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[191671_s_at] LIN-12 protein

Description R107.8 /REP_DB=WormBase Gene ID /WP=CE00274 /GEN=lin-12 /TR=SW:P14585 /GB=CAA78474.1 /SUBMIT=HINXTON /CHR=3 /FEA=Sanger Annotation /DEF=LIN-12 protein
Cluster 6grp_high1_10_10 > 54      4grp_high_8_8 > 45      6grp_total > 56      4grp_total > 42      6grp_cgc > 55      4grp_rule_based > L2      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 148
1 2 3 4 range
A 187.9
(-3)
P 		320.3
(3)
P 		227.4
(-1.2)
P 		286.3
(1.5)
A 		132
B 172.5
(-3)
P 		260.2
(1.9)
M 		279.1
(3)
P 		181.6
(-2.5)
P 		107
C 196.6
(-3)
P 		295.9
(3)
P 		291.6
(2.7)
P 		224.1
(-1.3)
A 		99
avr 185.7
(-3) 		292.1
(3) 		266
(1.5) 		230.7
(-0.5) 		106

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 153
1 2 3 4 5 6 range
A 228
(-1.2)
A 		311.1
(3)
P 		191.5
(-3)
A 		228.2
(-1.2)
P 		256.4
(0.3)
P 		292.1
(2)
P 		120
B 245.4
(0.4)
P 		255
(1)
P 		272.9
(2.1)
A 		266.4
(1.7)
P 		189.2
(-3)
P 		288
(3)
P 		99
C 250.3
(1.1)
P 		280.5
(2.4)
M 		294.2
(3)
P 		157.8
(-3)
A 		212
(-0.6)
P 		275.7
(2.2)
P 		136
avr 241.2
(-0.9) 		282.2
(2.7) 		252.9
(0.1) 		217.5
(-3) 		219.2
(-2.8) 		285.3
(3) 		68
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 64
1 2 3 4 range
A 68.4
(2.8)
P 		69.5
(3)
P 		59.5
(0.8)
P 		41.9
(-3)
A 		28
B 55
(0.8)
P 		64.3
(2.9)
M 		64.7
(3)
P 		38.7
(-3)
P 		26
C 65.1
(-0.4)
P 		85.1
(1.4)
P 		101.6
(3)
P 		37.8
(-3)
A 		64
avr 62.8
(0.9) 		73
(2.6) 		75.3
(3) 		39.5
(-3) 		36

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 79
1 2 3 4 5 6 range
A 42
(-3)
A 		110.6
(3)
P 		41.7
(-3)
A 		57.9
(-1.6)
P 		77.4
(0.1)
P 		71.1
(-0.4)
P 		69
B 85.4
(-0.2)
P 		84.9
(-0.3)
P 		66.3
(-3)
A 		70.6
(-2.4)
P 		76.9
(-1.5)
P 		107.4
(3)
P 		41
C 92.8
(3)
P 		85.6
(2.3)
M 		74.9
(1.2)
P 		31.7
(-3)
A 		68.6
(0.6)
P 		92.3
(3)
P 		61
avr 73.4
(-0) 		93.7
(3) 		61
(-1.9) 		53.4
(-3) 		74.3
(0.1) 		90.3
(2.5) 		40
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 191671_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.8080
Sequence Type Exemplar sequence
Representative Public ID R107.8 NCBI
Target Description R107.8 /REP_DB=WormBase Gene ID /WP=CE00274 /GEN=lin-12 /TR=SW:P14585 /GB=CAA78474.1 /SUBMIT=HINXTON /CHR=3 /FEA=Sanger Annotation /DEF=LIN-12 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_066606(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_066606 NCBI Caenorhabditis elegans abnormal cell LINeage family member (lin-12) (lin-12) mRNA, complete cds. 11/11 None
SNAP00000003029 ENSEMBL cdna:SNAP chromosome:CEL140:III:9060308:9066775:-1 11/11 None
GENEFINDER00000003031 ENSEMBL cdna:GeneFinder chromosome:CEL140:III:9060308:9071200:-1 11/11 None
R107.8 ENSEMBL cdna:known chromosome:CEL140:III:9060148:9071294:-1 gene:R107.8 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:9060303-9071290(-) 100.0 100.0
Public Domain and Genome References
Gene Title LIN-12 protein
Gene Symbol lin-12
Ensembl R107.8
Entrez Gene 176282 Entrez gene
SwissProt P14585 EMBL-EBI
WormBase CE00274 Wormbase
Functional Annotations
Gene Ontology
GO Biological Process (view graph)
ID Description Evidence Links
30154 cell differentiation inferred from electronic annotation QuickGO AmiGO
7219 Notch signaling pathway inferred from sequence similarity QuickGO AmiGO
GO Cellular Component (view graph)
ID Description Evidence Links
16020 membrane inferred from electronic annotation QuickGO AmiGO
5886 plasma membrane inferred from direct assay QuickGO AmiGO
16324 apical plasma membrane inferred from direct assay QuickGO AmiGO
GO Molecular Function (view graph)
ID Description Evidence Links
5198 structural molecule activity inferred from electronic annotation QuickGO AmiGO
5509 calcium ion binding inferred from electronic annotation QuickGO AmiGO
4888 transmembrane receptor activity inferred from sequence similarity QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast CAA78474 Hypothetical protein R107.8 [Caenorhabditis elegans] ref|NP_499007.1| abnormal cell LINeage family member (lin-12) [Caenorhabditis elegans] sp|P14585|LIN12_CAEEL Lin-12 protein precursor prf||1413328A lin 12 gene gb|AAA70191.1| lin-12 protein 0.0
blast AAP05764 notch-like transmembrane receptor LIN-12 [Caenorhabditis remanei] 0.0
blast AAP05765 notch-like transmembrane receptor LIN-12 [Caenorhabditis briggsae] gb|AAP05763.1| notch-like transmembrane receptor LIN-12 [Caenorhabditis briggsae] 0.0
Protein Domains
Database ID Description E-Value
Pfam IPR006209 EMBL-EBI EGF-like domain 8.2E-7
Pfam IPR006209 EMBL-EBI EGF-like domain 6.4E-8
Pfam IPR006209 EMBL-EBI EGF-like domain 1.7E-5
Pfam IPR006209 EMBL-EBI EGF-like domain 3.1E-10
Pfam IPR006209 EMBL-EBI EGF-like domain 2.4E-7
Pfam IPR006209 EMBL-EBI EGF-like domain 1.6E-6
Pfam IPR006209 EMBL-EBI EGF-like domain 1.1E-9
Pfam IPR006209 EMBL-EBI EGF-like domain 1.7E-7
Pfam IPR006209 EMBL-EBI EGF-like domain 4.2E-5
Pfam IPR006209 EMBL-EBI EGF-like domain 1.0E-9
Pfam IPR006209 EMBL-EBI EGF-like domain 9.6E-9
Pfam IPR006209 EMBL-EBI EGF-like domain 1.8E-6
Pfam IPR002110 EMBL-EBI Ankyrin 0.053
Pfam IPR002110 EMBL-EBI Ankyrin 1.7E-7
Pfam IPR002110 EMBL-EBI Ankyrin 31.0
Pfam IPR002110 EMBL-EBI Ankyrin 7.6E-4
Pfam IPR002110 EMBL-EBI Ankyrin 2.4E-7
Pfam IPR002110 EMBL-EBI Ankyrin 8.1E-11
Pfam IPR010660 EMBL-EBI NOTCH 2.3E-58
Pfam IPR000800 EMBL-EBI Notch (DSL) domain 9.2E-18
Pfam IPR000800 EMBL-EBI Notch (DSL) domain 1.5E-19
Pfam IPR000800 EMBL-EBI Notch (DSL) domain 6.3E-23
Pfam IPR006209 EMBL-EBI EGF-like domain 7.4E-4
Pfam IPR006209 EMBL-EBI EGF-like domain 6.4E-8
Pfam IPR006209 EMBL-EBI EGF-like domain 1.7E-5
Pfam IPR006209 EMBL-EBI EGF-like domain 3.1E-10
Pfam IPR006209 EMBL-EBI EGF-like domain 2.4E-7
Pfam IPR006209 EMBL-EBI EGF-like domain 1.6E-6
Pfam IPR006209 EMBL-EBI EGF-like domain 1.1E-9
Pfam IPR006209 EMBL-EBI EGF-like domain 1.7E-7
Pfam IPR006209 EMBL-EBI EGF-like domain 4.2E-5
Pfam IPR006209 EMBL-EBI EGF-like domain 1.0E-9
Pfam IPR006209 EMBL-EBI EGF-like domain 9.6E-9
Pfam IPR006209 EMBL-EBI EGF-like domain 1.8E-6
Pfam IPR002110 EMBL-EBI Ankyrin 0.053
Pfam IPR002110 EMBL-EBI Ankyrin 1.7E-7
Pfam IPR002110 EMBL-EBI Ankyrin 31.0
Pfam IPR002110 EMBL-EBI Ankyrin 7.6E-4
Pfam IPR002110 EMBL-EBI Ankyrin 2.4E-7
Pfam IPR002110 EMBL-EBI Ankyrin 8.1E-11
Pfam IPR010660 EMBL-EBI NOTCH 2.3E-58
Pfam IPR000800 EMBL-EBI Notch (DSL) domain 9.2E-18
Pfam IPR000800 EMBL-EBI Notch (DSL) domain 1.5E-19
Pfam IPR000800 EMBL-EBI Notch (DSL) domain 6.3E-23
Pfam IPR006209 EMBL-EBI EGF-like domain 8.2E-7
Pfam IPR006209 EMBL-EBI EGF-like domain 1.7E-5
Pfam IPR006209 EMBL-EBI EGF-like domain 3.1E-10
Pfam IPR006209 EMBL-EBI EGF-like domain 2.4E-7
Pfam IPR006209 EMBL-EBI EGF-like domain 1.6E-6
Pfam IPR006209 EMBL-EBI EGF-like domain 1.1E-9
Pfam IPR006209 EMBL-EBI EGF-like domain 1.7E-7
Pfam IPR006209 EMBL-EBI EGF-like domain 4.2E-5
Pfam IPR006209 EMBL-EBI EGF-like domain 1.0E-9
Pfam IPR006209 EMBL-EBI EGF-like domain 9.6E-9
Pfam IPR006209 EMBL-EBI EGF-like domain 1.8E-6
Pfam IPR002110 EMBL-EBI Ankyrin 0.053
Pfam IPR002110 EMBL-EBI Ankyrin 1.7E-7
Pfam IPR002110 EMBL-EBI Ankyrin 31.0
Pfam IPR002110 EMBL-EBI Ankyrin 7.6E-4
Pfam IPR002110 EMBL-EBI Ankyrin 2.4E-7
Pfam IPR002110 EMBL-EBI Ankyrin 8.1E-11
Pfam IPR010660 EMBL-EBI NOTCH 2.3E-58
Pfam IPR000800 EMBL-EBI Notch (DSL) domain 9.2E-18
Pfam IPR000800 EMBL-EBI Notch (DSL) domain 1.5E-19
Pfam IPR000800 EMBL-EBI Notch (DSL) domain 6.3E-23
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_499007.1 1 907-929
R107.8 1 907-929
SNAP00000003029 1 784-806
GENEFINDER00000003031 1 1043-1065
Sequence
Target Sequence 
>C. ELEGANS:191671_S_AT
gacgccgattatgttagctgcacaggaaggacgtattgaagttgtgatgtatttgattca
gcaaggggctagtgttgaagcggttgatgctacggatcatacggctcgtcaactcgctca
agcaaataaccatcacaatattgttgatatttttgatagatgtcgtccagaacgagaata
ttcaatggatcttcacatccaacatacccatcaaccacaaccttcaagaaaagtaactcg
agctccgaagaaacagacaagtcgaagcaaaaaagagtcagcttccaattctcgagactc
aactcatctgacacctccaccatcggatggatcaacgtcaacaccgtcaccacagcattt
tatgaataccactcatactacaccgacgagtttgaactatttgagcccagaatatcaaac
tgaagctggaagctcagaagcgttccaaccacaatgtggagcatttggaaatggcgaaat
gtggtatacaagagcttcaacatcgtacaccc

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GACGCCGATTATGTTAGCTGCACAG 112 379 3738 Antisense
GATGCTACGGATCATACGGCTCGTC 121 413 3823 Antisense
GCTCGTCAACTCGCTCAAGCAAATA 649 299 3841 Antisense
GGATCTTCACATCCAACATACCCAT 130 511 3924 Antisense
AGAGTCAGCTTCCAATTCTCGAGAC 308 67 4011 Antisense
TCTCGAGACTCAACTCATCTGACAC 361 611 4027 Antisense
GACACCTCCACCATCGGATGGATCA 41 369 4047 Antisense
GATGGATCAACGTCAACACCGTCAC 192 407 4063 Antisense
TGAATACCACTCATACTACACCGAC 675 573 4100 Antisense
GGAAGCTCAGAAGCGTTCCAACCAC 30 531 4165 Antisense
ACAAGAGCTTCAACATCGTACACCC 227 113 4225 Antisense
Sequence Source Affymetrix Proprietary Database