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[188614_at] collagen

Description W09G10.1 /REP_DB=WormBase Gene ID /WP=CE28512 /TR=O16640 /GB=AAB66109.1 /SUBMIT=ST.LOUIS /CHR=2 /FEA=Sanger Annotation /DEF=collagen
Cluster 6grp_total > 93      4grp_total > 60      6grp_cgc > 87      6grp_cgc_sub > 05      6grp_total_sub > Hat      6grp_rule_based > S5      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 71
1 2 3 4 range
A 10.7
(-2.7)
A 		24.5
(-1.2)
A 		62.9
(3)
A 		7.9
(-3)
A 		55
B 78.5
(3)
A 		44.9
(0.2)
A 		20.8
(-1.9)
A 		7.6
(-3)
A 		71
C 9.6
(-3)
A 		22.5
(-0.8)
A 		45.4
(3)
A 		12.6
(-2.5)
A 		36
avr 32.9
(1.2) 		30.6
(0.8) 		43
(3) 		9.4
(-3) 		34

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 2907
1 2 3 4 5 6 range
A 21
(-3)
A 		65.7
(-2.9)
A 		39.7
(-2.9)
A 		1465.6
(1.8)
P 		1840.7
(3)
P 		98.2
(-2.7)
P 		1820
B 29.1
(-3)
A 		40.9
(-3)
A 		29.6
(-3)
A 		1556.5
(0.5)
P 		2670.2
(3)
P 		135.2
(-2.8)
P 		2641
C 15.6
(-3)
A 		52.6
(-2.9)
A 		110.3
(-2.8)
A 		937.2
(-1.1)
P 		2922.2
(3)
P 		105.6
(-2.8)
A 		2907
avr 21.9
(-3) 		53.1
(-2.9) 		59.9
(-2.9) 		1319.8
(0.2) 		2477.7
(3) 		113
(-2.8) 		2456
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 24
1 2 3 4 range
A 3.9
(-1.9)
A 		5.3
(-1.4)
A 		16.4
(3)
A 		1.2
(-3)
A 		15
B 25
(3)
A 		11.1
(-0.6)
A 		4.8
(-2.2)
A 		1.6
(-3)
A 		23
C 3.2
(-2.5)
A 		6.5
(-1.1)
A 		15.8
(3)
A 		2.1
(-3)
A 		14
avr 10.7
(2.1) 		7.6
(0.4) 		12.3
(3) 		1.6
(-3) 		11

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 1081
1 2 3 4 5 6 range
A 3.9
(-3)
A 		23.4
(-2.8)
A 		8.6
(-2.9)
A 		371.7
(1)
P 		555.4
(3)
P 		23.9
(-2.8)
P 		552
B 10.1
(-3)
A 		13.6
(-3)
A 		7.2
(-3)
A 		412.3
(-0.7)
P 		1084.9
(3)
P 		50.4
(-2.8)
P 		1078
C 5.8
(-3)
A 		16
(-2.9)
A 		28.1
(-2.9)
A 		188.5
(-1.8)
P 		945.6
(3)
P 		35.3
(-2.8)
A 		940
avr 6.6
(-3) 		17.7
(-2.9) 		14.6
(-2.9) 		324.2
(-0.8) 		862
(3) 		36.5
(-2.8) 		855
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 188614_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.5160
Sequence Type Exemplar sequence
Representative Public ID W09G10.1 NCBI
Target Description W09G10.1 /REP_DB=WormBase Gene ID /WP=CE28512 /TR=O16640 /GB=AAB66109.1 /SUBMIT=ST.LOUIS /CHR=2 /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 Genome Target Overlap based pipeline to a RefSeq identifier using 1 transcript(s).
Annotation Grade This is a grade B annotation.
Annotation Transcript Cluster (# of Matching Probes) NM_062167
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
GENEFINDER00000024974 ENSEMBL cdna:GeneFinder chromosome:CEL140:II:3520735:3521403:-1 None
NM_062167 NCBI Caenorhabditis elegans W09G10.1 (collagen) mRNA, complete cds. A 
W09G10.1 ENSEMBL cdna:known chromosome:CEL140:II:3520735:3521403:-1 gene:W09G10.1 A 
SNAP00000024965 ENSEMBL cdna:SNAP chromosome:CEL140:II:3520735:3521403:-1 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
chrII:3520733-3521402(-) 100.0 100.0
Public Domain and Genome References
Gene Title collagen
Gene Symbol col-72
Ensembl W09G10.1
Entrez Gene 173698 Entrez gene
SwissProt O16640 EMBL-EBI
WormBase CE28512 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 AAB66109 Collagen protein 72 [Caenorhabditis elegans] ref|NP_494568.1| W09G10.1 [Caenorhabditis elegans] 2.0E-53
blast A88102 protein W09G10.1 [imported] - Caenorhabditis elegans 3.0E-50
blast CAE73812 Hypothetical protein CBG21362 [Caenorhabditis briggsae] 3.0E-20
Protein Domains
Database ID Description E-Value
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 6.4E-4
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 1.2E-12
Sequence
Target Sequence 
>C. ELEGANS:188614_AT
tcaacctggacaacctggagagcccggaatcactggaatgaccccaccaaccgattatca
aaacgagaaatcttgccgccagtgcccaccaggccacgtggacagccaggatacggagga
ccaccagggcccccagggcttccaggccaaccaggccaaaatggaaatggaggccgacca
ggaaacaatgggccaatgggacagcccggagagcctggaagagaaggacagccgggtaaa
gccggtggaccaggaagccctggaagagacggaatccgcggatcgaagggatccactgga
gataaggggccaaatggaccacccggacagaatgggccacctggatgggctggacgtgat
ggaaacatcggaccacaaggaacacctggaggacgtggagaaccaggaggcccaggaact
gatggattccctggattcgctggaaatcctggaccagatgtgagttacaatatattgagg
aagatcggggtgcaatttaatatttttcagggagctcct

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
TCAACCTGGACAACCTGGAGAGCCC 392 631 88 Antisense
GAGAGCCCGGAATCACTGGAATGAC 666 393 105 Antisense
CCCACCAACCGATTATCAAAACGAG 187 259 130 Antisense
GACAGCCAGGATACGGAGGACCACC 113 369 188 Antisense
GGCCAACCAGGCCAAAATGGAAATG 500 543 232 Antisense
GGAGGCCGACCAGGAAACAATGGGC 336 515 256 Antisense
GGCCAATGGGACAGCCCGGAGAGCC 17 543 278 Antisense
ACAGCCCGGAGAGCCTGGAAGAGAA 183 109 288 Antisense
ATCCTGGACCAGATGTGAGTTACAA 106 37 533 Antisense
GAGGAAGATCGGGGTGCAATTTAAT 392 403 564 Antisense
ATTTAATATTTTTCAGGGAGCTCCT 670 13 582 Antisense
Sequence Source Affymetrix Proprietary Database