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[194235_x_at]

Description C48813 /REP_DB=TREMBL Accession /5_PRIME_EXT_ID=F54A5.2 /5_PRIME_EXT_DB=WormBase Gene ID /GB=C48813 /WB_GENE_ID=F54A5.2 /WP=CE20860 /CHR=1 /FEA=Genomic Cluster /DEF=C.elegans cDNA clone yk461e8 : 5prime end, single read.
Cluster 6grp_highest_10_10 > 51      6grp_high1_10_10 > 26      4grp_highest_8_8 > 01      4grp_high_8_8 > 45      6grp_highest_nonorm > 60      6grp_total > 26      4grp_total > 51      6grp_highest_sub > De      6grp_high1_sub > De      6grp_total_sub > Cup      6grp_rule_based > S1      4grp_rule_based > L2      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 292
1 2 3 4 range
A 349.1
(-0.7)
P 		530.6
(3)
P 		441.2
(1.2)
P 		238.6
(-3)
P 		292
B 388.7
(0.3)
P 		459.9
(2.4)
P 		480.4
(3)
P 		278.8
(-3)
P 		202
C 324.9
(-3)
P 		509.3
(3)
P 		392.3
(-0.8)
P 		338.8
(-2.5)
P 		184
avr 354.2
(-1.1) 		499.9
(3) 		438
(1.3) 		285.4
(-3) 		215

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 328
1 2 3 4 5 6 range
A 496.3
(3)
P 		413.9
(0.8)
P 		322.6
(-1.6)
P 		279.1
(-2.8)
P 		270.8
(-3)
P 		308.1
(-2)
P 		226
B 554.7
(3)
P 		408.1
(-0.1)
P 		282.7
(-2.8)
P 		281.8
(-2.8)
P 		271
(-3)
P 		298.3
(-2.4)
P 		284
C 346.2
(0.8)
P 		414.8
(3)
P 		330.8
(0.3)
P 		272
(-1.6)
P 		226.6
(-3)
P 		283.8
(-1.2)
P 		188
avr 465.7
(3) 		412.3
(1.5) 		312
(-1.4) 		277.6
(-2.4) 		256.1
(-3) 		296.7
(-1.8) 		210
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 112
1 2 3 4 range
A 127.1
(3)
P 		115.2
(2.2)
P 		115.4
(2.2)
P 		34.9
(-3)
P 		92
B 123.9
(3)
P 		113.6
(2)
P 		111.3
(1.8)
P 		59.4
(-3)
P 		65
C 107.5
(0.4)
P 		146.4
(3)
P 		136.7
(2.3)
P 		57.1
(-3)
P 		89
avr 119.5
(2.5) 		125.1
(3) 		121.1
(2.7) 		50.5
(-3) 		75

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 138
1 2 3 4 5 6 range
A 91.5
(-1.3)
P 		147.2
(3)
P 		70.3
(-3)
P 		70.8
(-3)
P 		81.7
(-2.1)
P 		75
(-2.6)
P 		77
B 193
(3)
P 		135.8
(0.2)
P 		68.7
(-3)
P 		74.6
(-2.7)
P 		110.1
(-1)
P 		111.2
(-0.9)
P 		124
C 128.3
(3)
P 		126.6
(2.9)
P 		84.2
(-0.6)
P 		54.7
(-3)
P 		73.3
(-1.5)
P 		95
(0.3)
P 		74
avr 137.6
(3) 		136.5
(2.9) 		74.4
(-2.3) 		66.7
(-3) 		88.4
(-1.2) 		93.7
(-0.7) 		71
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 194235_x_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.22479
Sequence Type Exemplar sequence
Representative Public ID C48813 NCBI
Target Description C48813 /REP_DB=TREMBL Accession /5_PRIME_EXT_ID=F54A5.2 /5_PRIME_EXT_DB=WormBase Gene ID /GB=C48813 /WB_GENE_ID=F54A5.2 /WP=CE20860 /CHR=1 /FEA=Genomic Cluster /DEF=C.elegans cDNA clone yk461e8 : 5prime 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_058397(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_058397 NCBI Caenorhabditis elegans F54A5.2 (F54A5.2) mRNA, complete cds. 11/11 A 
GENEFINDER00000014310 ENSEMBL cdna:GeneFinder chromosome:CEL140:I:952589:974578:-1 11/11 None
F54A5.2 ENSEMBL cdna:known chromosome:CEL140:I:963715:969427:-1 gene:F54A5.2 11/11 A 
Annotation Notes
Cross Hybridizing mRNA Matched Probes Nature of Assignment Related Probesets by Grade
SNAP00000014306 6/11 Cross Hyb Matching Probes None
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrI:963715-969335(-) 94.18 100.0
Public Domain and Genome References
Gene Title
Ensembl F54A5.2
Entrez Gene 171678 Entrez gene
SwissProt Q9TYT4 EMBL-EBI
WormBase CE20860 Wormbase
Functional Annotations
Protein Similarities
Method ID Description E-Value
blast AAC78221 Hypothetical protein F54A5.2 [Caenorhabditis elegans] ref|NP_490798.1| F54A5.2 [Caenorhabditis elegans] 0.0
blast AAC78221 Hypothetical protein F54A5.2 [Caenorhabditis elegans] ref|NP_490798.1| F54A5.2 [Caenorhabditis elegans] 1.0E-124
blast AAC78222 Hypothetical protein F54A5.3a [Caenorhabditis elegans] ref|NP_490799.2| F54A5.3a [Caenorhabditis elegans] 1.0E-114
blast CAE61301 Hypothetical protein CBG05129 [Caenorhabditis briggsae] 1.0E-106
blast AAF60493 Abnormal cell migration protein 1, isoform b [Caenorhabditis elegans] ref|NP_001021744.1| abnormal cell MIGration family member (mig-1) [Caenorhabditis elegans] 7.0E-93
Protein Domains
Database ID Description E-Value
Pfam IPR001507 EMBL-EBI Endoglin/CD105 antigen 1.2E-4
Pfam IPR000980 EMBL-EBI SH2 motif 2.4E-12
Pfam IPR001507 EMBL-EBI Endoglin/CD105 antigen 1.2E-4
Pfam IPR006020 EMBL-EBI Phosphotyrosine interaction domain 2.8E-6
Pfam IPR000024 EMBL-EBI Frizzled CRD region 1.0E-68
Trans Membrane
ID Number Of Domains Domain Boundaries
GENEFINDER00000014310 5 10-32,516-538,558-580,587-604,619-636
Sequence
Target Sequence 
>C. ELEGANS:194235_X_AT
gtcgactaccgagttcgtgttctagacggcgacagtttggattcaaagcagctacaacgt
ccgttagcagttggtgatagagtgacgtacacagttgaaatgagcgatgatcagaatgga
cgaatcggaaggtgttgggcgaatgacgggatatccgagctaccactgtcggactcacac
ggatgctctttgcagacttctggggaggtgtggggagactttgaagtgactcgacgcaat
ggtaagaccatcttctacaaccacataaaggcctgggcattcccaacgagcaacgaggtg
aacatcttctgtaaccttcacgtctgtgtcacgtgtacccaggccgcgtgtcgtggacgg
gaacgtcgacataatcctcctcctcagcattcttcaaccgtctctgatcccttctcgtcg
acaatcgacgtgtccgacatctcgccaccgatcgccgtgcgaacatcgttccgtctgaaa
cgggaagctgtcgcacggctagagacatcacaaacaacgtcttccgtttcaacagattct
tcaactaattcgtcttcttcttc

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GTCGACTACCGAGTTCGTGTTCTAG 182 475 467 Antisense
GACGGGATATCCGAGCTACCACTGT 512 377 611 Antisense
CACGGATGCTCTTTGCAGACTTCTG 356 199 644 Antisense
TAAGACCATCTTCTACAACCACATA 571 637 709 Antisense
TAAAGGCCTGGGCATTCCCAACGAG 328 635 732 Antisense
TTCTGTAACCTTCACGTCTGTGTCA 296 689 773 Antisense
CGGGAACGTCGACATAATCCTCCTC 532 1 824 Antisense
CGACAATCGACGTGTCCGACATCTC 412 251 885 Antisense
GTGCGAACATCGTTCCGTCTGAAAC 130 479 923 Antisense
AACGTCTTCCGTTTCAACAGATTCT 169 143 982 Antisense
CTTCAACTAATTCGTCTTCTTCTTC 383 221 1005 Antisense
Sequence Source Affymetrix Proprietary Database