGF-like domain 8.2E-9
Pfam IPR006209 EMBL-EBI EGF-like domain 6.6E-8
Pfam IPR002172 EMBL-EBI Low density lipoprotein-receptor, class A 1.6E-12
Pfam IPR002172 EMBL-EBI Low density lipoprotein-receptor, class A 6.4E-11
Pfam IPR002172 EMBL-EBI Low density lipoprotein-receptor, class A 7.9E-11
Pfam IPR002172 EMBL-EBI Low density lipoprotein-receptor, class A 9.0E-11
Pfam IPR000033 EMBL-EBI Low-density lipoprotein receptor, YWTD repeat 4.0E-10
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_500815.2 1 789-811
T11F8.3.2 1 789-811
T11F8.3.1 1 789-811
SNAP00000002003 1 789-811
GENEFINDER00000002009 1 789-811
Sequence
Target Sequence 
>C. ELEGANS:191883_AT
agctttcccacattggatctgctttgatggccgaatactgcgaagctggtgtcgcgtgta
tgaatggaggagcctgccgtgaactacaaaatgagcacggaagagctcatcgcatcgttt
gtgattgtgagggtccatatgacgggcaatactgcgaacggctcaatccagagaagttct
ccgcaatggaagaggaagattcgtccttatggcttatcgttctgcttctcatttttctca
tcatcgttgcggtagtcggaattattgccttcctttggttttctcaacaagagcatatga
aagatgtgatttccactgcccgtgtccgtgttgataacatggctagaaaagcggaagatg
ctgcagctccaattgtcgagaagttccgcaaggtcactgataagcagaggagcacgcctc
ctagagaaggttgtcaaacggcaacaaacgttgacttcgtttcctacgagacaaatgctg
agaaaagaattcggatggactcttcgccgacgtcatacggaaaccccatgtacgatgaag
ttcctgaatcgtcaactggtttcgtcagatcggcttc

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
AGCTTTCCCACATTGGATCTGCTTT 192 79 2156 Antisense
GAATGGAGGAGCCTGCCGTGAACTA 621 331 2217 Antisense
CGGAAGAGCTCATCGCATCGTTTGT 672 241 2253 Antisense
GGCAATACTGCGAACGGCTCAATCC 654 533 2300 Antisense
TTATGGCTTATCGTTCTGCTTCTCA 636 681 2362 Antisense
TCTCATTTTTCTCATCATCGTTGCG 374 613 2382 Antisense
GAAAGATGTGATTTCCACTGCCCGT 132 361 2454 Antisense
GAAGATGCTGCAGCTCCAATTGTCG 33 339 2509 Antisense
GAGCACGCCTCCTAGAGAAGGTTGT 111 391 2565 Antisense
GAATTCGGATGGACTCTTCGCCGAC 558 323 2642 Antisense
CAACTGGTTTCGTCAGATCGGCTTC 13 189 2708 Antisense
Sequence Source Affymetrix Proprietary Database