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[188461_s_at] collagen

Description F29B9.9 /REP_DB=WormBase Gene ID /WP=CE09787 /TR=Q9GYI3 /GB=AAF99925.1 /SUBMIT=ST.LOUIS /CHR=4 /FEA=Sanger Annotation /DEF=collagen
Cluster 6grp_total > 93      4grp_total > 49      6grp_cgc > 88      6grp_total_sub > Hat      6grp_rule_based > S5      4grp_rule_based > L3      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 1061
1 2 3 4 range
A 7.6
(-3)
A 		982.6
(2.5)
P 		1068.6
(3)
P 		120.4
(-2.4)
A 		1061
B 18.7
(-3)
A 		669.4
(1.7)
P 		852.9
(3)
P 		66.5
(-2.7)
A 		834
C 23.7
(-3)
A 		663.2
(1.5)
P 		873.2
(3)
P 		39.3
(-2.9)
A 		850
avr 16.7
(-3) 		771.7
(2) 		931.6
(3) 		75.4
(-2.6) 		915

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 1522
1 2 3 4 5 6 range
A 51.3
(-3)
A 		399
(-0.9)
P 		305.9
(-1.5)
P 		673.7
(0.7)
P 		1051.3
(3)
P 		465.1
(-0.5)
P 		1000
B 41.2
(-3)
A 		272.9
(-1.6)
P 		350.3
(-1.1)
P 		603.7
(0.4)
P 		1039.5
(3)
P 		428.4
(-0.7)
P 		998
C 32.8
(-3)
A 		341.2
(-1.8)
P 		379
(-1.6)
P 		591.3
(-0.8)
P 		1554.5
(3)
P 		384.4
(-1.6)
P 		1522
avr 41.8
(-3) 		337.7
(-1.5) 		345.1
(-1.4) 		622.9
(-0) 		1215.1
(3) 		426
(-1) 		1173
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 302
1 2 3 4 range
A 2.8
(-3)
A 		213.3
(1.6)
P 		279.4
(3)
P 		17.6
(-2.7)
A 		277
B 6
(-3)
A 		165.3
(2)
P 		197.6
(3)
P 		14.2
(-2.7)
A 		192
C 7.9
(-3)
A 		190.7
(0.7)
P 		304.4
(3)
P 		6.6
(-3)
A 		298
avr 5.6
(-3) 		189.8
(1.3) 		260.5
(3) 		12.8
(-2.8) 		255

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 494
1 2 3 4 5 6 range
A 9.5
(-3)
A 		141.9
(-0.4)
P 		66.6
(-1.9)
P 		170.9
(0.1)
P 		317.2
(3)
P 		113.2
(-1)
P 		308
B 14.3
(-3)
A 		90.8
(-1.9)
P 		85.1
(-2)
P 		159.9
(-0.9)
P 		422.3
(3)
P 		159.7
(-0.9)
P 		408
C 12.2
(-3)
A 		104.1
(-1.9)
P 		96.5
(-2)
P 		118.9
(-1.7)
P 		503
(3)
P 		128.7
(-1.6)
P 		491
avr 12
(-3) 		112.3
(-1.5) 		82.7
(-1.9) 		149.9
(-0.9) 		414.2
(3) 		133.9
(-1.2) 		402
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 188461_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.10547
Sequence Type Exemplar sequence
Representative Public ID F29B9.9 NCBI
Target Description F29B9.9 /REP_DB=WormBase Gene ID /WP=CE09787 /TR=Q9GYI3 /GB=AAF99925.1 /SUBMIT=ST.LOUIS /CHR=4 /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_068206(10)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_068206 NCBI Caenorhabditis elegans F29B9.9 (collagen) mRNA, complete cds. 10/11 None
SNAP00000034766 ENSEMBL cdna:SNAP chromosome:CEL140:IV:4655821:4657578:-1 10/11 None
GENEFINDER00000034774 ENSEMBL cdna:GeneFinder chromosome:CEL140:IV:4655821:4657578:-1 10/11 None
F29B9.9 ENSEMBL cdna:known chromosome:CEL140:IV:4655821:4657578:-1 gene:F29B9.9 10/11 None
Annotation Notes
Cross Hybridizing mRNA Matched Probes Nature of Assignment Related Probesets by Grade
F29B9.4.1 11/11 Negative Strand Matching Probes None
F29B9.4.2 11/11 Negative Strand Matching Probes None
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrIV:4655826-4657584(-) 100.0 100.0
Public Domain and Genome References
Gene Title collagen
Gene Symbol col-111
Ensembl F29B9.9
Entrez Gene 177230 Entrez gene
SwissProt Q9GYI3 EMBL-EBI
WormBase CE34831 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 NP_500607 F29B9.9 [Caenorhabditis elegans] gb|AAF99925.2| Collagen protein 111 [Caenorhabditis elegans] 8.0E-64
blast CAE58561 Hypothetical protein CBG01723 [Caenorhabditis briggsae] 2.0E-50
Protein Domains
Database ID Description E-Value
Pfam IPR002486 EMBL-EBI Nematode cuticle collagen, N-terminal 1.6E-5
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 1.5E-4
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 4.3E-10
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 2.1E-5
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_500607.2 1 7-29
F29B9.9 1 7-29
SNAP00000034766 1 7-29
GENEFINDER00000034774 1 7-29
Sequence
Target Sequence 
>C. ELEGANS:188461_S_AT
gaacactcttccattttcgatttgttgtttcatttctaatagtaaactaaactctgaatt
ttcagcacccggaccacgtggagcaccgggatccgttggagaaccaggaccacagggtag
agatggaatgggtggtcgaccaggcaacatgggacgtcctggaccacctggaccagcggg
agatccgggacaagccggatcaaagggagcaccaggaacccacggaagacaaggaatgcc
aggagtacggtatcagctcggagagcccggaccagccggctacccaggaccacgtggagc
accaggaccagtcggaccaccgggagtcgccgaagaaggacctgatggcctaccaggacc
agctggaccaccaggaaagccaggaatgcctggaccaatggggacgccaggaggtccagg
agagccgggaattcctggatcagacgccgcctattgtccatgtccaaagagagaagcact
tgtcgaatcatccgtcatctcgcaagaggtgcca

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GAACACTCTTCCATTTTCGATTTGT 668 351 462 Antisense
GAGCACCGGGATCCGTTGGAGAACC 80 391 542 Antisense
GGTCGACCAGGCAACATGGGACGTC 237 503 595 Antisense
CCTGGACCAGCGGGAGATCCGGGAC 187 261 628 Antisense
AGCACCAGGAACCCACGGAAGACAA 509 73 669 Antisense
AGTACGGTATCAGCTCGGAGAGCCC 129 63 705 Antisense
GACCACCGGGAGTCGCCGAAGAAGG 612 383 776 Antisense
AAGGACCTGATGGCCTACCAGGACC 353 159 797 Antisense
GCCGGGAATTCCTGGATCAGACGCC 111 283 885 Antisense
AGCACTTGTCGAATCATCCGTCATC 372 77 936 Antisense
ATCCGTCATCTCGCAAGAGGTGCCA 334 37 951 Antisense
Sequence Source Affymetrix Proprietary Database