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[174152_s_at] collagen

Description C52339_rc /REP_DB=TREMBL Accession /GB=C52339 /CHR=2 /FEA=Genomic Cluster /DEF=C.elegans cDNA clone yk244c3 : 3prime end, single read.
Cluster 6grp_total > 93      4grp_total > 07      6grp_cgc > 88      6grp_total_sub > Hat      6grp_rule_based > S5      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 64
1 2 3 4 range
A 26.6
(-1.6)
A 		34.1
(2.1)
A 		36
(3)
A 		23.7
(-3)
A 		12
B 45.3
(3)
A 		40.9
(1.8)
A 		22.7
(-3)
A 		41
(1.9)
A 		23
C 62.3
(1.7)
A 		12.7
(-3)
A 		42.1
(-0.2)
A 		76.7
(3)
A 		64
avr 44.7
(2.2) 		29.2
(-3) 		33.6
(-1.5) 		47.1
(3) 		18

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 1506
1 2 3 4 5 6 range
A 31.1
(-3)
A 		39.6
(-3)
A 		73.6
(-2.8)
A 		432.7
(-1.4)
P 		1509.3
(3)
P 		232
(-2.2)
P 		1478
B 71.8
(-2.6)
A 		6.1
(-3)
A 		3.5
(-3)
A 		680.4
(0.9)
P 		1054.6
(3)
P 		316.2
(-1.2)
P 		1051
C 3.4
(-3)
A 		37
(-2.8)
A 		62.6
(-2.7)
A 		263.2
(-1.8)
P 		1267.8
(3)
P 		218.1
(-2)
P 		1264
avr 35.4
(-3) 		27.6
(-3) 		46.6
(-2.9) 		458.8
(-0.9) 		1277.2
(3) 		255.4
(-1.9) 		1250
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 17
1 2 3 4 range
A 9.7
(3)
A 		7.4
(0.8)
A 		9.4
(2.7)
A 		3.5
(-3)
A 		6
B 14.4
(3)
A 		10.1
(0.2)
A 		5.3
(-3)
A 		8.7
(-0.8)
A 		9
C 20.6
(3)
A 		3.6
(-3)
A 		14.7
(0.9)
A 		12.9
(0.3)
A 		17
avr 14.9
(3) 		7
(-3) 		9.8
(-0.9) 		8.4
(-1.9) 		8

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 455
1 2 3 4 5 6 range
A 5.7
(-3)
A 		14.1
(-2.9)
A 		16
(-2.9)
A 		109.7
(-1.6)
P 		455.5
(3)
P 		56.5
(-2.3)
P 		450
B 25
(-2.7)
A 		2
(-3)
A 		0.8
(-3)
A 		180.2
(-0.5)
P 		428.5
(3)
P 		117.9
(-1.4)
P 		428
C 1.2
(-3)
A 		11.3
(-2.9)
A 		15.9
(-2.8)
A 		52.9
(-2.2)
P 		410.3
(3)
P 		73
(-1.9)
P 		409
avr 10.6
(-3) 		9.1
(-3) 		10.9
(-3) 		114.3
(-1.5) 		431.4
(3) 		82.5
(-2) 		422
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 174152_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.20613
Sequence Type Exemplar sequence
Representative Public ID C52339 NCBI
Target Description C52339_rc /REP_DB=TREMBL Accession /GB=C52339 /CHR=2 /FEA=Genomic Cluster /DEF=C.elegans cDNA clone yk244c3 : 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_063910(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_063910 NCBI Caenorhabditis elegans C09G5.6 (collagen) mRNA, complete cds. 11/11 A 
SNAP00000014223 ENSEMBL cdna:SNAP chromosome:CEL140:II:10708925:10716248:1 10/11 None
GENEFINDER00000014235 ENSEMBL cdna:GeneFinder chromosome:CEL140:II:10708925:10711958:1 11/11 None
C09G5.6 ENSEMBL cdna:known chromosome:CEL140:II:10708871:10712036:1 gene:C09G5.6 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:10711708-10711988(+) 100.0 100.0
Public Domain and Genome References
Gene Title collagen
Gene Symbol bli-1
Ensembl C09G5.6
Entrez Gene 174653 Entrez gene
WormBase CE35827 Wormbase
Functional Annotations
Gene Ontology
GO Biological Process (view graph)
ID Description Evidence Links
6817 phosphate transport inferred from electronic annotation QuickGO AmiGO
GO Cellular Component (view graph)
ID Description Evidence Links
5737 cytoplasm inferred from electronic annotation QuickGO AmiGO
5578 extracellular matrix (sensu Metazoa) inferred from sequence similarity QuickGO AmiGO
GO Molecular Function (view graph)
ID Description Evidence Links
42302 structural constituent of cuticle inferred from electronic annotation QuickGO AmiGO
42329 structural constituent of cuticle (sensu Nematoda) inferred from sequence similarity QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast CAA86755 Hypothetical protein C09G5.6 [Caenorhabditis elegans] ref|NP_496311.2| C09G5.6 [Caenorhabditis elegans] 0.0
blast Q09457 Cuticle collagen bli-1 0.0
blast CAE59617 Hypothetical protein CBG03026 [Caenorhabditis briggsae] 0.0
Protein Domains
Database ID Description E-Value
Pfam IPR002486 EMBL-EBI Nematode cuticle collagen, N-terminal 5.7E-21
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 0.0015
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 3.5E-12
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 2.1E-6
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_496311.2 1 7-29
C09G5.6 1 7-29
SNAP00000014223 1 7-29
GENEFINDER00000014235 1 7-29
Sequence
Target Sequence 
>C. ELEGANS:174152_S_AT
cagttgaaacttccgtaccaatgcaacaagtaaaacctgaatcctctgcagaagaaaagc
cagttccacctgtacatgacaacttccagtcatccgagaaaagagctttttccaacgaaa
acccactaccatcagaacaaattccatacagaaggagaaatcgcttttacaggaaccact
attatgagaagtttct

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
CAGTTGAAACTTCCGTACCAATGCA 470 205 57 Antisense
GAAACTTCCGTACCAATGCAACAAG 230 357 62 Antisense
ACAAGTAAAACCTGAATCCTCTGCA 150 111 82 Antisense
TGAATCCTCTGCAGAAGAAAAGCCA 673 573 94 Antisense
AGAAAAGCCAGTTCCACCTGTACAT 334 73 109 Antisense
GTTCCACCTGTACATGACAACTTCC 8 441 119 Antisense
GACAACTTCCAGTCATCCGAGAAAA 36 367 134 Antisense
GAAAACCCACTACCATCAGAACAAA 230 355 173 Antisense
ACCATCAGAACAAATTCCATACAGA 133 87 184 Antisense
GAAATCGCTTTTACAGGAACCACTA 563 361 213 Antisense
GGAACCACTATTATGAGAAGTTTCT 210 531 228 Antisense
Sequence Source Affymetrix Proprietary Database