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[175372_s_at]

Description AV185564_rc /REP_DB=TREMBL Accession /GB=AV185564 /CHR=2 /FEA=Genomic Cluster /DEF=Caenorhabditis elegans cDNA clone:yk680a1 : 3prime end, single read.
Cluster 6grp_highest_10_10 > 0      6grp_high1_10_10 > 08      4grp_highest_8_8 > 0      4grp_high_8_8 > 44      6grp_highest_nonorm > 50      6grp_total > 09      4grp_total > 44      6grp_cgc > 0      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 525
1 2 3 4 range
A 626.2
(3)
P 		548.5
(1.6)
P 		532.6
(1.4)
P 		282.1
(-3)
P 		344
B 661.4
(3)
P 		648.6
(2.7)
P 		376.1
(-3)
P 		530.7
(0.3)
P 		285
C 371.5
(-3)
P 		807.1
(3)
P 		560.3
(-0.4)
P 		422.3
(-2.3)
P 		436
avr 553
(0.3) 		668.1
(3) 		489.7
(-1.2) 		411.7
(-3) 		256

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 600
1 2 3 4 5 6 range
A 838.5
(3)
P 		463.5
(-0.8)
P 		238.9
(-3)
P 		571.3
(0.3)
P 		412.1
(-1.3)
P 		493.3
(-0.5)
P 		600
B 461
(1.9)
P 		435.6
(1.4)
P 		238.9
(-3)
P 		510
(3)
P 		504.1
(2.9)
P 		370.5
(-0.1)
P 		271
C 582.4
(2)
P 		345
(-2.9)
P 		519.8
(0.7)
P 		632.1
(3)
P 		439.5
(-1)
P 		340.3
(-3)
P 		292
avr 627.3
(3) 		414.7
(-1.3) 		332.5
(-3) 		571.1
(1.9) 		451.9
(-0.6) 		401.4
(-1.6) 		295
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 191
1 2 3 4 range
A 228
(3)
P 		119.1
(-0.5)
P 		139.2
(0.1)
P 		41.3
(-3)
P 		187
B 210.9
(3)
P 		160.2
(0.5)
P 		87.1
(-3)
P 		113.1
(-1.7)
P 		124
C 123
(-1.1)
P 		232
(3)
P 		195.3
(1.6)
P 		71.2
(-3)
P 		161
avr 187.3
(3) 		170.4
(2.1) 		140.5
(0.5) 		75.2
(-3) 		112

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 164
1 2 3 4 5 6 range
A 154.6
(2.5)
P 		164.9
(3)
P 		52
(-3)
P 		144.9
(1.9)
P 		124.3
(0.8)
P 		120.1
(0.6)
P 		113
B 160.4
(1.2)
P 		145
(0.6)
P 		58
(-3)
P 		135.1
(0.2)
P 		204.8
(3)
P 		138.2
(0.3)
P 		147
C 215.9
(3)
P 		105.3
(-3)
P 		132.3
(-1.5)
P 		127.1
(-1.8)
P 		142.2
(-1)
P 		113.9
(-2.5)
P 		111
avr 177
(3) 		138.4
(0.6) 		80.8
(-3) 		135.7
(0.4) 		157.1
(1.8) 		124.1
(-0.3) 		96
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 175372_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.20656
Sequence Type Exemplar sequence
Representative Public ID AV185564 NCBI
Target Description AV185564_rc /REP_DB=TREMBL Accession /GB=AV185564 /CHR=2 /FEA=Genomic Cluster /DEF=Caenorhabditis elegans cDNA clone:yk680a1 : 3prime end, single read.
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_062405(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_062405 NCBI Caenorhabditis elegans Variable ABnormal morphology family member (vab-1) (vab-1) mRNA, complete cds. 11/11 None
M03A1.1b ENSEMBL cdna:known chromosome:CEL140:II:4572001:4590938:1 gene:M03A1.1 11/11 A 
Annotation Notes
There are no noteworthy cross hybridizing mRNAs found for this probe set.
Splice Variants
Entrez Total Refseq Isoforms Total Detected By This Probeset Refseq Probesets
173794 2 1 NM_062405 175372_s_at (11)
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrII:4590596-4590887(+) 100.0 100.0
Public Domain and Genome References
Ensembl M03A1.1
Functional Annotations
Protein Similarities
Method ID Description E-Value
blast AAK77621 Variable abnormal morphology protein 1, isoform b [Caenorhabditis elegans] ref|NP_494806.1| Variable ABnormal morphology family member (vab-1) [Caenorhabditis elegans] sp|O61460|VAB1_CAEEL Ephrin receptor 1 precursor (Tyrosine-protein kinase Eph receptor) (Variable abnormal protein 1) gb|AAC38970.1| Eph receptor tyrosine kinase [Caenorhabditis elegans] 0.0
blast AAK77620 Variable abnormal morphology protein 1, isoform a [Caenorhabditis elegans] ref|NP_494807.1| Variable ABnormal morphology family member (vab-1) [Caenorhabditis elegans] 0.0
blast CAE67856 Hypothetical protein CBG13447 [Caenorhabditis briggsae] 0.0
Protein Domains
Database ID Description E-Value
Pfam IPR003961 EMBL-EBI Fibronectin, type III 1.4E-10
Pfam IPR003961 EMBL-EBI Fibronectin, type III 2.4E-10
Pfam IPR001090 EMBL-EBI Ephrin receptor, ligand binding 3.6E-10
Pfam IPR001090 EMBL-EBI Ephrin receptor, ligand binding 9.7E-5
Pfam IPR000719 EMBL-EBI Protein kinase 5.2E-61
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_494806.1 2 558-580,776-798
M03A1.1b 2 558-580,776-798
Sequence
Target Sequence 
>C. ELEGANS:175372_S_AT
gatatgtgcattttcaaaactgttatgggtagccgattcgatattatgttttcctctgtg
tctttaaatcctttttttctgcatttttccccctaatgttcccctctccccgatgatatg
atctactcaacaaatttagtattttagcaacgatttgtaagcctccacc

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GATATGTGCATTTTCAAAACTGTTA 480 425 15 Antisense
AACTGTTATGGGTAGCCGATTCGAT 260 143 32 Antisense
GCCGATTCGATATTATGTTTTCCTC 322 283 46 Antisense
ATATTATGTTTTCCTCTGTGTCTTT 590 19 55 Antisense
GTTTTCCTCTGTGTCTTTAAATCCT 372 447 62 Antisense
TCCTCTGTGTCTTTAAATCCTTTTT 628 591 66 Antisense
GTCTTTAAATCCTTTTTTTCTGCAT 452 469 74 Antisense
CCTCTCCCCGATGATATGATCTACT 593 267 117 Antisense
CCCCGATGATATGATCTACTCAACA 451 261 122 Antisense
ATTTAGTATTTTAGCAACGATTTGT 669 13 148 Antisense
TAGCAACGATTTGTAAGCCTCCACC 299 651 159 Antisense
Sequence Source Affymetrix Proprietary Database