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[172711_x_at] collagen

Description F59F5.4 /REP_DB=WormBase Gene ID /WP=CE03445 /TR=Q21047 /GB=CAA90658.1 /SUBMIT=HINXTON /CHR=X /FEA=Sanger Annotation /DEF=collagen
Cluster 6grp_total > 83      4grp_total > 31      6grp_total_sub > Hat      6grp_rule_based > S5      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 25
1 2 3 4 range
A 22.2
(3)
P 		1.5
(-3)
A 		1.8
(-2.9)
A 		3.4
(-2.4)
A 		21
B 10
(3)
A 		7.1
(-2.8)
A 		8.1
(-0.8)
A 		7
(-3)
A 		3
C 20.5
(1.4)
A 		3
(-3)
A 		10.3
(-1.1)
A 		26.6
(3)
A 		24
avr 17.6
(3) 		3.9
(-3) 		6.7
(-1.8) 		12.3
(0.7) 		14

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 102
1 2 3 4 5 6 range
A 6.6
(-3)
A 		14.3
(-2)
A 		19.5
(-1.4)
A 		53.6
(3)
P 		13.9
(-2.1)
A 		17.4
(-1.6)
A 		47
B 11.9
(-3)
A 		17.7
(-2.6)
P 		35.4
(-1.5)
A 		39.7
(-1.2)
P 		105.1
(3)
P 		18.2
(-2.6)
M 		93
C 3.6
(-3)
A 		14.8
(-1.9)
A 		18.1
(-1.5)
A 		61.2
(2.9)
M 		62.6
(3)
P 		16.6
(-1.7)
A 		59
avr 7.4
(-3) 		15.6
(-2.1) 		24.3
(-1.1) 		51.5
(2) 		60.5
(3) 		17.4
(-1.9) 		53
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 8
1 2 3 4 range
A 8.1
(3)
P 		0.3
(-3)
A 		0.5
(-2.8)
A 		0.5
(-2.8)
A 		8
B 3.2
(3)
A 		1.8
(-1.9)
A 		1.9
(-1.6)
A 		1.5
(-3)
A 		2
C 6.8
(3)
A 		0.9
(-3)
A 		3.6
(-0.3)
A 		4.5
(0.7)
A 		6
avr 6
(3) 		1
(-3) 		2
(-1.8) 		2.2
(-1.6) 		5

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 42
1 2 3 4 5 6 range
A 1.2
(-3)
A 		5.1
(-1.1)
A 		4.3
(-1.5)
A 		13.6
(3)
P 		4.2
(-1.5)
A 		4.2
(-1.5)
A 		12
B 4.1
(-3)
A 		5.9
(-2.7)
P 		8.6
(-2.3)
A 		10.5
(-2)
P 		42.7
(3)
P 		6.8
(-2.6)
M 		39
C 1.3
(-3)
A 		4.5
(-2)
A 		4.6
(-2)
A 		12.3
(0.5)
M 		20.3
(3)
P 		5.6
(-1.6)
A 		19
avr 2.2
(-3) 		5.2
(-2.1) 		5.8
(-1.9) 		12.1
(-0.1) 		22.4
(3) 		5.5
(-2) 		20
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 172711_x_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.16802
Sequence Type Exemplar sequence
Representative Public ID F59F5.4 NCBI
Target Description F59F5.4 /REP_DB=WormBase Gene ID /WP=CE03445 /TR=Q21047 /GB=CAA90658.1 /SUBMIT=HINXTON /CHR=X /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_077365(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_077365 NCBI Caenorhabditis elegans F59F5.4 (collagen) mRNA, complete cds. 11/11 None
F59F5.4 ENSEMBL cdna:known chromosome:CEL140:X:10542968:10543336:1 gene:F59F5.4 11/11 None
Annotation Notes
Cross Hybridizing mRNA Matched Probes Nature of Assignment Related Probesets by Grade
SNAP00000005592 4/11 Cross Hyb Matching Probes None
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrX:10542967-10543336(+) 100.0 100.0
Public Domain and Genome References
Gene Title collagen
Ensembl F59F5.4
Entrez Gene 186635 Entrez gene
SwissProt Q21047 EMBL-EBI
WormBase CE03445 Wormbase
Functional Annotations
Protein Similarities
Method ID Description E-Value
blast CAA90658 Hypothetical protein F59F5.4 [Caenorhabditis elegans] ref|NP_509766.1| F59F5.4 [Caenorhabditis elegans] 6.0E-48
blast CAE60799 Hypothetical protein CBG04491 [Caenorhabditis briggsae] 1.0E-14
Protein Domains
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_509766.1 1 13-35
F59F5.4 1 13-35
Sequence
Target Sequence 
>C. ELEGANS:172711_X_AT
tactcgaaaatatgcataccagacagttttggcaattgcagcaacattatccatcatttc
tgtaataacaattttcatgacattcccatgtttctacacttattttgcaagggtaaaaat
ggatttgcaacatgaaatgaagttttgcaagaaatctgccgaaaaagtgttctactttgt
taatgaagtaggatactttgatcgaaaaagagaaatgagtcttgatatttcacaatgcca
a

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
TACTCGAAAATATGCATACCAGACA 425 645 21 Antisense
ACCAGACAGTTTTGGCAATTGCAGC 556 81 38 Antisense
TGCAGCAACATTATCCATCATTTCT 79 579 57 Antisense
TATCCATCATTTCTGTAATAACAAT 196 657 68 Antisense
ATTTTCATGACATTCCCATGTTTCT 367 15 91 Antisense
ACATTCCCATGTTTCTACACTTATT 385 105 100 Antisense
GTTTCTACACTTATTTTGCAAGGGT 294 447 110 Antisense
AGTTTTGCAAGAAATCTGCCGAAAA 577 63 161 Antisense
AATCTGCCGAAAAAGTGTTCTACTT 93 169 173 Antisense
AAGTGTTCTACTTTGTTAATGAAGT 67 159 185 Antisense
GAGTCTTGATATTTCACAATGCCAA 465 399 237 Antisense
Sequence Source Affymetrix Proprietary Database