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[188473_s_at] collagen

Description ZK1010.7 /REP_DB=WormBase Gene ID /WP=CE15507 /TR=O18286 /GB=CAB04973.1 /SUBMIT=HINXTON /CHR=3 /FEA=Sanger Annotation /DEF=collagen
Cluster 6grp_high1_10_10 > 91      6grp_total > 93      4grp_total > 57      6grp_cgc > 98      6grp_high1_sub > 05      6grp_total_sub > Hat      4grp_rule_based > L3      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 5079
1 2 3 4 range
A 70.1
(-2.9)
A 		4251.8
(2.7)
P 		4477.3
(3)
P 		7
(-3)
A 		4470
B 80.6
(-2.9)
A 		3783.6
(1.5)
P 		5086.1
(3)
P 		25.9
(-3)
A 		5060
C 68.5
(-2.9)
A 		3648.4
(2.4)
P 		4026.9
(3)
P 		15.7
(-3)
A 		4011
avr 73.1
(-2.9) 		3894.6
(2.2) 		4530.1
(3) 		16.2
(-3) 		4514

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 6696
1 2 3 4 5 6 range
A 569.3
(-3)
A 		2313.1
(-1)
P 		1790.2
(-1.6)
P 		3760.3
(0.7)
P 		5805.1
(3)
P 		2246.5
(-1.1)
P 		5236
B 580.7
(-3)
M 		2391.2
(-0.8)
P 		2379
(-0.8)
P 		3277.3
(0.2)
P 		5574.6
(3)
P 		2182
(-1.1)
P 		4994
C 804
(-3)
P 		2215.1
(-1.7)
P 		1984.5
(-1.9)
P 		3086
(-0.9)
P 		7264.9
(3)
P 		1741.2
(-2.1)
P 		6461
avr 651.3
(-3) 		2306.5
(-1.2) 		2051.2
(-1.5) 		3374.5
(-0.1) 		6214.9
(3) 		2056.6
(-1.5) 		5564
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 1403
1 2 3 4 range
A 25.5
(-2.9)
A 		923
(1.7)
P 		1170.4
(3)
P 		1
(-3)
A 		1169
B 25.7
(-2.9)
A 		934.5
(1.8)
P 		1178.6
(3)
P 		5.5
(-3)
A 		1173
C 22.7
(-2.9)
A 		1048.9
(1.5)
P 		1403.5
(3)
P 		2.6
(-3)
A 		1401
avr 24.6
(-2.9) 		968.8
(1.6) 		1250.8
(3) 		3
(-3) 		1248

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 2246
1 2 3 4 5 6 range
A 104.9
(-3)
A 		822.6
(-0.4)
P 		389.9
(-2)
P 		953.7
(0.1)
P 		1751.7
(3)
P 		547
(-1.4)
P 		1647
B 202.1
(-3)
M 		795.9
(-1.3)
P 		577.7
(-1.9)
P 		868.1
(-1.1)
P 		2264.9
(3)
P 		813.6
(-1.2)
P 		2063
C 298
(-3)
P 		675.9
(-1.9)
P 		505.1
(-2.4)
P 		620.6
(-2.1)
P 		2350.8
(3)
P 		582.9
(-2.2)
P 		2053
avr 201.7
(-3) 		764.8
(-1.2) 		490.9
(-2.1) 		814.1
(-1.1) 		2122.5
(3) 		647.8
(-1.6) 		1921
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 188473_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.6935
Sequence Type Exemplar sequence
Representative Public ID ZK1010.7 NCBI
Target Description ZK1010.7 /REP_DB=WormBase Gene ID /WP=CE15507 /TR=O18286 /GB=CAB04973.1 /SUBMIT=HINXTON /CHR=3 /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_067299(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_067299 NCBI Caenorhabditis elegans ZK1010.7 (collagen) mRNA, complete cds. 11/11 None
SNAP00000035101 ENSEMBL cdna:SNAP chromosome:CEL140:III:12984057:12993209:-1 11/11 None
GENEFINDER00000035107 ENSEMBL cdna:GeneFinder chromosome:CEL140:III:12992196:12993209:-1 11/11 None
ZK1010.7 ENSEMBL cdna:known chromosome:CEL140:III:12991921:12993225:-1 gene:ZK1010.7 11/11 A 
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
chrIII:12992191-12993205(-) 100.0 100.0
Public Domain and Genome References
Gene Title collagen
Gene Symbol col-97
Ensembl ZK1010.7
Entrez Gene 176721 Entrez gene
SwissProt O18286 EMBL-EBI
WormBase CE15507 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 CAB04971 Hypothetical protein ZK1010.5 [Caenorhabditis elegans] ref|NP_499698.1| ZK1010.5 [Caenorhabditis elegans] 0.0
blast CAB04973 Hypothetical protein ZK1010.7 [Caenorhabditis elegans] ref|NP_499700.1| ZK1010.7 [Caenorhabditis elegans] 7.0E-64
blast CAE69571 Hypothetical protein CBG15783 [Caenorhabditis briggsae] 3.0E-63
blast CAB04973 Hypothetical protein ZK1010.7 [Caenorhabditis elegans] ref|NP_499700.1| ZK1010.7 [Caenorhabditis elegans] 5.0E-62
blast CAE69571 Hypothetical protein CBG15783 [Caenorhabditis briggsae] 2.0E-61
blast CAD66221 Hypothetical protein Y41C4A.19 [Caenorhabditis elegans] ref|NP_871711.1| Y41C4A.19 [Caenorhabditis elegans] 5.0E-19
Protein Domains
Database ID Description E-Value
Pfam IPR002486 EMBL-EBI Nematode cuticle collagen, N-terminal 3.9E-8
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 3.1E-4
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 1.4E-6
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 8.6E-13
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_499700.1 1 13-35
ZK1010.7 1 13-35
SNAP00000035101 2 13-35,1046-1068
GENEFINDER00000035107 1 13-35
Sequence
Target Sequence 
>C. ELEGANS:188473_S_AT
ccaggtcttcctggaccagacggaccaccaggaaagaacggagctccaggacggccggga
gctccaggagcacctggattcccaggacgcccaccagcagtgtgtgaggagatcaccgag
ccaccatgcacaccatgcccaccaggagagccaggaccaccaggaccaccaggagatgct
ggaaacccgggacaatcggggcatccaggaagaaatggaaatgatggaggagttggacca
caaggaccaccaggaccacccggaaacaacggagaaggaggaagagatggaccacgtgga
gagcaaggaagaccagcaatctccactccagctctgccaggagatccaggagcaccagga
gaaccgggaccatctggacttccaggagatcaaggacaagctggccgtccaggatc

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
CCAGGTCTTCCTGGACCAGACGGAC 551 267 316 Antisense
GAGCTCCAGGACGGCCGGGAGCTCC 654 385 356 Antisense
ACGCCCACCAGCAGTGTGTGAGGAG 103 91 402 Antisense
GTGTGAGGAGATCACCGAGCCACCA 110 489 417 Antisense
AGATGCTGGAAACCCGGGACAATCG 268 67 489 Antisense
GGGACAATCGGGGCATCCAGGAAGA 230 495 504 Antisense
GACCACGTGGAGAGCAAGGAAGACC 2 385 605 Antisense
CAAGGAAGACCAGCAATCTCCACTC 571 183 619 Antisense
TCCAGCTCTGCCAGGAGATCCAGGA 620 589 642 Antisense
CCAGGAGAACCGGGACCATCTGGAC 213 271 670 Antisense
AAGGACAAGCTGGCCGTCCAGGATC 461 161 707 Antisense
Sequence Source Affymetrix Proprietary Database