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[188275_at] collagen

Description C01H6.1 /REP_DB=WormBase Gene ID /WP=CE05184 /TR=Q17582 /GB=CAA95780.1 /SUBMIT=HINXTON /CHR=1 /FEA=Sanger Annotation /DEF=collagen
Cluster 6grp_total > 92      4grp_total > 50      6grp_cgc > 98      4grp_rule_based > L2      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 185
1 2 3 4 range
A 43.3
(-2.3)
A 		196
(3)
P 		163.6
(1.9)
A 		23.3
(-3)
A 		173
B 19.1
(-2.7)
A 		177.2
(3)
A 		174.8
(2.9)
A 		10.6
(-3)
A 		167
C 75.1
(-0.7)
A 		181.3
(3)
A 		158.5
(2.2)
A 		10.7
(-3)
A 		171
avr 45.8
(-1.9) 		184.8
(3) 		165.6
(2.3) 		14.9
(-3) 		170

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 271
1 2 3 4 5 6 range
A 15.2
(-3)
A 		133.5
(1)
A 		52.1
(-1.8)
A 		193
(3)
P 		192.3
(3)
P 		77.9
(-0.9)
A 		178
B 55.5
(-3)
A 		155.9
(0.3)
A 		84.7
(-2)
A 		133.2
(-0.5)
A 		239.6
(3)
P 		94.7
(-1.7)
A 		184
C 53.3
(-2.7)
A 		118.1
(-1.1)
A 		118.3
(-1.1)
A 		199.4
(0.9)
P 		286.4
(3)
P 		39.2
(-3)
A 		247
avr 41.3
(-3) 		135.8
(-0.1) 		85
(-1.7) 		175.2
(1.1) 		239.4
(3) 		70.6
(-2.1) 		198
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 53
1 2 3 4 range
A 15.8
(-1.1)
A 		42.6
(3)
P 		42.8
(3)
A 		3.4
(-3)
A 		39
B 6.1
(-2.5)
A 		43.8
(3)
A 		40.5
(2.5)
A 		2.3
(-3)
A 		42
C 24.9
(-0.4)
A 		52.1
(2.7)
A 		55.2
(3)
A 		1.8
(-3)
A 		53
avr 15.6
(-1.2) 		46.2
(3) 		46.2
(3) 		2.5
(-3) 		44

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 95
1 2 3 4 5 6 range
A 2.8
(-3)
A 		47.5
(1.9)
A 		11.3
(-2.1)
A 		48.9
(2)
P 		58
(3)
P 		19
(-1.2)
A 		55
B 19.3
(-3)
A 		51.9
(-0.5)
A 		20.6
(-2.9)
A 		35.3
(-1.8)
A 		97.4
(3)
P 		35.3
(-1.8)
A 		78
C 19.8
(-2.5)
A 		36
(-1.3)
A 		30.1
(-1.7)
A 		40.1
(-1)
P 		92.7
(3)
P 		13.1
(-3)
A 		80
avr 14
(-3) 		45.1
(-0.3) 		20.7
(-2.4) 		41.4
(-0.6) 		82.7
(3) 		22.5
(-2.3) 		69
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 188275_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.515
Sequence Type Exemplar sequence
Representative Public ID C01H6.1 NCBI
Target Description C01H6.1 /REP_DB=WormBase Gene ID /WP=CE05184 /TR=Q17582 /GB=CAA95780.1 /SUBMIT=HINXTON /CHR=1 /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_059634(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_059634 NCBI Caenorhabditis elegans C01H6.1 (collagen) mRNA, complete cds. 11/11 None
SNAP00000008115 ENSEMBL cdna:SNAP chromosome:CEL140:I:7210373:7211639:-1 11/11 None
GENEFINDER00000008127 ENSEMBL cdna:GeneFinder chromosome:CEL140:I:7210373:7211639:-1 11/11 None
C01H6.1 ENSEMBL cdna:known chromosome:CEL140:I:7210373:7211639:-1 gene:C01H6.1 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
chrI:7210303-7211570(-) 100.0 100.0
Public Domain and Genome References
Gene Title collagen
Gene Symbol col-61
Ensembl C01H6.1
Entrez Gene 182090 Entrez gene
SwissProt Q17582 EMBL-EBI
WormBase CE05184 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 CAA95780 Hypothetical protein C01H6.1 [Caenorhabditis elegans] ref|NP_492035.1| C01H6.1 [Caenorhabditis elegans] 1.0E-123
blast CAE74251 Hypothetical protein CBG21938 [Caenorhabditis briggsae] 1.0E-104
blast CAE64784 Hypothetical protein CBG09577 [Caenorhabditis briggsae] 8.0E-44
Protein Domains
Database ID Description E-Value
Pfam IPR002486 EMBL-EBI Nematode cuticle collagen, N-terminal 1.6E-22
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 0.0018
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 1.7E-12
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 0.0011
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 2.2E-4
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_492035.1 1 7-29
C01H6.1 1 7-29
SNAP00000008115 1 7-29
GENEFINDER00000008127 1 7-29
Sequence
Target Sequence 
>C. ELEGANS:188275_AT
ggcccaccaggaaactctggttctccaggaaatccaggatcacgtggagtacctggtgaa
gataatcatcagatatatgaaccaatacaatgcccacttccatcacgtgattgcattatt
tgccctgtaggactcccaggttatccagggcgagatggtcttccaggagagccaggtcct
aatggaaaaccaggaaatccgggatatagaggggaagatggaaagccagggcgtccaggt
gaacctggctccagtggattaccaggcaggccaggatctgatggaaaaccgggacttcct
ggaagagatgggaagaaaggaataggattgcctggaagaatgggtagacctggattcgct
ggaaaagaaggccaaccaggtattaatggaaaaccaggtcgaatgggattgcctggtcca
gccgggcctgaaggaaagcctggatatcctggaatgttgggaagggatggaattccagga
gaaccaggactggctggaggtccaggacctgatgctggttact

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GGCCCACCAGGAAACTCTGGTTCTC 543 541 337 Antisense
TGAACCAATACAATGCCCACTTCCA 602 573 414 Antisense
CCCACTTCCATCACGTGATTGCATT 672 257 429 Antisense
TGCATTATTTGCCCTGTAGGACTCC 336 579 448 Antisense
GTAGGACTCCCAGGTTATCCAGGGC 446 453 463 Antisense
ATCCAGGGCGAGATGGTCTTCCAGG 403 39 479 Antisense
GGCGTCCAGGTGAACCTGGCTCCAG 94 541 566 Antisense
GGCTCCAGTGGATTACCAGGCAGGC 159 539 583 Antisense
GTCGAATGGGATTGCCTGGTCCAGC 515 471 734 Antisense
GGTCCAGCCGGGCCTGAAGGAAAGC 632 497 751 Antisense
GGTCCAGGACCTGATGCTGGTTACT 221 491 835 Antisense
Sequence Source Affymetrix Proprietary Database