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[172826_x_at] collagen

Description F11G11.10 /REP_DB=WormBase Gene ID /WP=CE27952 /GEN=col-17 /TR=P91248 /GB=AAB37841.2 /SUBMIT=ST.LOUIS /CHR=2 /FEA=Sanger Annotation /DEF=collagen
Cluster 6grp_highest_10_10 > 08      6grp_high1_10_10 > 52      4grp_high_8_8 > 54      6grp_highest_nonorm > 08      6grp_total > 20      4grp_total > 49      6grp_cgc > 74      6grp_high1_sub > 03      6grp_cgc_sub > 02_03_04_05      6grp_total_sub > Hat      6grp_rule_based > S3      4grp_rule_based > L2      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 41758
1 2 3 4 range
A 3950.2
(-2.6)
P 		42407.6
(3)
P 		38017.5
(2.4)
P 		838.6
(-3)
M 		41569
B 3685.1
(-2.5)
P 		34351.4
(2.4)
P 		38126.2
(3)
P 		649.2
(-3)
P 		37477
C 3788.2
(-2.4)
P 		32420.1
(3)
P 		30308.4
(2.6)
P 		656
(-3)
P 		31764
avr 3807.8
(-2.5) 		36393
(3) 		35484
(2.8) 		714.6
(-3) 		35678

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 18942
1 2 3 4 5 6 range
A 8349
(-3)
P 		25164.7
(3)
P 		22521.9
(2.1)
P 		21457
(1.7)
P 		18126.2
(0.5)
P 		11514.2
(-1.9)
P 		16816
B 6794
(-3)
P 		23471
(2.4)
P 		25342.7
(3)
P 		20505.5
(1.4)
P 		17889.9
(0.6)
P 		10339.6
(-1.9)
P 		18549
C 6888.5
(-3)
P 		23704.4
(2.4)
P 		25736.2
(3)
P 		20811
(1.4)
P 		20463.9
(1.3)
P 		9297.8
(-2.2)
P 		18848
avr 7343.8
(-3) 		24113.4
(2.9) 		24533.6
(3) 		20924.5
(1.7) 		18826.7
(1) 		10383.9
(-1.9) 		17190
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 10453
1 2 3 4 range
A 1438.3
(-2.2)
P 		9205.5
(2.6)
P 		9938.5
(3)
P 		122.7
(-3)
M 		9816
B 1175.2
(-2.3)
P 		8484
(2.8)
P 		8834.7
(3)
P 		138.3
(-3)
P 		8696
C 1254
(-2.3)
P 		9321
(2.3)
P 		10563.4
(3)
P 		110.6
(-3)
P 		10453
avr 1289.2
(-2.3) 		9003.5
(2.5) 		9778.9
(3) 		123.9
(-3) 		9655

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 7411
1 2 3 4 5 6 range
A 1539.1
(-3)
P 		8949.8
(3)
P 		4904.8
(-0.3)
P 		5442
(0.2)
P 		5469.7
(0.2)
P 		2803.3
(-2)
P 		7411
B 2364
(-3)
P 		7812.5
(3)
P 		6154
(1.2)
P 		5431.2
(0.4)
P 		7268.4
(2.4)
P 		3855.6
(-1.4)
P 		5449
C 2553.3
(-3)
P 		7232.9
(3)
P 		6550.3
(2.1)
P 		4185.1
(-0.9)
P 		6621.8
(2.2)
P 		3112.5
(-2.3)
P 		4680
avr 2152.1
(-3) 		7998.4
(3) 		5869.7
(0.8) 		5019.4
(-0.1) 		6453.3
(1.4) 		3257.1
(-1.9) 		5846
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 172826_x_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.5032
Sequence Type Exemplar sequence
Representative Public ID F11G11.10 NCBI
Target Description F11G11.10 /REP_DB=WormBase Gene ID /WP=CE27952 /GEN=col-17 /TR=P91248 /GB=AAB37841.2 /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 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_062477(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_062477 NCBI Caenorhabditis elegans F11G11.10 (collagen) mRNA, complete cds. 11/11 None
SNAP00000005484 ENSEMBL cdna:SNAP chromosome:CEL140:II:4866709:4867560:-1 11/11 None
GENEFINDER00000005492 ENSEMBL cdna:GeneFinder chromosome:CEL140:II:4866709:4867560:-1 11/11 None
F11G11.10 ENSEMBL cdna:known chromosome:CEL140:II:4866430:4867560:-1 gene:F11G11.10 11/11 None
Annotation Notes
Cross Hybridizing mRNA Matched Probes Nature of Assignment Related Probesets by Grade
NM_067008 1/11 Cross Hyb Matching Probes A 
NM_067009 1/11 Cross Hyb Matching Probes A 
NM_181982 1/11 Cross Hyb Matching Probes None
NM_073276 1/11 Cross Hyb Matching Probes A 
NM_073277 1/11 Cross Hyb Matching Probes A 
NM_077291 1/11 Cross Hyb Matching Probes None
NM_182407 1/11 Cross Hyb Matching Probes None
NM_067504 1/11 Cross Hyb Matching Probes A 
NM_068749 1/11 Cross Hyb Matching Probes A 
NM_072974 1/11 Cross Hyb Matching Probes None
NM_070299 1/11 Cross Hyb Matching Probes A 
NM_001029722 1/11 Cross Hyb Matching Probes None
NM_069971 1/11 Cross Hyb Matching Probes A 
NM_001029723 1/11 Cross Hyb Matching Probes None
NM_076658 1/11 Cross Hyb Matching Probes A 
NM_076659 1/11 Cross Hyb Matching Probes A 
NM_075994 1/11 Cross Hyb Matching Probes A 
NM_062479 6/11 Cross Hyb Matching Probes A 
NM_067302 1/11 Cross Hyb Matching Probes A 
NM_073882 1/11 Cross Hyb Matching Probes A 
NM_073883 1/11 Cross Hyb Matching Probes A 
NM_067007 1/11 Cross Hyb Matching Probes A 
NM_072673 1/11 Cross Hyb Matching Probes A 
NM_060535 1/11 Cross Hyb Matching Probes A 
NM_061234 1/11 Cross Hyb Matching Probes A 
SNAP00000013576 1/11 Cross Hyb Matching Probes None
GENEFINDER00000013583 1/11 Cross Hyb Matching Probes None
SNAP00000005486 6/11 Cross Hyb Matching Probes None
GENEFINDER00000005502 6/11 Cross Hyb Matching Probes None
SNAP00000043178 1/11 Cross Hyb Matching Probes None
GENEFINDER00000043184 1/11 Cross Hyb Matching Probes None
SNAP00000036390 1/11 Cross Hyb Matching Probes None
GENEFINDER00000036401 2/11 Cross Hyb Matching Probes None
SNAP00000036391 2/11 Cross Hyb Matching Probes None
GENEFINDER00000036400 2/11 Cross Hyb Matching Probes None
SNAP00000036392 2/11 Cross Hyb Matching Probes None
GENEFINDER00000036395 2/11 Cross Hyb Matching Probes None
SNAP00000034887 1/11 Cross Hyb Matching Probes None
GENEFINDER00000034916 1/11 Cross Hyb Matching Probes None
GENEFINDER00000000294 1/11 Cross Hyb Matching Probes None
SNAP00000015232 1/11 Cross Hyb Matching Probes None
GENEFINDER00000015234 1/11 Cross Hyb Matching Probes None
SNAP00000033329 1/11 Cross Hyb Matching Probes None
GENEFINDER00000033337 1/11 Cross Hyb Matching Probes None
SNAP00000035582 1/11 Cross Hyb Matching Probes None
GENEFINDER00000035589 1/11 Cross Hyb Matching Probes None
SNAP00000043808 1/11 Cross Hyb Matching Probes None
GENEFINDER00000043818 1/11 Cross Hyb Matching Probes None
SNAP00000002596 1/11 Cross Hyb Matching Probes None
GENEFINDER00000002614 1/11 Cross Hyb Matching Probes None
SNAP00000002816 1/11 Cross Hyb Matching Probes None
SNAP00000002817 1/11 Cross Hyb Matching Probes None
GENEFINDER00000002822 1/11 Cross Hyb Matching Probes None
GENEFINDER00000002824 1/11 Cross Hyb Matching Probes None
SNAP00000007051 1/11 Cross Hyb Matching Probes None
SNAP00000007052 1/11 Cross Hyb Matching Probes None
GENEFINDER00000007058 1/11 Cross Hyb Matching Probes None
GENEFINDER00000007063 1/11 Cross Hyb Matching Probes None
SNAP00000025313 1/11 Cross Hyb Matching Probes None
GENEFINDER00000025319 1/11 Cross Hyb Matching Probes None
SNAP00000029183 1/11 Cross Hyb Matching Probes None
GENEFINDER00000029193 1/11 Cross Hyb Matching Probes None
SNAP00000029184 1/11 Cross Hyb Matching Probes None
GENEFINDER00000029190 1/11 Cross Hyb Matching Probes None
SNAP00000008502 1/11 Cross Hyb Matching Probes None
GENEFINDER00000008503 1/11 Cross Hyb Matching Probes None
SNAP00000003213 1/11 Cross Hyb Matching Probes None
GENEFINDER00000003228 1/11 Cross Hyb Matching Probes None
K08C9.4 1/11 Cross Hyb Matching Probes A 
C01B12.1 1/11 Cross Hyb Matching Probes A 
F11G11.12 6/11 Cross Hyb Matching Probes A 
W05B2.6 1/11 Cross Hyb Matching Probes A 
W05B2.5 1/11 Cross Hyb Matching Probes A 
W05B2.1 1/11 Cross Hyb Matching Probes A 
Y41C4A.19 1/11 Cross Hyb Matching Probes None
F14F7.1.2 1/11 Cross Hyb Matching Probes A 
F14F7.1.1 1/11 Cross Hyb Matching Probes A 
F14F7.1.3 1/11 Cross Hyb Matching Probes A 
K02D7.3 1/11 Cross Hyb Matching Probes A 
D2024.8 1/11 Cross Hyb Matching Probes A 
F08G5.4 1/11 Cross Hyb Matching Probes A 
F52B11.4 1/11 Cross Hyb Matching Probes A 
ZC513.8 1/11 Cross Hyb Matching Probes A 
B0222.7 1/11 Cross Hyb Matching Probes A 
F15H10.2 1/11 Cross Hyb Matching Probes A 
F15H10.1.1 1/11 Cross Hyb Matching Probes A 
F57B1.3 1/11 Cross Hyb Matching Probes A 
F57B1.4.1 1/11 Cross Hyb Matching Probes A 
F57B1.4.3 1/11 Cross Hyb Matching Probes None
F57B1.4.2 1/11 Cross Hyb Matching Probes A 
Y69H2.14.2 1/11 Cross Hyb Matching Probes None
Y69H2.14.3 1/11 Cross Hyb Matching Probes None
Y69H2.14.1 1/11 Cross Hyb Matching Probes None
EGAP7.1.1 1/11 Cross Hyb Matching Probes None
EGAP7.1.2 1/11 Cross Hyb Matching Probes None
T07H6.3a 1/11 Cross Hyb Matching Probes A 
T07H6.3b.3 1/11 Cross Hyb Matching Probes None
T07H6.3b.2 1/11 Cross Hyb Matching Probes A 
T10E10.2.1 1/11 Cross Hyb Matching Probes A 
T10E10.1 1/11 Cross Hyb Matching Probes A 
ZC373.7 1/11 Cross Hyb Matching Probes A 
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrII:4866707-4867559(-) 89.67 100.0
chrII:4869762-4873077(-) 86.74 93.08
Public Domain and Genome References
Gene Title collagen
Gene Symbol col-17
Ensembl F11G11.10
Entrez Gene 173839 Entrez gene
SwissProt P91248 EMBL-EBI
WormBase CE31783 Wormbase
Functional Annotations
Protein Similarities
Method ID Description E-Value
blast NP_494878 F11G11.10 [Caenorhabditis elegans] gb|AAB37841.3| Collagen protein 17 [Caenorhabditis elegans] 1.0E-145
blast AAA62504 collagen 1.0E-140
blast NP_494880 F11G11.12 [Caenorhabditis elegans] gb|AAB37843.1| Collagen protein 73 [Caenorhabditis elegans] 1.0E-57
blast CAE56956 Hypothetical protein CBG24806 [Caenorhabditis briggsae] 2.0E-57
blast CAB50767 putative cuticular collagen protein [Ascaris suum] emb|CAB85465.1| putative cuticular collagen [Ascaris suum] 1.0E-33
Protein Domains
Database ID Description E-Value
Pfam IPR002486 EMBL-EBI Nematode cuticle collagen, N-terminal 3.2E-9
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 8.8E-4
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 4.3E-12
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 3.8E-14
Trans Membrane
ID Number Of Domains Domain Boundaries
SNAP00000005484 1 16-38
GENEFINDER00000005492 1 16-38
Sequence
Target Sequence 
>C. ELEGANS:172826_X_AT
gagccgtgagaagcgtcaaacctaccaatgctgctcttgtggaatcggaccagctggatc
cgttggaaacccaggacaagacggagccccaggaaatgacggaagaccaggagccccagg
agctccaggaccagatgctccaaatgatcatgttcaaccaacccccgccgatttctgctt
cgagtgcccaccaggaccagccggaaacgccggaaacccaggaccaaagggaccaccagg
acagccaggagcaccaggagagcaaggaccaaatggacgcccaggaaccccaggagcccc
aggaccacaaggaccaccaggaaccccaggacaagacggaactccaggacaaccaggagc
cccaggacaagtccgcaccgtcccagccccaccagggaacccaggacagccaggagagcc
aggagcccaaggaccaccaggaccagacggacacccaggaagcgctggaccacaaggacc
accaggaccacaaggagat

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GAGCCGTGAGAAGCGTCAAACCTAC 257 385 243 Antisense
TCAAACCTACCAATGCTGCTCTTGT 461 629 258 Antisense
GGACCAGCTGGATCCGTTGGAAACC 321 523 289 Antisense
AATGACGGAAGACCAGGAGCCCCAG 135 163 337 Antisense
GAGCTCCAGGACCAGATGCTCCAAA 439 387 362 Antisense
AAATGATCATGTTCAACCAACCCCC 620 119 384 Antisense
GGACCAAAGGGACCACCAGGACAGC 7 523 463 Antisense
GAACTCCAGGACAACCAGGAGCCCC 199 349 581 Antisense
AGGACAGCCAGGAGAGCCAGGAGCC 390 55 645 Antisense
CAGGAAGCGCTGGACCACAAGGACC 17 209 698 Antisense
AGGACCACCAGGACCACAAGGAGAT 236 55 717 Antisense
Sequence Source Affymetrix Proprietary Database