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[188573_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 > 50      6grp_cgc > 89      6grp_total_sub > Hat      6grp_rule_based > S5      4grp_rule_based > L2      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 100
1 2 3 4 range
A 39.9
(-2.9)
A 		117.5
(3)
A 		91.4
(1)
A 		38.2
(-3)
A 		79
B 32.9
(-2.5)
A 		98.8
(3)
A 		88.3
(2.1)
A 		26.7
(-3)
A 		72
C 44
(-3)
A 		126.2
(3)
A 		102.4
(1.3)
A 		50.8
(-2.5)
A 		82
avr 38.9
(-3) 		114.2
(3) 		94
(1.4) 		38.6
(-3) 		76

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 309
1 2 3 4 5 6 range
A 73.2
(-0.6)
A 		104.2
(0.6)
A 		12.9
(-3)
A 		71.6
(-0.7)
A 		160.2
(2.9)
P 		163.8
(3)
P 		151
B 51.6
(-2.4)
A 		29.4
(-3)
A 		67.2
(-1.9)
A 		70.5
(-1.8)
A 		236.2
(3)
P 		166.7
(1)
P 		207
C 12.3
(-3)
A 		83.1
(-1.6)
A 		13.1
(-3)
A 		75.4
(-1.8)
A 		321.5
(3)
P 		93.1
(-1.4)
P 		309
avr 45.7
(-2.6) 		72.2
(-1.8) 		31.1
(-3) 		72.5
(-1.8) 		239.3
(3) 		141.2
(0.2) 		208
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 31
1 2 3 4 range
A 14.5
(-0.3)
A 		25.5
(3)
A 		23.9
(2.5)
A 		5.6
(-3)
A 		20
B 10.5
(-1.5)
A 		24.4
(3)
A 		20.5
(1.7)
A 		5.7
(-3)
A 		19
C 14.6
(-1.7)
A 		36.3
(3)
A 		35.7
(2.9)
A 		8.6
(-3)
A 		28
avr 13.2
(-1.2) 		28.7
(3) 		26.7
(2.5) 		6.6
(-3) 		22

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 101
1 2 3 4 5 6 range
A 13.5
(-1.6)
A 		37
(1.5)
A 		2.8
(-3)
A 		18.1
(-1)
A 		48.3
(3)
P 		39.9
(1.9)
P 		46
B 18
(-2.4)
A 		9.8
(-3)
A 		16.3
(-2.5)
A 		18.7
(-2.4)
A 		96
(3)
P 		62.2
(0.6)
P 		86
C 4.6
(-2.9)
A 		25.3
(-1.7)
A 		3.3
(-3)
A 		15.2
(-2.3)
A 		104
(3)
P 		31.2
(-1.3)
P 		101
avr 12
(-2.6) 		24
(-1.7) 		7.5
(-3) 		17.3
(-2.2) 		82.8
(3) 		44.4
(-0.1) 		75
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 188573_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_061577(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_061577 NCBI Caenorhabditis elegans H17B01.2 (collagen) mRNA, complete cds. 11/11 A 
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
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 H17B01.2
Entrez Gene 186749 Entrez gene
SwissProt O61209 EMBL-EBI
WormBase CE11592 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 AAK39331 Hypothetical protein Y51H7C.13 [Caenorhabditis elegans] ref|NP_493976.2| Y51H7C.13 [Caenorhabditis elegans] 2.0E-31
Protein Domains
Trans Membrane
ID Number Of Domains Domain Boundaries
SNAP00000040926 1 21-38
Sequence
Target Sequence 
>C. ELEGANS:188573_AT
acagtaccacagcaatggaccaccctaccaccaggcccagagccaaccccgggacaagga
ccttctggagaatgctgctacatcgaccttcgcagaatccaggttaccgtatcctgtgga
gtctccattggaaatcagtgctgccatcaatcttgctcgggaacctaccagcgtcaaatc
aacttgaactactacattctaacacaaatcttccgtaacctcccatccagaattcaatgc
tcagaggctgttcgtctgggattagtgagatctacagagattcaaggattttgtacatct
agagtaatcccaggaggtccagtaaaccaaccatcgacagcattcccaccaaacccgaat
ggaccagaagtcccagtgaccacaggaggtcccattcatcctgcctacccaattgtgccg
accagagggtacccaccaactacagtaaccccaccaaacccatatggaccaaaggatgct
tatattacatctgacccaaaacccaactcaggctccacacttgttgcaccatttttcgct

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
ACAGTACCACAGCAATGGACCACCC 226 107 1036 Antisense
ACATCTAGAGTAATCCCAGGAGGTC 579 103 1330 Antisense
GGAGGTCCAGTAAACCAACCATCGA 643 515 1348 Antisense
CCAGTAAACCAACCATCGACAGCAT 451 269 1354 Antisense
CAGAAGTCCCAGTGACCACAGGAGG 267 205 1400 Antisense
ACCACAGGAGGTCCCATTCATCCTG 87 85 1414 Antisense
CTACCCAATTGTGCCGACCAGAGGG 277 225 1440 Antisense
AATTGTGCCGACCAGAGGGTACCCA 334 177 1446 Antisense
GGATGCTTATATTACATCTGACCCA 370 513 1509 Antisense
TATTACATCTGACCCAAAACCCAAC 676 657 1518 Antisense
CACACTTGTTGCACCATTTTTCGCT 436 195 1551 Antisense
Sequence Source Affymetrix Proprietary Database