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[186974_s_at]

Description Y49F6B.10 /REP_DB=WormBase Gene ID /WP=CE25334 /TR=Q9N4U2 /GB=AAF60736.1 /SUBMIT=ST.LOUIS /CHR=2 /FEA=Sanger Annotation
Cluster 6grp_total > 94      4grp_total > 50      6grp_cgc > 78      6grp_cgc_sub > In      6grp_total_sub > Hat      6grp_rule_based > S5      4grp_rule_based > L2      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 210
1 2 3 4 range
A 182.8
(-0.2)
A 		288
(3)
A 		182
(-0.2)
A 		88.5
(-3)
A 		200
B 116.7
(-2.4)
A 		281.2
(2.7)
A 		292.1
(3)
A 		97.2
(-3)
A 		195
C 157.2
(-1.2)
A 		298
(3)
A 		269.6
(2.2)
A 		96.2
(-3)
A 		202
avr 152.2
(-1.2) 		289.1
(3) 		247.9
(1.7) 		94
(-3) 		195

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 3142
1 2 3 4 5 6 range
A 109.6
(-3)
A 		172.4
(-2.8)
P 		183.7
(-2.8)
A 		928.2
(-0.7)
P 		2209.5
(3)
P 		2201.3
(3)
P 		2100
B 151.3
(-3)
A 		156.4
(-3)
A 		244.7
(-2.8)
A 		826.6
(-1.4)
P 		2649.4
(3)
P 		2187.9
(1.9)
P 		2498
C 145.1
(-3)
A 		150.8
(-3)
M 		152.8
(-3)
A 		764.5
(-1.8)
P 		3251.7
(3)
P 		1629.1
(-0.1)
P 		3107
avr 135.3
(-3) 		159.9
(-2.9) 		193.7
(-2.9) 		839.8
(-1.4) 		2703.5
(3) 		2006.1
(1.4) 		2568
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 81
1 2 3 4 range
A 66.6
(3)
A 		62.5
(2.5)
A 		47.6
(0.9)
A 		13
(-3)
A 		54
B 37.2
(-1)
A 		69.4
(3)
A 		67.7
(2.8)
A 		20.7
(-3)
A 		49
C 52.1
(-0.2)
A 		85.7
(2.4)
A 		94
(3)
A 		16.2
(-3)
A 		78
avr 52
(0.8) 		72.5
(3) 		69.8
(2.7) 		16.6
(-3) 		56

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 1056
1 2 3 4 5 6 range
A 20.2
(-3)
A 		61.3
(-2.6)
P 		40
(-2.8)
A 		235.4
(-1)
P 		666.7
(3)
P 		535.9
(1.8)
P 		647
B 52.7
(-3)
A 		52.1
(-3)
A 		59.4
(-3)
A 		218.9
(-2)
P 		1076.4
(3)
P 		815.9
(1.5)
P 		1024
C 53.8
(-2.9)
A 		46
(-3)
M 		38.9
(-3)
A 		153.7
(-2.3)
P 		1052.2
(3)
P 		545.4
(-0)
P 		1013
avr 42.2
(-3) 		53.1
(-2.9) 		46.1
(-3) 		202.7
(-1.9) 		931.8
(3) 		632.4
(1) 		890
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 186974_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.5595
Sequence Type Exemplar sequence
Representative Public ID Y49F6B.10 NCBI
Target Description Y49F6B.10 /REP_DB=WormBase Gene ID /WP=CE25334 /TR=Q9N4U2 /GB=AAF60736.1 /SUBMIT=ST.LOUIS /CHR=2 /FEA=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_062161(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_062161 NCBI Caenorhabditis elegans COLlagen family member (col-71) (col-71) mRNA, complete cds. 11/11 None
SNAP00000021101 ENSEMBL cdna:SNAP chromosome:CEL140:II:3500142:3513717:-1 11/11 None
GENEFINDER00000021105 ENSEMBL cdna:GeneFinder chromosome:CEL140:II:3500142:3502439:-1 11/11 None
Y49F6B.10 ENSEMBL cdna:known chromosome:CEL140:II:3500080:3502444:-1 gene:Y49F6B.10 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
chrII:3500140-3502438(-) 100.0 100.0
Public Domain and Genome References
Gene Title
Gene Symbol col-71
Ensembl Y49F6B.10
Entrez Gene 173695 Entrez gene
SwissProt Q9N4U2 EMBL-EBI
WormBase CE25334 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_494562 COLlagen family member (col-71) [Caenorhabditis elegans] gb|AAF60736.1| Collagen protein 71 [Caenorhabditis elegans] 6.0E-97
blast NP_494562 COLlagen family member (col-71) [Caenorhabditis elegans] gb|AAF60736.1| Collagen protein 71 [Caenorhabditis elegans] 1.0E-96
blast CAE70951 Hypothetical protein CBG17762 [Caenorhabditis briggsae] 1.0E-65
blast CAE70951 Hypothetical protein CBG17762 [Caenorhabditis briggsae] 2.0E-65
blast CAB55014 Hypothetical protein Y57A10A.11 [Caenorhabditis elegans] ref|NP_496589.1| ROLler: helically twisted, animals roll when moving family member (rol-1) [Caenorhabditis elegans] 3.0E-17
Protein Domains
Database ID Description E-Value
Pfam IPR002486 EMBL-EBI Nematode cuticle collagen, N-terminal 2.2E-5
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 8.2E-4
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 5.2E-12
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 9.9E-13
Pfam IPR002486 EMBL-EBI Nematode cuticle collagen, N-terminal 2.2E-5
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 8.2E-4
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 5.2E-12
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 9.9E-13
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_494562.1 1 38-60
Y49F6B.10 1 38-60
SNAP00000021101 2 13-35,256-278
GENEFINDER00000021105 1 38-60
Sequence
Target Sequence 
>C. ELEGANS:186974_S_AT
cgaaggaacgtgccacgactgctgccttccaggcccaccaggcccaccaggacctccagg
ccgtccaggaccaaacggaaaggccggcgccaacggactcaacggaaacccaggaagacc
accagaggctccatgtgagccagtaaccccaccaccatgcccaccatgcccagcaggacc
aaagggagcccctggacaagccgggtacccgggagccgacgggcaacctggatcgcaggg
agacaatggagagaagggatcagacggtgctgctggagagaaaggacgtccaggaccact
tggaaagatcggagagccgggagcaactggagagacgggagagaacgctgagaatagtga
gccgactccaggaccacaaggaccaccgggagccattggaccagttggatcacgtggaac
tccaggacatcctggagaagatggagaagctggagctccgggagcacctggagagaatgg
aactgacggagagaatggagaagatggagttcctggagttccag

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
CGAAGGAACGTGCCACGACTGCTGC 525 253 504 Antisense
TCCAGGCCGTCCAGGACCAAACGGA 455 587 558 Antisense
AGACCACCAGAGGCTCCATGTGAGC 76 71 619 Antisense
GACGGGCAACCTGGATCGCAGGGAG 466 375 721 Antisense
GAAGGGATCAGACGGTGCTGCTGGA 419 335 756 Antisense
GGTGCTGCTGGAGAGAAAGGACGTC 678 501 769 Antisense
ATCGGAGAGCCGGGAGCAACTGGAG 596 33 811 Antisense
AGAATAGTGAGCCGACTCCAGGACC 625 73 854 Antisense
CACCGGGAGCCATTGGACCAGTTGG 488 199 887 Antisense
GACCAGTTGGATCACGTGGAACTCC 321 383 902 Antisense
GAAGATGGAGTTCCTGGAGTTCCAG 580 335 1003 Antisense
Sequence Source Affymetrix Proprietary Database