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[188574_s_at] collagen

Description H17B01.2 /REP_DB=WormBase Gene ID /WP=CE11592 /TR=O61209 /GB=AAK31537.1 /SUBMIT=ST.LOUIS /CHR=2 /FEA=Sanger Annotation /DEF=collagen
Cluster 6grp_total > 94      4grp_total > 15      6grp_cgc > 89      6grp_total_sub > Hat      6grp_rule_based > S5      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 55
1 2 3 4 range
A 6.5
(-1.4)
A 		4.1
(-3)
A 		8.3
(-0.3)
A 		13.3
(3)
A 		9
B 49.5
(3)
A 		4.4
(-3)
A 		10.3
(-2.2)
A 		5.3
(-2.9)
A 		45
C 18.2
(-1.5)
A 		5.7
(-2.8)
A 		4.1
(-3)
A 		59.3
(3)
A 		55
avr 24.7
(2.6) 		4.7
(-3) 		7.6
(-2.2) 		26
(3) 		21

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 1629
1 2 3 4 5 6 range
A 4
(-3)
A 		7.7
(-3)
A 		14.9
(-2.9)
A 		234.4
(-1.8)
A 		1147.5
(3)
P 		607.4
(0.2)
P 		1144
B 10.5
(-3)
A 		7.2
(-3)
A 		5.6
(-3)
A 		149.2
(-2.3)
P 		1251.3
(3)
P 		456.7
(-0.8)
P 		1246
C 9.1
(-3)
A 		6
(-3)
A 		9.2
(-3)
A 		166.9
(-2.4)
A 		1632.8
(3)
P 		345.3
(-1.7)
P 		1627
avr 7.9
(-3) 		7
(-3) 		9.9
(-3) 		183.5
(-2.2) 		1343.9
(3) 		469.8
(-0.9) 		1337
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 15
1 2 3 4 range
A 2.4
(3)
A 		0.9
(-3)
A 		2.2
(2.2)
A 		2
(1.4)
A 		2
B 15.8
(3)
A 		1.1
(-3)
A 		2.4
(-2.5)
A 		1.1
(-3)
A 		15
C 6
(0.2)
A 		1.6
(-2.9)
A 		1.4
(-3)
A 		10
(3)
A 		9
avr 8.1
(3) 		1.2
(-3) 		2
(-2.3) 		4.4
(-0.2) 		7

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 528
1 2 3 4 5 6 range
A 0.7
(-3)
A 		2.8
(-3)
A 		3.2
(-3)
A 		59.4
(-2)
A 		346.3
(3)
P 		147.9
(-0.4)
P 		346
B 3.7
(-3)
A 		2.4
(-3)
A 		1.4
(-3)
A 		39.5
(-2.5)
P 		508.4
(3)
P 		170.3
(-1)
P 		507
C 3.4
(-3)
A 		1.8
(-3)
A 		2.4
(-3)
A 		33.6
(-2.6)
A 		528.3
(3)
P 		115.6
(-1.7)
P 		527
avr 2.6
(-3) 		2.3
(-3) 		2.3
(-3) 		44.2
(-2.5) 		461
(3) 		144.6
(-1.1) 		459
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 188574_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.5515
Sequence Type Exemplar sequence
Representative Public ID H17B01.2 NCBI
Target Description H17B01.2 /REP_DB=WormBase Gene ID /WP=CE11592 /TR=O61209 /GB=AAK31537.1 /SUBMIT=ST.LOUIS /CHR=2 /FEA=Sanger Annotation /DEF=collagen
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_061576(11), NM_061577(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_061576 NCBI Caenorhabditis elegans Y51H7C.1 (Y51H7C.1) mRNA, complete cds. 11/11 A 
NM_061577 NCBI Caenorhabditis elegans H17B01.2 (collagen) mRNA, complete cds. 11/11 A 
SNAP00000035536 ENSEMBL cdna:SNAP chromosome:CEL140:II:1461925:1469560:1 11/11 None
GENEFINDER00000035538 ENSEMBL cdna:GeneFinder chromosome:CEL140:II:1467753:1469560:1 11/11 None
SNAP00000040926 ENSEMBL cdna:SNAP chromosome:CEL140:II:1470210:1472266:1 11/11 None
GENEFINDER00000040937 ENSEMBL cdna:GeneFinder chromosome:CEL140:II:1470571:1472266:1 11/11 None
Y51H7C.1 ENSEMBL cdna:known chromosome:CEL140:II:1467733:1469600:1 gene:Y51H7C.1 11/11 A 
H17B01.2 ENSEMBL cdna:known chromosome:CEL140:II:1470046:1472266:1 gene:H17B01.2 11/11 A 
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
chrII:1470044-1472265(+) 97.8 100.0
Public Domain and Genome References
Gene Title collagen

Gene Symbol col-70
Ensembl Y51H7C.1
H17B01.2
Entrez Gene 186749 Entrez gene
190173 Entrez gene
SwissProt O61209 EMBL-EBI
Q9N3I0 EMBL-EBI
WormBase CE11592 Wormbase
CE22358 Wormbase
Functional Annotations
Protein Similarities
Method ID Description E-Value
blast AAK31537 Collagen protein 70 [Caenorhabditis elegans] ref|NP_493978.1| H17B01.2 [Caenorhabditis elegans] 1.0E-130
blast AAK39336 Hypothetical protein Y51H7C.1 [Caenorhabditis elegans] ref|NP_493977.1| Y51H7C.1 [Caenorhabditis elegans] 1.0E-113
blast AAK39336 Hypothetical protein Y51H7C.1 [Caenorhabditis elegans] ref|NP_493977.1| Y51H7C.1 [Caenorhabditis elegans] 1.0E-75
Protein Domains
Trans Membrane
ID Number Of Domains Domain Boundaries
SNAP00000040926 1 21-38
Sequence
Target Sequence 
>C. ELEGANS:188574_S_AT
ctacatcgaccttcgcagaatccaggttaccgtatcctgtggagtctccattggaaatca
gtgctgccatcaatcttgctcgggaacctaccagcgtcaaatcaacttgaactactacat
tctaacacaaatcttccgtaacctcccatccagaattcaatgctcagaggctgttcgtct
gggattagtgagatctacagagattcaaggattttgtacatctagagtaatcccaggagg
tccagtaaaccaaccatcgacagcattcccaccaaacccgaatggaccagaagtcccagt
gaccacaggaggtcccattcatcctgcctacccaattgtgccgaccagagggtacccacc
aactacagtaaccccaccaaacccatatggaccaaagg

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
CTACATCGACCTTCGCAGAATCCAG 163 225 1113 Antisense
CGTATCCTGTGGAGTCTCCATTGGA 428 247 1143 Antisense
TGGAGTCTCCATTGGAAATCAGTGC 457 549 1152 Antisense
AATCAGTGCTGCCATCAATCTTGCT 125 171 1168 Antisense
GAACCTACCAGCGTCAAATCAACTT 23 345 1196 Antisense
AAATCAACTTGAACTACTACATTCT 264 117 1211 Antisense
ACTACATTCTAACACAAATCTTCCG 554 99 1226 Antisense
TCTAACACAAATCTTCCGTAACCTC 692 607 1233 Antisense
TAACCTCCCATCCAGAATTCAATGC 465 637 1251 Antisense
GCTGTTCGTCTGGGATTAGTGAGAT 467 295 1282 Antisense
CCACCAAACCCATATGGACCAAAGG 548 261 1486 Antisense
Sequence Source Affymetrix Proprietary Database