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[190348_at] collagen

Description C09G5.6 /REP_DB=WormBase Gene ID /WP=CE01486 /GEN=bli-1 /TR=SW:Q09457 /GB=CAA86755.1 /SUBMIT=HINXTON /CHR=2 /FEA=Sanger Annotation /DEF=collagen
Cluster 6grp_total > 93      4grp_total > 16      6grp_cgc > 88      6grp_total_sub > Hat      6grp_rule_based > S5      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 72
1 2 3 4 range
A 6.7
(-3)
A 		14.1
(-2.4)
A 		21.6
(-1.7)
A 		75.4
(3)
A 		69
B 6.6
(-2.8)
A 		5.9
(-3)
A 		14.6
(-0.4)
A 		25.7
(3)
A 		20
C 6.4
(-1.9)
A 		13.2
(0.7)
A 		19
(3)
A 		3.7
(-3)
A 		15
avr 6.6
(-3) 		11.1
(-2) 		18.4
(-0.5) 		34.9
(3) 		28

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 746
1 2 3 4 5 6 range
A 2.9
(-3)
A 		8.2
(-2.9)
A 		4.9
(-3)
A 		251.7
(-0)
P 		503.2
(3)
P 		108
(-1.7)
P 		500
B 6
(-3)
A 		20
(-2.8)
A 		10.3
(-2.9)
A 		259.2
(0.2)
P 		481.1
(3)
P 		92.7
(-1.9)
P 		475
C 3.6
(-3)
A 		58.3
(-2.6)
A 		24.4
(-2.8)
A 		200.8
(-1.4)
P 		749.1
(3)
P 		80
(-2.4)
P 		746
avr 4.2
(-3) 		28.8
(-2.7) 		13.2
(-2.9) 		237.2
(-0.6) 		577.8
(3) 		93.6
(-2.1) 		574
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 10
1 2 3 4 range
A 2.4
(-3)
A 		3.1
(-2.5)
A 		5.6
(-0.8)
A 		11
(3)
A 		9
B 2.1
(-2.1)
A 		1.5
(-3)
A 		3.4
(-0.2)
A 		5.5
(3)
A 		4
C 2.1
(-1.5)
A 		3.8
(0.2)
A 		6.6
(3)
A 		0.6
(-3)
A 		6
avr 2.2
(-3) 		2.8
(-2) 		5.2
(2.1) 		5.7
(3) 		4

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 242
1 2 3 4 5 6 range
A 0.5
(-3)
A 		2.9
(-2.9)
A 		1.1
(-3)
A 		63.8
(-0.5)
P 		151.9
(3)
P 		26.3
(-2)
P 		151
B 2.1
(-3)
A 		6.6
(-2.9)
A 		2.5
(-3)
A 		68.7
(-0.9)
P 		195.5
(3)
P 		34.6
(-2)
P 		193
C 1.3
(-3)
A 		17.8
(-2.6)
A 		6.2
(-2.9)
A 		40.4
(-2)
P 		242.4
(3)
P 		26.8
(-2.4)
P 		241
avr 1.3
(-3) 		9.1
(-2.8) 		3.3
(-2.9) 		57.6
(-1.3) 		196.6
(3) 		29.2
(-2.1) 		195
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 190348_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.3277
Sequence Type Exemplar sequence
Representative Public ID C09G5.6 NCBI
Target Description C09G5.6 /REP_DB=WormBase Gene ID /WP=CE01486 /GEN=bli-1 /TR=SW:Q09457 /GB=CAA86755.1 /SUBMIT=HINXTON /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_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 11/11 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:10708921-10711955(+) 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:190348_AT
ttgagatcatcagacacccagaaagaggatacgatcgtcgtcagccatcttatgaggatt
cgaagccaagacaagaggagccaagacgatatgaaacggaagctgagccacgctatgaag
aagttccacggaaagagacacatcctccaggatttggaagaccaaaatctgaggaaaatc
caagggaaacaggaagaacttactcagaagaagcaatgccacctgtgcaacaaactgaga
aatataatggagataaaagaaagaagaatcagccagagtatgaggatatttcaaaaccag
aagaggataaagaaagagcaatggaaaaacaccacaagaagcctaataagttccaagaaa
aacaatgggaagagcatagaaagagccaggaactcaggaattcgagagagcatggaggac
aagttccagt

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
TTGAGATCATCAGACACCCAGAAAG 652 703 2276 Antisense
GAGGATACGATCGTCGTCAGCCATC 472 403 2300 Antisense
GTCGTCAGCCATCTTATGAGGATTC 412 473 2312 Antisense
TGAGGATTCGAAGCCAAGACAAGAG 378 563 2328 Antisense
GAAACGGAAGCTGAGCCACGCTATG 604 355 2368 Antisense
GCCACGCTATGAAGAAGTTCCACGG 655 277 2382 Antisense
GGAAAGAGACACATCCTCCAGGATT 148 527 2405 Antisense
GAAGCAATGCCACCTGTGCAACAAA 260 341 2485 Antisense
GAAAAACACCACAAGAAGCCTAATA 498 355 2599 Antisense
AGAGCCAGGAACTCAGGAATTCGAG 290 67 2657 Antisense
GAGAGCATGGAGGACAAGTTCCAGT 254 395 2681 Antisense
Sequence Source Affymetrix Proprietary Database