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[188589_at] collagen

Description F33D11.3 /REP_DB=WormBase Gene ID /WP=CE09893 /TR=O44774 /GB=AAB96697.1 /SUBMIT=ST.LOUIS /CHR=1 /FEA=Sanger Annotation /DEF=collagen
Cluster 6grp_highest_10_10 > 44      6grp_high1_10_10 > 43      6grp_highest_nonorm > 52      6grp_total > 20      4grp_total > 49      6grp_highest_sub > 02      6grp_cgc > 73      6grp_high1_sub > 02      6grp_cgc_sub > 02_03      6grp_total_sub > Hat      6grp_rule_based > S2      4grp_rule_based > L3      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 2508
1 2 3 4 range
A 163.2
(-2.8)
A 		2122.1
(3)
P 		2071.3
(2.8)
P 		109.4
(-3)
A 		2013
B 173.8
(-2.8)
M 		2076.9
(1.8)
P 		2550.4
(3)
P 		107.9
(-3)
A 		2443
C 202.5
(-2.5)
P 		1792.4
(2.1)
P 		2089.3
(3)
P 		42.8
(-3)
A 		2047
avr 179.8
(-2.7) 		1997.1
(2.3) 		2237
(3) 		86.7
(-3) 		2150

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 1292
1 2 3 4 5 6 range
A 171.4
(-3)
P 		1222.2
(3)
P 		956.9
(1.5)
P 		1190.1
(2.8)
P 		348
(-2)
P 		237.5
(-2.6)
P 		1051
B 216.9
(-3)
P 		1399.1
(3)
P 		991
(0.9)
P 		801.7
(-0)
P 		412.5
(-2)
P 		212.8
(-3)
P 		1186
C 107
(-3)
P 		1124.2
(3)
P 		956.1
(2)
P 		832.1
(1.3)
P 		366.7
(-1.5)
P 		158.8
(-2.7)
P 		1017
avr 165.1
(-3) 		1248.5
(3) 		968
(1.4) 		941.3
(1.3) 		375.7
(-1.8) 		203
(-2.8) 		1083
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 721
1 2 3 4 range
A 59.4
(-2.5)
A 		460.6
(2.1)
P 		541.5
(3)
P 		16
(-3)
A 		526
B 55.4
(-2.7)
M 		512.9
(2.2)
P 		591
(3)
P 		23
(-3)
A 		568
C 67
(-2.5)
P 		515.3
(1.2)
P 		728.2
(3)
P 		7.2
(-3)
A 		721
avr 60.6
(-2.6) 		496.3
(1.8) 		620.2
(3) 		15.4
(-3) 		605

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 434
1 2 3 4 5 6 range
A 31.6
(-3)
P 		434.7
(3)
P 		208.4
(-0.4)
P 		301.8
(1)
P 		105
(-1.9)
P 		57.8
(-2.6)
P 		403
B 75.5
(-3)
P 		465.7
(3)
P 		240.6
(-0.5)
P 		212.3
(-0.9)
P 		167.6
(-1.6)
P 		79.3
(-2.9)
P 		390
C 39.7
(-3)
P 		343
(3)
P 		243.3
(1)
P 		167.3
(-0.5)
P 		118.7
(-1.4)
P 		53.2
(-2.7)
P 		303
avr 48.9
(-3) 		414.5
(3) 		230.8
(-0) 		227.1
(-0.1) 		130.4
(-1.7) 		63.4
(-2.8) 		366
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 188589_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.620
Sequence Type Exemplar sequence
Representative Public ID F33D11.3 NCBI
Target Description F33D11.3 /REP_DB=WormBase Gene ID /WP=CE09893 /TR=O44774 /GB=AAB96697.1 /SUBMIT=ST.LOUIS /CHR=1 /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_059293(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_059293 NCBI Caenorhabditis elegans F33D11.3 (collagen) mRNA, complete cds. 11/11 None
GENEFINDER00000028964 ENSEMBL cdna:GeneFinder chromosome:CEL140:I:5850850:5852101:1 11/11 None
F33D11.3 ENSEMBL cdna:known chromosome:CEL140:I:5850850:5852101:1 gene:F33D11.3 11/11 None
Annotation Notes
Cross Hybridizing mRNA Matched Probes Nature of Assignment Related Probesets by Grade
SNAP00000028950 3/11 Cross Hyb Matching Probes None
SNAP00000028951 8/11 Cross Hyb Matching Probes None
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrI:5850849-5852101(+) 100.0 100.0
Public Domain and Genome References
Gene Title collagen
Gene Symbol col-54
Ensembl F33D11.3
Entrez Gene 185226 Entrez gene
SwissProt O44774 EMBL-EBI
WormBase CE09893 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 AAB96697 Collagen protein 54 [Caenorhabditis elegans] ref|NP_491694.1| F33D11.3 [Caenorhabditis elegans] 4.0E-84
blast CAE60416 Hypothetical protein CBG04022 [Caenorhabditis briggsae] 3.0E-69
blast CAB04587 Hypothetical protein K08C9.4 [Caenorhabditis elegans] ref|NP_492936.1| COLlagen family member (col-65) [Caenorhabditis elegans] 1.0E-15
Protein Domains
Database ID Description E-Value
Pfam IPR002486 EMBL-EBI Nematode cuticle collagen, N-terminal 1.5E-19
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 2.6E-4
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 1.1E-11
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 7.2E-10
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_491694.1 1 7-29
F33D11.3 1 7-29
GENEFINDER00000028964 1 7-29
Sequence
Target Sequence 
>C. ELEGANS:188589_AT
gtcatgtggctgcccatgtgcaaacggtccaaataactgccctccgggagaagcaggacc
accgggagctccaggaacaccaggagccgacggagaagctggaaatccaggaaaagatgg
agctgccggatcttcgttggtatttgaagatgagaagcttccatgcattaaatgcccagc
tggtgaaccaggaccacaaggacctgatggtgcaccaggtgcaccaggaccagatggaca
gccaggagctccaggatccaacggaaatccaggatctgccggagaacaaggatcagaagg
agaaccaggagatgctggagcaacaggagaaattggagttgcaggagcaccaggaaagaa
tggaaaccgtggatctggtgctccaggagctccaggtccagaaggaccaattggagaacc
aggaaaagatggacaacaaggaccacatggagatgttggaggtgatggaactgaaggaat
tcaaggagcaccaggaaaagatggagaaaatggatctgatggagttgcaggaagtgatgg
agctccaggagcaccaggaccagatgctgcctattgttcatgtccagcaag

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GTCATGTGGCTGCCCATGTGCAAAC 81 467 234 Antisense
GCAAACGGTCCAAATAACTGCCCTC 13 319 253 Antisense
ACTGCCCTCCGGGAGAAGCAGGACC 454 91 269 Antisense
AAAGATGGAGCTGCCGGATCTTCGT 334 123 346 Antisense
CTGCCGGATCTTCGTTGGTATTTGA 133 237 356 Antisense
GAGAAGCTTCCATGCATTAAATGCC 300 391 385 Antisense
TAAATGCCCAGCTGGTGAACCAGGA 463 639 402 Antisense
GAAATCCAGGATCTGCCGGAGAACA 631 361 497 Antisense
AAACCGTGGATCTGGTGCTCCAGGA 495 125 597 Antisense
CAGGAGCTCCAGGTCCAGAAGGACC 130 209 617 Antisense
CTGCCTATTGTTCATGTCCAGCAAG 267 237 800 Antisense
Sequence Source Affymetrix Proprietary Database