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[172723_x_at]

Description B0222.8 /REP_DB=WormBase Gene ID /WP=CE06699 /GEN=col-10 /TR=Q17460 /GB=AAA92325.1 /SUBMIT=ST.LOUIS /CHR=5 /FEA=Sanger Annotation
Cluster 6grp_highest_10_10 > 15      6grp_high1_10_10 > 40      4grp_highest_8_8 > 16      4grp_high_8_8 > 52      6grp_highest_nonorm > 09      6grp_total > 41      4grp_total > 59      6grp_highest_sub > 03      6grp_cgc > 83      6grp_high1_sub > 03      6grp_cgc_sub > 03      6grp_total_sub > Hat      6grp_rule_based > S3      4grp_rule_based > L2      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 49035
1 2 3 4 range
A 34276.4
(1.1)
P 		49804.9
(3)
P 		44954.3
(2.4)
P 		1854.6
(-3)
P 		47950
B 35568.9
(1.1)
P 		42807.3
(2)
P 		50715.7
(3)
P 		1680.7
(-3)
P 		49035
C 35581.4
(2.4)
P 		39157.3
(3)
P 		36069.5
(2.5)
P 		2033.5
(-3)
P 		37124
avr 35142.2
(1.7) 		43923.2
(3) 		43913.2
(3) 		1856.3
(-3) 		42067

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 28510
1 2 3 4 5 6 range
A 39394.1
(-1)
P 		41489.6
(-0.4)
P 		53622.8
(3)
P 		41178.4
(-0.5)
P 		32220.2
(-3)
P 		34281
(-2.4)
P 		21403
B 36987.1
(0.1)
P 		36832.4
(0.1)
P 		47774.8
(3)
P 		41171.2
(1.2)
P 		27190.1
(-2.5)
P 		25412.5
(-3)
P 		22362
C 33794.2
(-0.6)
P 		39088.6
(0.9)
P 		46643.4
(3)
P 		44735.1
(2.5)
P 		35380.2
(-0.1)
P 		25112.9
(-3)
P 		21531
avr 36725.1
(-0.6) 		39136.9
(0.1) 		49347
(3) 		42361.6
(1) 		31596.8
(-2.1) 		28268.8
(-3) 		21078
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 12300
1 2 3 4 range
A 12480
(3)
P 		10811.3
(2.2)
P 		11751.9
(2.6)
P 		271.5
(-3)
P 		12209
B 11342.6
(2.8)
P 		10572.4
(2.4)
P 		11752
(3)
P 		358.2
(-3)
P 		11394
C 11778.4
(2.6)
P 		11258
(2.4)
P 		12571.3
(3)
P 		342.9
(-3)
P 		12228
avr 11867
(2.9) 		10880.6
(2.4) 		12025.1
(3) 		324.2
(-3) 		11701

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 7494
1 2 3 4 5 6 range
A 7262
(-3)
P 		14755.7
(3)
P 		11677.9
(0.5)
P 		10443.8
(-0.5)
P 		9722.6
(-1)
P 		8346.4
(-2.1)
P 		7494
B 12869.7
(3)
P 		12260
(1.9)
P 		11601.1
(0.8)
P 		10904.8
(-0.5)
P 		11047
(-0.2)
P 		9476.2
(-3)
P 		3394
C 12526
(3)
P 		11927.1
(2.1)
P 		11871.5
(2)
P 		8996.3
(-2.1)
P 		11448.5
(1.4)
P 		8406.7
(-3)
P 		4119
avr 10885.9
(0) 		12980.9
(3) 		11716.8
(1.2) 		10115
(-1.1) 		10739.4
(-0.2) 		8743.1
(-3) 		4238
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 172723_x_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.11335
Sequence Type Exemplar sequence
Representative Public ID B0222.8 NCBI
Target Description B0222.8 /REP_DB=WormBase Gene ID /WP=CE06699 /GEN=col-10 /TR=Q17460 /GB=AAA92325.1 /SUBMIT=ST.LOUIS /CHR=5 /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_072973(10), NM_072975(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_072973 NCBI Caenorhabditis elegans COLlagen family member (col-144) (col-144) mRNA, complete cds. 10/11 A 
NM_072975 NCBI Caenorhabditis elegans COLlagen family member (col-10) (col-10) mRNA, complete cds. 11/11 A 
SNAP00000023008 ENSEMBL cdna:SNAP chromosome:CEL140:V:9162280:9163212:-1 10/11 None
SNAP00000023010 ENSEMBL cdna:SNAP chromosome:CEL140:V:9166941:9167875:-1 11/11 None
GENEFINDER00000023016 ENSEMBL cdna:GeneFinder chromosome:CEL140:V:9166941:9167875:-1 11/11 None
GENEFINDER00000023019 ENSEMBL cdna:GeneFinder chromosome:CEL140:V:9162280:9163248:-1 10/11 None
B0222.6 ENSEMBL cdna:known chromosome:CEL140:V:9162221:9163248:-1 gene:B0222.6 10/11 A 
B0222.8 ENSEMBL cdna:known chromosome:CEL140:V:9166882:9167892:-1 gene:B0222.8 11/11 A 
Annotation Notes
Cross Hybridizing mRNA Matched Probes Nature of Assignment Related Probesets by Grade
NM_066413 1/11 Cross Hyb Matching Probes A 
NM_069125 1/11 Cross Hyb Matching Probes A 
NM_069126 1/11 Cross Hyb Matching Probes A 
NM_072974 1/11 Cross Hyb Matching Probes A 
NM_069971 1/11 Cross Hyb Matching Probes A 
NM_001029723 1/11 Cross Hyb Matching Probes None
NM_182455 1/11 Cross Hyb Matching Probes A 
NM_171268 1/11 Cross Hyb Matching Probes A 
NM_182305 1/11 Cross Hyb Matching Probes A 
NM_067693 1/11 Cross Hyb Matching Probes None
NM_059194 1/11 Cross Hyb Matching Probes A 
NM_073933 1/11 Cross Hyb Matching Probes A 
NM_001027491 1/11 Cross Hyb Matching Probes None
NM_077559 1/11 Cross Hyb Matching Probes A 
NM_077620 1/11 Cross Hyb Matching Probes A 
NM_062478 1/11 Cross Hyb Matching Probes A 
SNAP00000014505 1/11 Cross Hyb Matching Probes None
GENEFINDER00000014522 1/11 Cross Hyb Matching Probes None
SNAP00000005485 1/11 Cross Hyb Matching Probes None
GENEFINDER00000005498 1/11 Cross Hyb Matching Probes None
SNAP00000034500 1/11 Cross Hyb Matching Probes None
GENEFINDER00000034516 1/11 Cross Hyb Matching Probes None
SNAP00000032557 1/11 Cross Hyb Matching Probes None
GENEFINDER00000032568 1/11 Cross Hyb Matching Probes None
SNAP00000005654 1/11 Cross Hyb Matching Probes None
SNAP00000005655 1/11 Cross Hyb Matching Probes None
GENEFINDER00000005663 1/11 Cross Hyb Matching Probes None
GENEFINDER00000005664 1/11 Cross Hyb Matching Probes None
SNAP00000027314 1/11 Cross Hyb Matching Probes None
GENEFINDER00000027318 1/11 Cross Hyb Matching Probes None
SNAP00000036194 1/11 Cross Hyb Matching Probes None
GENEFINDER00000036201 1/11 Cross Hyb Matching Probes None
SNAP00000043808 1/11 Cross Hyb Matching Probes None
GENEFINDER00000043818 1/11 Cross Hyb Matching Probes None
SNAP00000011428 1/11 Cross Hyb Matching Probes None
GENEFINDER00000011431 1/11 Cross Hyb Matching Probes None
SNAP00000023009 1/11 Cross Hyb Matching Probes None
GENEFINDER00000023017 1/11 Cross Hyb Matching Probes None
GENEFINDER00000028425 1/11 Cross Hyb Matching Probes None
SNAP00000029185 1/11 Cross Hyb Matching Probes None
GENEFINDER00000029188 1/11 Cross Hyb Matching Probes None
SNAP00000037973 1/11 Cross Hyb Matching Probes None
GENEFINDER00000037983 1/11 Cross Hyb Matching Probes None
SNAP00000031753 1/11 Cross Hyb Matching Probes None
GENEFINDER00000031755 1/11 Cross Hyb Matching Probes None
F27C1.8 1/11 Cross Hyb Matching Probes A 
F11G11.11.2 1/11 Cross Hyb Matching Probes None
F09G8.6 1/11 Cross Hyb Matching Probes A 
K04H4.1a 1/11 Cross Hyb Matching Probes A 
Y77E11A.15 1/11 Cross Hyb Matching Probes A 
C34H4.4a 1/11 Cross Hyb Matching Probes None
C34H4.4b 1/11 Cross Hyb Matching Probes A 
T28C6.4 1/11 Cross Hyb Matching Probes A 
T28C6.6 1/11 Cross Hyb Matching Probes A 
F08G5.4 1/11 Cross Hyb Matching Probes A 
B0222.7 1/11 Cross Hyb Matching Probes A 
Y2H9A.3 1/11 Cross Hyb Matching Probes A 
T07H6.3b.3 1/11 Cross Hyb Matching Probes None
T10E10.5 1/11 Cross Hyb Matching Probes A 
C44C10.1 1/11 Cross Hyb Matching Probes A 
W03G11.1 1/11 Cross Hyb Matching Probes A 
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrV:9166941-9167876(-) 85.99 100.0
chrV:9162280-9165575(-) 84.07 98.08
Public Domain and Genome References
Gene Title

Gene Symbol col-144
col-10
Ensembl B0222.6
B0222.8
Entrez Gene 179296 Entrez gene
179298 Entrez gene
SwissProt Q17458 EMBL-EBI
Q17460 EMBL-EBI
WormBase CE30585 Wormbase
CE06699 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 AAA92325 Collagen protein 10 [Caenorhabditis elegans] ref|NP_505376.1| COLlagen family member (col-10) [Caenorhabditis elegans] 4.0E-58
blast CAE72121 Hypothetical protein CBG19217 [Caenorhabditis briggsae] 6.0E-56
blast AAA92324 Collagen protein 145 [Caenorhabditis elegans] ref|NP_505375.1| COLlagen family member (col-145) [Caenorhabditis elegans] 1.0E-55
Protein Domains
Database ID Description E-Value
Pfam IPR002486 EMBL-EBI Nematode cuticle collagen, N-terminal 5.6E-29
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 7.7E-4
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 2.0E-12
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 9.5E-9
Pfam IPR002486 EMBL-EBI Nematode cuticle collagen, N-terminal 7.7E-29
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 7.7E-4
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 2.0E-12
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 9.5E-9
Pfam IPR002486 EMBL-EBI Nematode cuticle collagen, N-terminal 5.6E-29
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_505374.2 1 16-38
NP_505376.1 1 5-27
B0222.6 1 16-38
B0222.8 1 5-27
SNAP00000023008 1 5-27
SNAP00000023010 1 5-27
GENEFINDER00000023016 1 5-27
GENEFINDER00000023019 1 16-38
Sequence
Target Sequence 
>C. ELEGANS:172723_X_AT
ctcccagcttggtgccaatgcgagccaactaagccaacttgcccaccaggaccaccagga
ccaccaggacagccaggagccccaggaaccccaggagccccaggaccaaagggagacgac
aacaccgctaccttcgctccactcacctgcgccccagtctcccaagactgcgtcaagtgc
ccagaaggaccagctggaccagccggaccagaaggaccagccggaccagccggaccagac
ggacaaccaggagcaccaggaaacgctggaaacccaggatccgacggacaaccaggagcc
ccaggagacaacggacaagacggagccccaggacaagacggacaaccaggagccccagga
caagacggacaacgtggatccggagccccaggaggaccaggagccccaggaaacgctgga
ccagctggaccagccggacaagacggagccccaggacaagacggacaaccaggaccagcc
ggaccagctggacaagatggagccccaggaaacgctggatccgatggacaaccaggagcc
ccaggaggaccaggacttccaggaaacgatgccgcttattgcgcttgc

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
CTCCCAGCTTGGTGCCAATGCGAGC 101 235 274 Antisense
GACTGCGTCAAGTGCCCAGAAGGAC 602 373 439 Antisense
GAAGGACCAGCTGGACCAGCCGGAC 186 333 457 Antisense
GGACCAGACGGACAACCAGGAGCAC 393 523 505 Antisense
AGGATCCGACGGACAACCAGGAGCC 225 57 549 Antisense
AACGCTGGACCAGCTGGACCAGCCG 271 145 685 Antisense
ACAAGACGGACAACCAGGACCAGCC 182 113 729 Antisense
GGACCAGCCGGACCAGCTGGACAAG 455 523 745 Antisense
GGATCCGATGGACAACCAGGAGCCC 208 511 790 Antisense
CCCAGGAGGACCAGGACTTCCAGGA 231 259 813 Antisense
AAACGATGCCGCTTATTGCGCTTGC 360 127 837 Antisense
Sequence Source Affymetrix Proprietary Database