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[189795_at] cuticular collagen

Description F58F6.2 /REP_DB=WormBase Gene ID /WP=CE17137 /TR=O44173 /GB=AAB88359.1 /SUBMIT=ST.LOUIS /CHR=4 /FEA=Sanger Annotation /DEF=cuticular collagen
Cluster 6grp_total > 93      4grp_total > 49      6grp_cgc > 98      6grp_total_sub > Hat      6grp_rule_based > S5      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 16
1 2 3 4 range
A 5.3
(-3)
A 		10.6
(-0.5)
A 		18
(3)
A 		8.2
(-1.6)
A 		13
B 3.8
(-2.3)
A 		6.7
(-0.8)
A 		14.3
(3)
A 		2.4
(-3)
A 		12
C 4.1
(-2.8)
A 		18.7
(3)
A 		8.1
(-1.2)
A 		3.6
(-3)
A 		15
avr 4.4
(-3) 		12
(2) 		13.5
(3) 		4.7
(-2.8) 		9

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 52
1 2 3 4 5 6 range
A 7.8
(-2.7)
A 		6.5
(-2.8)
A 		5.2
(-3)
A 		7.6
(-2.7)
A 		56
(3)
A 		8.6
(-2.6)
A 		51
B 5.8
(-2.8)
A 		7.2
(-2.6)
A 		4.3
(-3)
A 		11.9
(-2)
A 		51.3
(3)
A 		4.8
(-2.9)
A 		47
C 5.5
(-2.6)
A 		4.1
(-3)
A 		4.1
(-3)
A 		25.7
(2.5)
A 		27.7
(3)
A 		4.9
(-2.8)
A 		24
avr 6.4
(-2.7) 		5.9
(-2.8) 		4.5
(-3) 		15.1
(-1.4) 		45
(3) 		6.1
(-2.8) 		41
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 5
1 2 3 4 range
A 1.9
(-1.8)
A 		2.3
(-1.1)
A 		4.7
(3)
A 		1.2
(-3)
A 		4
B 1.2
(-1.5)
A 		1.7
(-0.4)
A 		3.3
(3)
A 		0.5
(-3)
A 		3
C 1.3
(-2.1)
A 		5.4
(3)
A 		2.8
(-0.3)
A 		0.6
(-3)
A 		5
avr 1.5
(-1.5) 		3.1
(1.9) 		3.6
(3) 		0.8
(-3) 		3

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 20
1 2 3 4 5 6 range
A 1.4
(-2.9)
A 		2.3
(-2.5)
A 		1.1
(-3)
A 		1.9
(-2.7)
A 		16.9
(3)
A 		2.1
(-2.6)
A 		16
B 2
(-2.7)
A 		2.4
(-2.6)
A 		1.1
(-3)
A 		3.1
(-2.4)
A 		20.8
(3)
A 		1.8
(-2.8)
A 		20
C 2
(-2.3)
A 		1.3
(-2.8)
A 		1
(-3)
A 		5.2
(0.2)
A 		9
(3)
A 		1.6
(-2.6)
A 		8
avr 1.8
(-2.7) 		2
(-2.6) 		1.1
(-3) 		3.4
(-2) 		15.6
(3) 		1.8
(-2.7) 		15
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 189795_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.10667
Sequence Type Exemplar sequence
Representative Public ID F58F6.2 NCBI
Target Description F58F6.2 /REP_DB=WormBase Gene ID /WP=CE17137 /TR=O44173 /GB=AAB88359.1 /SUBMIT=ST.LOUIS /CHR=4 /FEA=Sanger Annotation /DEF=cuticular 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_067670(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_067670 NCBI Caenorhabditis elegans COLlagen family member (col-105) (col-105) mRNA, complete cds. 11/11 None
SNAP00000017983 ENSEMBL cdna:SNAP chromosome:CEL140:IV:1357815:1358419:-1 10/11 None
GENEFINDER00000017987 ENSEMBL cdna:GeneFinder chromosome:CEL140:IV:1357453:1359831:-1 11/11 None
F58F6.2 ENSEMBL cdna:known chromosome:CEL140:IV:1357815:1359224:-1 gene:F58F6.2 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:1357820-1359230(-) 99.89 100.0
Public Domain and Genome References
Gene Title cuticular collagen
Gene Symbol col-105
Ensembl F58F6.2
Entrez Gene 186529 Entrez gene
SwissProt O44173 EMBL-EBI
WormBase CE17137 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 AAB88359 Collagen protein 105 [Caenorhabditis elegans] ref|NP_500071.1| COLlagen family member (col-105) [Caenorhabditis elegans] 2.0E-74
blast AAB88359 Collagen protein 105 [Caenorhabditis elegans] ref|NP_500071.1| COLlagen family member (col-105) [Caenorhabditis elegans] 3.0E-72
blast CAE70204 Hypothetical protein CBG16679 [Caenorhabditis briggsae] 2.0E-38
blast CAE70204 Hypothetical protein CBG16679 [Caenorhabditis briggsae] 3.0E-38
blast AAB88359 Collagen protein 105 [Caenorhabditis elegans] ref|NP_500071.1| COLlagen family member (col-105) [Caenorhabditis elegans] 8.0E-32
blast CAA92729 Hypothetical protein C29F4.1 [Caenorhabditis elegans] ref|NP_502107.1| C29F4.1 [Caenorhabditis elegans] 2.0E-20
Protein Domains
Database ID Description E-Value
Pfam IPR002486 EMBL-EBI Nematode cuticle collagen, N-terminal 3.4E-9
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 4.3E-12
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 1.2E-11
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 4.3E-12
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 1.2E-11
Pfam IPR002486 EMBL-EBI Nematode cuticle collagen, N-terminal 3.4E-9
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 4.3E-12
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 1.2E-11
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_500071.1 1 13-35
F58F6.2 1 13-35
GENEFINDER00000017987 1 21-43
Sequence
Target Sequence 
>C. ELEGANS:189795_AT
gatgggtgctgtatacagggcgcccctgggccaacgggcgaaccagggcgtccaggccgc
ccgggtaagcccggtgttcctgggatgcctggcaaccccggcaaaccaccccagcagccg
tgtgagctagttaccccgccaccgtgctctccttgtcctgcaggtcctccgggcaaaccg
ggacctcagggcgccccgggtgacatcggccagccgggtaacccgggcgagcggggcatg
gacggggagcccgggccgccaggacccacaggtcctcctggggagcctgggctacctggc
gcccagggaataaccggacagcctggtgttaacgcagagccagtggcgtatagggcaggc
gcgccaggacctcctggtgagcctggaccaccaggtgcgcacggggatcctggggatctt
ggcgaagaggggccgcccgggttacccggaccgaaaggcccacccggtgcatctggaatt
cctggaaacgatgggccgccaggagctcggggacaaccgggat

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GATGGGTGCTGTATACAGGGCGCCC 580 407 274 Antisense
CAGCAGCCGTGTGAGCTAGTTACCC 707 199 385 Antisense
TAACCCGGGCGAGCGGGGCATGGAC 114 1 492 Antisense
GCGCCCAGGGAATAACCGGACAGCC 636 281 572 Antisense
GACAGCCTGGTGTTAACGCAGAGCC 170 369 590 Antisense
GCCAGTGGCGTATAGGGCAGGCGCG 405 281 612 Antisense
CCAGGACCTCCTGGTGAGCCTGGAC 291 271 637 Antisense
CACCAGGTGCGCACGGGGATCCTGG 383 197 662 Antisense
GGGGATCTTGGCGAAGAGGGGCCGC 667 495 685 Antisense
GAATTCCTGGAAACGATGGGCCGCC 218 323 749 Antisense
CCAGGAGCTCGGGGACAACCGGGAT 311 269 772 Antisense
Sequence Source Affymetrix Proprietary Database