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[190036_at] collagen

Description F54B11.1 /REP_DB=WormBase Gene ID /WP=CE05925 /GEN=col-9 /TR=Q20744 /GB=CAA94141.1 /SUBMIT=HINXTON /CHR=X /FEA=Sanger Annotation /DEF=collagen
Cluster 6grp_total > 92      4grp_total > 56      6grp_cgc > 98      4grp_rule_based > L3      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 51
1 2 3 4 range
A 10.9
(-3)
A 		31.4
(3)
A 		17.4
(-1.1)
A 		19.6
(-0.5)
A 		21
B 4.3
(-3)
A 		8.7
(-2.5)
A 		53.4
(3)
A 		6.3
(-2.8)
A 		49
C 10.5
(-2.5)
A 		11.2
(-2.5)
A 		55.7
(3)
A 		6.8
(-3)
A 		49
avr 8.6
(-3) 		17.1
(-1.5) 		42.2
(3) 		10.9
(-2.6) 		34

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 47
1 2 3 4 5 6 range
A 24.5
(3)
A 		19.3
(1)
A 		13
(-1.4)
A 		8.8
(-3)
A 		17.8
(0.4)
A 		22.6
(2.3)
A 		16
B 10.9
(-2.3)
A 		7
(-3)
A 		25.5
(0.1)
A 		18.9
(-1)
A 		21.6
(-0.6)
A 		42.8
(3)
A 		36
C 33
(0.3)
A 		53.9
(3)
A 		31.1
(0.1)
A 		48.6
(2.3)
A 		44.2
(1.8)
A 		7
(-3)
A 		47
avr 22.8
(-3) 		26.7
(1.6) 		23.2
(-2.5) 		25.4
(0.1) 		27.9
(3) 		24.1
(-1.5) 		5
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 18
1 2 3 4 range
A 4
(-1.3)
A 		6.8
(3)
A 		4.5
(-0.5)
A 		2.9
(-3)
A 		4
B 1.4
(-2.9)
A 		2.2
(-2.5)
A 		12.4
(3)
A 		1.3
(-3)
A 		11
C 3.5
(-2.2)
A 		3.2
(-2.3)
A 		19.4
(3)
A 		1.1
(-3)
A 		18
avr 3
(-2.3) 		4.1
(-1.7) 		12.1
(3) 		1.8
(-3) 		10

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 14
1 2 3 4 5 6 range
A 4.5
(-0.1)
A 		6.9
(3)
A 		2.8
(-2.2)
A 		2.2
(-3)
A 		5.4
(1.1)
A 		5.5
(1.2)
A 		5
B 3.8
(-2.3)
A 		2.3
(-3)
A 		6.2
(-1.3)
A 		5
(-1.8)
A 		8.8
(-0.1)
A 		15.9
(3)
A 		14
C 12.2
(1.2)
A 		16.4
(3)
A 		7.9
(-0.6)
A 		9.8
(0.2)
A 		14.3
(2.1)
A 		2.3
(-3)
A 		14
avr 6.8
(-1.2) 		8.5
(1.5) 		5.6
(-3) 		5.7
(-2.8) 		9.5
(3) 		7.9
(0.5) 		4
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 190036_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.17516
Sequence Type Exemplar sequence
Representative Public ID F54B11.1 NCBI
Target Description F54B11.1 /REP_DB=WormBase Gene ID /WP=CE05925 /GEN=col-9 /TR=Q20744 /GB=CAA94141.1 /SUBMIT=HINXTON /CHR=X /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_077872(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_077872 NCBI Caenorhabditis elegans F54B11.1 (collagen) mRNA, complete cds. 11/11 None
SNAP00000008287 ENSEMBL cdna:SNAP chromosome:CEL140:X:13589954:13591126:1 11/11 None
GENEFINDER00000008298 ENSEMBL cdna:GeneFinder chromosome:CEL140:X:13590302:13591126:1 11/11 None
F54B11.1 ENSEMBL cdna:known chromosome:CEL140:X:13589954:13591126:1 gene:F54B11.1 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:13589953-13591126(+) 100.0 100.0
Public Domain and Genome References
Gene Title collagen
Gene Symbol col-9
Ensembl F54B11.1
Entrez Gene 186210 Entrez gene
SwissProt Q20744 EMBL-EBI
WormBase CE05925 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
Protein Similarities
Method ID Description E-Value
blast CAA94141 Hypothetical protein F54B11.1 [Caenorhabditis elegans] ref|NP_510273.1| F54B11.1 [Caenorhabditis elegans] 5.0E-72
blast CAA94141 Hypothetical protein F54B11.1 [Caenorhabditis elegans] ref|NP_510273.1| F54B11.1 [Caenorhabditis elegans] 4.0E-33
blast CAE63118 Hypothetical protein CBG07415 [Caenorhabditis briggsae] 1.0E-21
blast CAE63146 Hypothetical protein CBG07448 [Caenorhabditis briggsae] 2.0E-19
Protein Domains
Database ID Description E-Value
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 6.9E-4
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 6.9E-4
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_510273.1 1 15-37
F54B11.1 1 15-37
SNAP00000008287 1 15-37
Sequence
Target Sequence 
>C. ELEGANS:190036_AT
tggccacccaggaaaaccaggtcgaccaggaagaccaggtggtcacgggatgccaggaat
gcccggactaggcgcatcgccttgccaacctagaactcaatcacagtgtcaacaatgtcc
acagggacccccaggccctccaggtctgaacggacagcccggcctgcccggtggaatggg
gccaccaggtcagtcaatgtcaaacgtactaccaggacctctaggaccaccaggaccgcc
cgggcagcctggtaaccacggtttggcagggcaaccaggaagtcctggacaatcggtgct
gggcggaatcgtcgggtttgctgcaccaggcccaatgggtcctcctggactaatggggcc
accaggcttggatgcacaaaatggagcaaatggctttggcccgccaggactgccaggacc
accaggaccaccaggaagaccaggaagcgacggtaatcctggagttcc

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
TGGCCACCCAGGAAAACCAGGTCGA 370 543 459 Antisense
ACCAGGTGGTCACGGGATGCCAGGA 495 85 492 Antisense
CCTTGCCAACCTAGAACTCAATCAC 315 267 538 Antisense
GTCAACAATGTCCACAGGGACCCCC 225 463 566 Antisense
GCCACCAGGTCAGTCAATGTCAAAC 385 279 639 Antisense
ATGTCAAACGTACTACCAGGACCTC 328 47 655 Antisense
GCAGCCTGGTAACCACGGTTTGGCA 111 313 702 Antisense
GACAATCGGTGCTGGGCGGAATCGT 209 365 746 Antisense
GGGTCCTCCTGGACTAATGGGGCCA 17 493 795 Antisense
GGCCACCAGGCTTGGATGCACAAAA 92 545 815 Antisense
GAAGCGACGGTAATCCTGGAGTTCC 599 341 902 Antisense
Sequence Source Affymetrix Proprietary Database