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[192755_s_at] cuticle collagen (CC02)

Description W01B6.7 /REP_DB=WormBase Gene ID /WP=CE03759 /GEN=col-2 /TR=SW:P17656 /GB=CAA92620.1 /SUBMIT=HINXTON /CHR=4 /FEA=Sanger Annotation /DEF=cuticle collagen (CC02)
Cluster 6grp_total > 83      4grp_total > 41      6grp_cgc > 87      6grp_cgc_sub > 05      6grp_total_sub > Hat      6grp_rule_based > S5      4grp_rule_based > L2      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 289
1 2 3 4 range
A 36.6
(-3)
A 		325.2
(3)
A 		196.1
(0.3)
A 		136.3
(-0.9)
A 		289
B 87.4
(-3)
A 		177.6
(0.1)
A 		263.2
(3)
A 		93.7
(-2.8)
P 		176
C 96.7
(-3)
A 		220.1
(3)
A 		212.5
(2.6)
A 		115.3
(-2.1)
A 		123
avr 73.6
(-3) 		241
(3) 		223.9
(2.4) 		115.1
(-1.5) 		167

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 27297
1 2 3 4 5 6 range
A 75.5
(-3)
A 		110.9
(-3)
A 		190.1
(-3)
P 		22543.5
(2.3)
P 		25357.1
(3)
P 		8500.1
(-1)
P 		25282
B 112.9
(-3)
A 		154.1
(-3)
A 		208.6
(-3)
P 		19755
(2.1)
P 		23194
(3)
P 		7037.3
(-1.2)
P 		23081
C 107.9
(-3)
A 		126.5
(-3)
A 		193
(-3)
P 		19385.3
(1.2)
P 		27372.4
(3)
P 		5559.8
(-1.8)
P 		27265
avr 98.8
(-3) 		130.5
(-3) 		197.2
(-3) 		20561.3
(1.9) 		25307.8
(3) 		7032.4
(-1.3) 		25209
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 61
1 2 3 4 range
A 13.3
(-3)
A 		70.6
(3)
A 		51.3
(1)
A 		19.9
(-2.3)
A 		57
B 27.9
(-1.8)
A 		43.9
(0.5)
A 		61
(3)
A 		20
(-3)
P 		41
C 32
(-1.6)
A 		63.3
(1.8)
A 		74.1
(3)
A 		19.4
(-3)
A 		55
avr 24.4
(-2.3) 		59.3
(2.6) 		62.1
(3) 		19.8
(-3) 		42

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 9410
1 2 3 4 5 6 range
A 13.9
(-3)
A 		39.4
(-3)
A 		41.4
(-3)
P 		5717.6
(1.5)
P 		7651.7
(3)
P 		2069.5
(-1.4)
P 		7638
B 39.3
(-3)
A 		51.3
(-3)
A 		50.6
(-3)
P 		5232.4
(0.3)
P 		9423.4
(3)
P 		2624.2
(-1.3)
P 		9384
C 40
(-3)
A 		38.6
(-3)
A 		49.1
(-3)
P 		3898.4
(-0.4)
P 		8857.3
(3)
P 		1861.2
(-1.8)
P 		8819
avr 31.1
(-3) 		43.1
(-3) 		47
(-3) 		4949.5
(0.4) 		8644.1
(3) 		2185
(-1.5) 		8613
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 192755_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.9928
Sequence Type Exemplar sequence
Representative Public ID W01B6.7 NCBI
Target Description W01B6.7 /REP_DB=WormBase Gene ID /WP=CE03759 /GEN=col-2 /TR=SW:P17656 /GB=CAA92620.1 /SUBMIT=HINXTON /CHR=4 /FEA=Sanger Annotation /DEF=cuticle collagen (CC02)
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_069428(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_069428 NCBI Caenorhabditis elegans COLlagen family member (col-2) (col-2) mRNA, complete cds. 11/11 None
SNAP00000040433 ENSEMBL cdna:SNAP chromosome:CEL140:IV:10084457:10085847:-1 11/11 None
GENEFINDER00000040439 ENSEMBL cdna:GeneFinder chromosome:CEL140:IV:10084457:10085409:-1 11/11 None
W01B6.7 ENSEMBL cdna:known chromosome:CEL140:IV:10084426:10085410:-1 gene:W01B6.7 11/11 None
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
chrIV:10084462-10085415(-) 86.31 100.0
Public Domain and Genome References
Gene Title cuticle collagen (CC02)
Gene Symbol col-2
Ensembl W01B6.7
Entrez Gene 177872 Entrez gene
SwissProt P17656 EMBL-EBI
WormBase CE03759 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
GO Molecular Function (view graph)
ID Description Evidence Links
42302 structural constituent of cuticle inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast CAA92620 Hypothetical protein W01B6.7 [Caenorhabditis elegans] ref|NP_501829.1| COLlagen family member (col-2) [Caenorhabditis elegans] gb|AAP97869.1| COLlagen structural gene, probable dorsal and ventral cuticle component, from embryo to adult, but maximal in dauer (28.0 kD) (col-2) [Caenorhabditis elegans] sp|P17656|COL2_CAEEL Cuticle collagen 2 precursor emb|CAA23464.1| unnamed protein product [Caenorhabditis elegans] gb|AAA27990.1| collagen 5.0E-30
blast CAA92620 Hypothetical protein W01B6.7 [Caenorhabditis elegans] ref|NP_501829.1| COLlagen family member (col-2) [Caenorhabditis elegans] gb|AAP97869.1| COLlagen structural gene, probable dorsal and ventral cuticle component, from embryo to adult, but maximal in dauer (28.0 kD) (col-2) [Caenorhabditis elegans] sp|P17656|COL2_CAEEL Cuticle collagen 2 precursor emb|CAA23464.1| unnamed protein product [Caenorhabditis elegans] gb|AAA27990.1| collagen 6.0E-30
blast CAE59934 Hypothetical protein CBG03420 [Caenorhabditis briggsae] 5.0E-29
blast CAE59934 Hypothetical protein CBG03420 [Caenorhabditis briggsae] 6.0E-29
blast CAE61462 Hypothetical protein CBG05354 [Caenorhabditis briggsae] 1.0E-15
Protein Domains
Database ID Description E-Value
Pfam IPR002486 EMBL-EBI Nematode cuticle collagen, N-terminal 1.1E-14
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 3.1E-6
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 0.0019
Pfam IPR002486 EMBL-EBI Nematode cuticle collagen, N-terminal 1.1E-14
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 3.1E-6
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 0.0019
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_501829.1 1 12-34
W01B6.7 1 12-34
SNAP00000040433 1 39-61
GENEFINDER00000040439 1 12-34
Sequence
Target Sequence 
>C. ELEGANS:192755_S_AT
aggcggcggaggatgtgatggatgctgcaatcctggaccaccaggaccaggtggatctcc
cggaaaaccaggaaagccaggaaagccaggagctccaggagccccaggaaatccaggaaa
aggagcatcagctccatgtgagccagttactcaaccaccatgccaaccatgcccaggagg
accaccaggaccagctggtccagccggaccaccaggaccaccgggaccagatggaaaccc
aggatcaccagccggaccatcaggcccaggaccagccggaccaccaggaccagcaggacc
agccggaaacgacggagccccaggagccccaggaggaccaggagaaccaggagcatccga
gcaaggaggaccaggagagccaggaccagctggaccaccaggaccagccggaccagccgg
aaatgacggagccccaggaaccggaggaccaggaccagctggaccaaagggaccaccagg
agctgctggagcaccaggagctgacggaaacccaggaggaccaggaaccgctggaaagcc
aggaggagaaggagagaagggaatctgccccaagtattgtgctatc

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
AGGCGGCGGAGGATGTGATGGATGC 127 55 291 Antisense
GGCGGAGGATGTGATGGATGCTGCA 397 541 295 Antisense
GATGGATGCTGCAATCCTGGACCAC 521 407 307 Antisense
CCAGGTGGATCTCCCGGAAAACCAG 273 269 337 Antisense
TCCATGTGAGCCAGTTACTCAACCA 435 589 423 Antisense
TGTGAGCCAGTTACTCAACCACCAT 403 555 427 Antisense
CAGGAGAACCAGGAGCATCCGAGCA 409 209 629 Antisense
GAACCAGGAGCATCCGAGCAAGGAG 476 345 634 Antisense
GAGCATCCGAGCAAGGAGGACCAGG 395 387 641 Antisense
GGACCAGGAACCGCTGGAAAGCCAG 618 519 808 Antisense
AATCTGCCCCAAGTATTGTGCTATC 531 169 852 Antisense
Sequence Source Affymetrix Proprietary Database