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[190085_at] collagen

Description F54B11.2 /REP_DB=WormBase Gene ID /WP=CE05926 /GEN=col-9 /TR=Q20739 /GB=CAA94136.1 /SUBMIT=HINXTON /CHR=X /FEA=Sanger Annotation /DEF=collagen
Cluster 6grp_total > 93      4grp_total > 48      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 60
1 2 3 4 range
A 4.6
(-2.9)
A 		62.9
(3)
A 		53.1
(2)
A 		3.8
(-3)
A 		59
B 15.1
(-0.6)
A 		18.3
(0.1)
A 		33.2
(3)
A 		2.7
(-3)
A 		31
C 5.3
(-3)
A 		23.8
(-0.4)
A 		48.5
(3)
A 		26.4
(-0.1)
A 		43
avr 8.3
(-3) 		35
(1.4) 		44.9
(3) 		11
(-2.6) 		37

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 5134
1 2 3 4 5 6 range
A 48.8
(-2.9)
A 		12.4
(-3)
A 		20.8
(-3)
A 		2270.6
(1.4)
P 		3125.4
(3)
P 		438.8
(-2.2)
P 		3113
B 11
(-3)
A 		4.6
(-3)
A 		22.1
(-3)
A 		1723.5
(-0)
P 		3488.7
(3)
P 		207.1
(-2.7)
P 		3484
C 40.9
(-3)
A 		26.4
(-3)
A 		35.9
(-3)
A 		1259.7
(-1.6)
P 		5138.7
(3)
P 		172.2
(-2.8)
P 		5112
avr 33.6
(-3) 		14.5
(-3) 		26.3
(-3) 		1751.3
(-0.3) 		3917.6
(3) 		272.7
(-2.6) 		3903
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 16
1 2 3 4 range
A 1.7
(-2.5)
A 		13.7
(2.9)
A 		13.9
(3)
A 		0.6
(-3)
A 		13
B 4.8
(0.5)
A 		4.5
(0.3)
A 		7.7
(3)
A 		0.6
(-3)
A 		7
C 1.7
(-3)
A 		6.8
(-1)
A 		16.9
(3)
A 		4.4
(-1.9)
A 		15
avr 2.7
(-2.6) 		8.3
(0.5) 		12.8
(3) 		1.9
(-3) 		11

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 1661
1 2 3 4 5 6 range
A 9
(-3)
A 		4.4
(-3)
A 		4.5
(-3)
A 		575.9
(0.7)
P 		943.1
(3)
P 		106.8
(-2.3)
P 		939
B 3.8
(-3)
A 		1.5
(-3)
A 		5.4
(-3)
A 		456.5
(-1.1)
P 		1417.4
(3)
P 		77.2
(-2.7)
P 		1416
C 15.2
(-3)
A 		8.1
(-3)
A 		9.1
(-3)
A 		253.3
(-2.1)
P 		1662.8
(3)
P 		57.7
(-2.8)
P 		1655
avr 9.3
(-3) 		4.7
(-3) 		6.3
(-3) 		428.6
(-1.1) 		1341.1
(3) 		80.6
(-2.7) 		1336
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 190085_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.17968
Sequence Type Exemplar sequence
Representative Public ID F54B11.2 NCBI
Target Description F54B11.2 /REP_DB=WormBase Gene ID /WP=CE05926 /GEN=col-9 /TR=Q20739 /GB=CAA94136.1 /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_077873(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_077873 NCBI Caenorhabditis elegans F54B11.2 (collagen) mRNA, complete cds. 11/11 None
SNAP00000008288 ENSEMBL cdna:SNAP chromosome:CEL140:X:13591417:13592380:1 11/11 None
GENEFINDER00000008299 ENSEMBL cdna:GeneFinder chromosome:CEL140:X:13591417:13592380:1 11/11 None
F54B11.2 ENSEMBL cdna:known chromosome:CEL140:X:13591417:13592380:1 gene:F54B11.2 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
chrX:13591416-13592380(+) 94.21 100.0
Public Domain and Genome References
Gene Title collagen
Gene Symbol col-44
Ensembl F54B11.2
Entrez Gene 186211 Entrez gene
SwissProt Q20739 EMBL-EBI
WormBase CE05926 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 CAA94136 Hypothetical protein F54B11.2 [Caenorhabditis elegans] ref|NP_510274.1| F54B11.2 [Caenorhabditis elegans] 1.0E-43
blast CAE63117 Hypothetical protein CBG07414 [Caenorhabditis briggsae] 1.0E-34
blast CAE63136 Hypothetical protein CBG07436 [Caenorhabditis briggsae] 6.0E-30
Protein Domains
Database ID Description E-Value
Pfam IPR002486 EMBL-EBI Nematode cuticle collagen, N-terminal 4.3E-5
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 3.8E-10
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 1.5E-4
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_510274.1 1 15-37
F54B11.2 1 15-37
SNAP00000008288 1 15-37
GENEFINDER00000008299 1 15-37
Sequence
Target Sequence 
>C. ELEGANS:190085_AT
caagcggcggtcaatgtgaaggatgctgcaatccaggtccaccaggagttgctggtaacc
ctggaaagcctggaaaaccaggaaagccaggagcaccaggaaacccgggtgcaccaggaa
aaggagcagctgttccatgcgaagccaagactccaccgccatgcaagccatgcccagcag
gaccaccaggaccaccaggaccagacggaccagctggaccagcaggaccagacggagaag
ccggttcaccagccgcaccatccccaccaggaccaccaggaccatcaggacctgcagggc
ctgcaggaaacgacggagccgccggaactccaggaccagatgggccagctggagagagca
cctatccagagcca

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
CAAGCGGCGGTCAATGTGAAGGATG 409 185 302 Antisense
GAGTTGCTGGTAACCCTGGAAAGCC 109 397 347 Antisense
AGCACCAGGAAACCCGGGTGCACCA 508 73 393 Antisense
CCCGGGTGCACCAGGAAAAGGAGCA 218 233 405 Antisense
GAAAAGGAGCAGCTGTTCCATGCGA 47 355 419 Antisense
GCTGTTCCATGCGAAGCCAAGACTC 300 295 430 Antisense
AGACGGAGAAGCCGGTTCACCAGCC 147 69 531 Antisense
AGGACCATCAGGACCTGCAGGGCCT 22 57 579 Antisense
TGCAGGGCCTGCAGGAAACGACGGA 670 573 594 Antisense
GATGGGCCAGCTGGAGAGAGCACCT 525 407 640 Antisense
TGGAGAGAGCACCTATCCAGAGCCA 431 549 651 Antisense
Sequence Source Affymetrix Proprietary Database