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[189486_at] cuticle collagen

Description F02D10.1 /REP_DB=WormBase Gene ID /WP=CE03136 /TR=Q19111 /GB=CAA91932.1 /SUBMIT=HINXTON /CHR=X /FEA=Sanger Annotation /DEF=cuticle collagen
Cluster 6grp_total > 93      4grp_total > 10      6grp_cgc > 88      6grp_total_sub > Hat      6grp_rule_based > S5      4grp_rule_based > L4      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 215
1 2 3 4 range
A 29.2
(-3)
A 		42.7
(-2.5)
A 		29
(-3)
A 		210.5
(3)
P 		182
B 40.5
(-3)
A 		82.5
(-1.8)
A 		102.5
(-1.2)
A 		243.8
(3)
P 		203
C 53.8
(-2.9)
P 		100.3
(-1.4)
P 		50.4
(-3)
A 		242
(3)
P 		192
avr 41.2
(-3) 		75.2
(-1.9) 		60.6
(-2.4) 		232.1
(3) 		191

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 7234
1 2 3 4 5 6 range
A 19.4
(-3)
A 		65.3
(-2.9)
A 		22.3
(-3)
A 		3240.7
(0.8)
P 		5092.4
(3)
P 		962.4
(-1.9)
P 		5073
B 19.6
(-3)
A 		36.9
(-3)
A 		78.9
(-2.9)
M 		2330.6
(-0.7)
P 		5969.2
(3)
P 		1101.7
(-1.9)
P 		5950
C 61
(-3)
P 		37.4
(-3)
A 		87.9
(-3)
A 		2254.6
(-1.2)
P 		7253.3
(3)
P 		837.3
(-2.3)
P 		7216
avr 33.3
(-3) 		46.5
(-3) 		63
(-3) 		2608.6
(-0.5) 		6105
(3) 		967.1
(-2.1) 		6072
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 44
1 2 3 4 range
A 10.6
(-2.2)
A 		9.3
(-2.6)
A 		7.6
(-3)
A 		30.8
(3)
P 		23
B 12.9
(-3)
A 		20.4
(-1.8)
A 		23.8
(-1.3)
A 		51.9
(3)
P 		39
C 17.8
(-2.9)
P 		28.8
(-0.1)
P 		17.6
(-3)
A 		40.8
(3)
P 		23
avr 13.8
(-3) 		19.5
(-1.8) 		16.3
(-2.5) 		41.2
(3) 		27

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 2422
1 2 3 4 5 6 range
A 3.6
(-3)
A 		23.2
(-2.9)
A 		4.8
(-3)
A 		821.9
(0.2)
P 		1536.7
(3)
P 		234.3
(-2.1)
P 		1533
B 6.8
(-3)
A 		12.3
(-3)
A 		19.1
(-3)
M 		617.3
(-1.5)
P 		2425.2
(3)
P 		410.8
(-2)
P 		2418
C 22.6
(-3)
P 		11.4
(-3)
A 		22.4
(-3)
A 		453.4
(-1.9)
P 		2347.1
(3)
P 		280.3
(-2.3)
P 		2336
avr 11
(-3) 		15.6
(-3) 		15.4
(-3) 		630.9
(-1.2) 		2103
(3) 		308.5
(-2.1) 		2092
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 189486_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.17362
Sequence Type Exemplar sequence
Representative Public ID F02D10.1 NCBI
Target Description F02D10.1 /REP_DB=WormBase Gene ID /WP=CE03136 /TR=Q19111 /GB=CAA91932.1 /SUBMIT=HINXTON /CHR=X /FEA=Sanger Annotation /DEF=cuticle 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_077846(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_077846 NCBI Caenorhabditis elegans COLlagen family member (col-183) (col-183) mRNA, complete cds. 11/11 None
SNAP00000039146 ENSEMBL cdna:SNAP chromosome:CEL140:X:13466658:13467657:-1 11/11 None
GENEFINDER00000039152 ENSEMBL cdna:GeneFinder chromosome:CEL140:X:13466658:13467657:-1 11/11 None
F02D10.1 ENSEMBL cdna:known chromosome:CEL140:X:13466658:13467657:-1 gene:F02D10.1 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
chrX:13466657-13467657(-) 89.17 100.0
Public Domain and Genome References
Gene Title cuticle collagen
Gene Symbol col-183
Ensembl F02D10.1
Entrez Gene 184081 Entrez gene
SwissProt Q19111 EMBL-EBI
WormBase CE03136 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 CAA91932 Hypothetical protein F02D10.1 [Caenorhabditis elegans] ref|NP_510247.1| COLlagen family member (col-183) [Caenorhabditis elegans] 4.0E-39
blast CAE63146 Hypothetical protein CBG07448 [Caenorhabditis briggsae] 9.0E-35
blast CAE63118 Hypothetical protein CBG07415 [Caenorhabditis briggsae] 5.0E-22
Protein Domains
Database ID Description E-Value
Pfam IPR002486 EMBL-EBI Nematode cuticle collagen, N-terminal 6.3E-8
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 2.0E-4
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 1.2E-5
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_510247.1 1 15-37
F02D10.1 1 15-37
SNAP00000039146 1 15-37
GENEFINDER00000039152 1 15-37
Sequence
Target Sequence 
>C. ELEGANS:189486_AT
gaggcggtgggtgtacaggatgctgtaacccaggtccaccaggaccaggaggaagaccag
gaaagccaggaaccccaggaaaacctggtgcaccaggaaatccaggagcttctggaaagg
gtgcagcagctccctgcgagccatctacaccaccaccatgccaaccatgcccagctggac
ctccaggaccaccaggaccagatggaactccaggagagccaggaggcccaggaccagcag
gatccccagctggaccatcaggaccaggaccagctggaccaccaggaccagcaggaccac
ctggaaacgatggacaaccaggacagccaggagggccaggacaagatggagcaagcagtg
ctggaggagaagctggaccaggacctgcaggaccacctggaccagccggaccagcgggac
cagacggacaaagtggaagtggatctgctggaggaccaggaccaaagggaccaccaggac
ctgctggacaacccggaagtgat

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GAGGCGGTGGGTGTACAGGATGCTG 692 403 338 Antisense
TACAGGATGCTGTAACCCAGGTCCA 39 645 351 Antisense
ACCCCAGGAAAACCTGGTGCACCAG 478 85 409 Antisense
AAACCTGGTGCACCAGGAAATCCAG 307 123 418 Antisense
GGAGCTTCTGGAAAGGGTGCAGCAG 489 519 442 Antisense
TGGAAAGGGTGCAGCAGCTCCCTGC 203 547 450 Antisense
AAGATGGAGCAAGCAGTGCTGGAGG 9 155 680 Antisense
GAAGCTGGACCAGGACCTGCAGGAC 194 343 706 Antisense
ACCAGCGGGACCAGACGGACAAAGT 363 85 747 Antisense
AAGTGGAAGTGGATCTGCTGGAGGA 568 159 768 Antisense
ACCTGCTGGACAACCCGGAAGTGAT 225 87 816 Antisense
Sequence Source Affymetrix Proprietary Database