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[189272_at] cuticle collagen

Description R09A8.4 /REP_DB=WormBase Gene ID /WP=CE03540 /TR=Q21855 /GB=CAA92006.1 /SUBMIT=HINXTON /CHR=X /FEA=Sanger Annotation /DEF=cuticle collagen
Cluster 6grp_total > 93      4grp_total > 56      6grp_cgc > 98      6grp_total_sub > Hat      6grp_rule_based > S5      4grp_rule_based > L3      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 838
1 2 3 4 range
A 28.9
(-2.9)
A 		634.4
(2.7)
M 		667.6
(3)
P 		19.7
(-3)
A 		648
B 29.6
(-3)
A 		614.9
(1.3)
A 		850.7
(3)
P 		55.8
(-2.8)
A 		821
C 81.4
(-2.4)
A 		569.3
(1.8)
A 		712.1
(3)
P 		12.3
(-3)
A 		700
avr 46.6
(-2.9) 		606.2
(1.8) 		743.5
(3) 		29.3
(-3) 		714

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 665
1 2 3 4 5 6 range
A 131.2
(-3)
A 		294.1
(-0.7)
A 		266.3
(-1.1)
A 		465.2
(1.7)
A 		557.2
(3)
P 		240.8
(-1.5)
A 		426
B 157.5
(-3)
A 		241.8
(-1.8)
A 		346.6
(-0.3)
A 		399.9
(0.5)
A 		576.4
(3)
P 		276.1
(-1.3)
A 		419
C 232.6
(-3)
A 		297.7
(-2.3)
A 		255.1
(-2.7)
A 		333.6
(-1.9)
A 		796.2
(3)
A 		229.2
(-3)
A 		567
avr 173.8
(-3) 		277.9
(-1.7) 		289.3
(-1.5) 		399.6
(-0.1) 		643.3
(3) 		248.7
(-2) 		470
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 246
1 2 3 4 range
A 10.5
(-2.7)
A 		137.7
(1.7)
M 		174.5
(3)
P 		2.9
(-3)
A 		172
B 9.5
(-3)
A 		151.9
(1.6)
A 		197.1
(3)
P 		11.9
(-2.9)
A 		188
C 26.9
(-2.4)
A 		163.7
(0.9)
A 		248.2
(3)
P 		2.1
(-3)
A 		246
avr 15.6
(-2.7) 		151.1
(1.3) 		206.6
(3) 		5.6
(-3) 		201

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 233
1 2 3 4 5 6 range
A 24.2
(-3)
A 		104.6
(0.4)
A 		58
(-1.6)
A 		118
(0.9)
A 		168.2
(3)
P 		58.6
(-1.6)
A 		144
B 54.8
(-3)
A 		80.5
(-2.1)
A 		84.2
(-2)
A 		105.9
(-1.3)
A 		234.2
(3)
P 		103
(-1.4)
A 		179
C 86.2
(-2.3)
A 		90.8
(-2.2)
A 		64.9
(-3)
A 		67.1
(-2.9)
A 		257.6
(3)
A 		76.7
(-2.6)
A 		193
avr 55.1
(-3) 		92
(-1.7) 		69
(-2.5) 		97
(-1.5) 		220
(3) 		79.4
(-2.1) 		165
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 189272_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.17770
Sequence Type Exemplar sequence
Representative Public ID R09A8.4 NCBI
Target Description R09A8.4 /REP_DB=WormBase Gene ID /WP=CE03540 /TR=Q21855 /GB=CAA92006.1 /SUBMIT=HINXTON /CHR=X /FEA=Sanger Annotation /DEF=cuticle 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_077709(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_077709 NCBI Caenorhabditis elegans COLlagen family member (col-182) (col-182) mRNA, complete cds. 11/11 None
SNAP00000001741 ENSEMBL cdna:SNAP chromosome:CEL140:X:12636074:12636977:-1 9/11 None
GENEFINDER00000001745 ENSEMBL cdna:GeneFinder chromosome:CEL140:X:12636074:12636977:-1 9/11 None
R09A8.4 ENSEMBL cdna:known chromosome:CEL140:X:12636074:12636532:-1 gene:R09A8.4 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
chrX:12636073-12636532(-) 100.0 100.0
Public Domain and Genome References
Gene Title cuticle collagen
Gene Symbol col-182
Ensembl R09A8.4
Entrez Gene 187723 Entrez gene
SwissProt Q21855 EMBL-EBI
WormBase CE03540 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
Protein Similarities
Method ID Description E-Value
blast CAE57231 Hypothetical protein CBG00101 [Caenorhabditis briggsae] 2.0E-81
blast CAE57231 Hypothetical protein CBG00101 [Caenorhabditis briggsae] 6.0E-26
blast CAA92006 Hypothetical protein R09A8.4 [Caenorhabditis elegans] ref|NP_510110.1| COLlagen family member (col-182) [Caenorhabditis elegans] 6.0E-25
blast CAA92006 Hypothetical protein R09A8.4 [Caenorhabditis elegans] ref|NP_510110.1| COLlagen family member (col-182) [Caenorhabditis elegans] 2.0E-19
blast CAA92006 Hypothetical protein R09A8.4 [Caenorhabditis elegans] ref|NP_510110.1| COLlagen family member (col-182) [Caenorhabditis elegans] 3.0E-18
blast CAE57231 Hypothetical protein CBG00101 [Caenorhabditis briggsae] 7.0E-17
blast CAE73812 Hypothetical protein CBG21362 [Caenorhabditis briggsae] 3.0E-16
Protein Domains
Database ID Description E-Value
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 2.4E-9
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 1.3E-11
Pfam IPR002486 EMBL-EBI Nematode cuticle collagen, N-terminal 3.3E-5
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 3.7E-6
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 1.4E-11
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 1.3E-11
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 2.4E-9
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 1.3E-11
Trans Membrane
ID Number Of Domains Domain Boundaries
SNAP00000001741 1 7-29
GENEFINDER00000001745 1 7-29
Sequence
Target Sequence 
>C. ELEGANS:189272_AT
ggaccaccgggaacaactatatccagggatatccaggacagccaggaccacaaggacttc
caggaaaccagggagatcaaggagagatcggacgcgaaggatcaccaggagcccagggag
ctccaggagatatgggaatgatgggagaggcaggaaaggaaggcgagaagggagctccag
gaagagagggagttcgtggagagaagggaccatctggaccaccaggacttccaggactcg
ttggaccaaagggattctctggaaacagtgggccaccaggaagcccaggagagccagggc
cagaaggagagcaaggaccagctggaaaggatggagctccaggttacgatggtggattcg
gaaactatggagaggcaggacagccaggagaggatgccggata

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GGACCACCGGGAACAACTATATCCA 400 521 32 Antisense
ATATCCAGGGATATCCAGGACAGCC 670 9 50 Antisense
CGGACGCGAAGGATCACCAGGAGCC 271 243 120 Antisense
GAGCCCAGGGAGCTCCAGGAGATAT 608 385 140 Antisense
GGAAGGCGAGAAGGGAGCTCCAGGA 649 531 189 Antisense
CTCGTTGGACCAAAGGGATTCTCTG 518 27 268 Antisense
GATTCTCTGGAAACAGTGGGCCACC 99 433 284 Antisense
GGCCACCAGGAAGCCCAGGAGAGCC 18 543 302 Antisense
GAGAGCCAGGGCCAGAAGGAGAGCA 62 395 320 Antisense
GGATGGAGCTCCAGGTTACGATGGT 407 515 360 Antisense
GACAGCCAGGAGAGGATGCCGGATA 172 369 410 Antisense
Sequence Source Affymetrix Proprietary Database