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[189561_at] cuticle collagen

Description W03G11.1 /REP_DB=WormBase Gene ID /WP=CE26826 /TR=Q23150 /GB=CAA91544.2 /SUBMIT=HINXTON /CHR=X /FEA=Sanger Annotation /DEF=cuticle collagen
Cluster 6grp_high1_10_10 > 91      6grp_total > 93      4grp_total > 25      6grp_cgc > 89      6grp_high1_sub > 05      6grp_total_sub > Hat      6grp_rule_based > S5      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 89
1 2 3 4 range
A 34.6
(-3)
A 		73.2
(-0.2)
A 		81.3
(0.4)
A 		117
(3)
P 		82
B 54.7
(-3)
P 		92.8
(0.5)
A 		97
(0.9)
A 		119.1
(3)
P 		64
C 52.5
(0.2)
A 		72.7
(3)
A 		30.1
(-3)
P 		64.4
(1.8)
P 		43
avr 47.3
(-3) 		79.6
(0.7) 		69.5
(-0.5) 		100.2
(3) 		53

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 6532
1 2 3 4 5 6 range
A 56
(-3)
A 		125.8
(-2.9)
P 		129.2
(-2.9)
P 		426.4
(-2.6)
P 		5813.1
(3)
P 		1544.2
(-1.4)
P 		5757
B 79.3
(-3)
P 		100.6
(-3)
P 		75
(-3)
A 		341.9
(-2.7)
P 		6143.4
(3)
P 		1468.5
(-1.6)
P 		6068
C 95.6
(-3)
P 		102.9
(-3)
P 		106.1
(-3)
P 		399.5
(-2.7)
P 		6588.4
(3)
P 		1163.3
(-2)
P 		6493
avr 77
(-3) 		109.8
(-3) 		103.4
(-3) 		389.3
(-2.7) 		6181.6
(3) 		1392
(-1.7) 		6105
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 15
1 2 3 4 range
A 12.6
(-3)
A 		15.9
(-0.7)
A 		21.3
(3)
A 		17.1
(0.1)
P 		9
B 17.4
(-3)
P 		22.9
(1.1)
A 		22.5
(0.8)
A 		25.4
(3)
P 		8
C 17.4
(1)
A 		20.9
(3)
A 		10.5
(-3)
P 		10.9
(-2.8)
P 		10
avr 15.8
(-3) 		19.9
(3) 		18.1
(0.4) 		17.8
(-0.1) 		4

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 2486
1 2 3 4 5 6 range
A 10.3
(-3)
A 		44.7
(-2.9)
P 		28.1
(-2.9)
P 		108.1
(-2.7)
P 		1754.1
(3)
P 		376
(-1.7)
P 		1744
B 27.6
(-3)
P 		33.5
(-3)
P 		18.2
(-3)
A 		90.5
(-2.8)
P 		2496
(3)
P 		547.6
(-1.7)
P 		2478
C 35.4
(-3)
P 		31.4
(-3)
P 		27
(-3)
P 		80.3
(-2.8)
P 		2131.9
(3)
P 		389.4
(-2)
P 		2105
avr 24.4
(-3) 		36.5
(-3) 		24.4
(-3) 		93
(-2.8) 		2127.3
(3) 		437.7
(-1.8) 		2103
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 189561_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.17207
Sequence Type Exemplar sequence
Representative Public ID W03G11.1 NCBI
Target Description W03G11.1 /REP_DB=WormBase Gene ID /WP=CE26826 /TR=Q23150 /GB=CAA91544.2 /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_077620(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_077620 NCBI Caenorhabditis elegans COLlagen family member (col-181) (col-181) mRNA, complete cds. 11/11 None
SNAP00000031753 ENSEMBL cdna:SNAP chromosome:CEL140:X:12105061:12105906:1 11/11 None
GENEFINDER00000031755 ENSEMBL cdna:GeneFinder chromosome:CEL140:X:12105061:12105906:1 11/11 None
W03G11.1 ENSEMBL cdna:known chromosome:CEL140:X:12104851:12106002:1 gene:W03G11.1 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:12105066-12105906(+) 100.0 100.0
Public Domain and Genome References
Gene Title cuticle collagen
Gene Symbol col-181
Ensembl W03G11.1
Entrez Gene 181378 Entrez gene
SwissProt Q23150 EMBL-EBI
WormBase CE26826 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 CAA91544 Hypothetical protein W03G11.1 [Caenorhabditis elegans] ref|NP_510021.1| COLlagen family member (col-181) [Caenorhabditis elegans] 1.0E-113
blast CAE69873 Hypothetical protein CBG16210 [Caenorhabditis briggsae] 1.0E-94
blast CAA91544 Hypothetical protein W03G11.1 [Caenorhabditis elegans] ref|NP_510021.1| COLlagen family member (col-181) [Caenorhabditis elegans] 2.0E-84
blast CAE69873 Hypothetical protein CBG16210 [Caenorhabditis briggsae] 5.0E-80
blast CAE56956 Hypothetical protein CBG24806 [Caenorhabditis briggsae] 1.0E-25
Protein Domains
Database ID Description E-Value
Pfam IPR002486 EMBL-EBI Nematode cuticle collagen, N-terminal 8.8E-7
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 3.3E-4
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 7.8E-7
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 5.1E-12
Pfam IPR002486 EMBL-EBI Nematode cuticle collagen, N-terminal 8.8E-7
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 3.3E-4
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 7.8E-7
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 5.1E-12
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_510021.1 1 66-88
W03G11.1 1 66-88
SNAP00000031753 1 12-34
GENEFINDER00000031755 1 12-34
Sequence
Target Sequence 
>C. ELEGANS:189561_AT
gagctccaagaaaggcacgtgctgctgagggaacctgctgctcctgcggagttggatcag
ctggaccaccaggaccaccaggatttgatggatccgctggaaaggatggatcaaacggac
gtccaggaaacccaggagaggatgctgatggagatgactacaagccagatgcaagccaat
tctgcttcgactgcccagaggctccagctggaccaccaggacgtccaggaccagacggag
agaacggaggagctggagagccaggacgtgacggacttgctggacgcccaggagctcgtg
gatcaccaggaccacgtggaccatctggaaacccaggagctgatggaccagcaggacaac
ttggaccacaaggaggatcaaacgttgcaccatctccagccggagagccaggagcaccag
gagcccaaggaccaaagggaccaccaggagccgctggacgtccaggacgcgacggacaac
caggagcaccaggagaccaaggagagaatggaccagacggagccccaggaaaatctggtt
ccg

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GAGCTCCAAGAAAGGCACGTGCTGC 113 387 224 Antisense
AAGGCACGTGCTGCTGAGGGAACCT 675 159 235 Antisense
GCTCCTGCGGAGTTGGATCAGCTGG 470 297 263 Antisense
ACCACCAGGATTTGATGGATCCGCT 356 85 297 Antisense
GGATGGATCAAACGGACGTCCAGGA 194 515 327 Antisense
GATGACTACAAGCCAGATGCAAGCC 508 411 376 Antisense
GATGCAAGCCAATTCTGCTTCGACT 157 413 391 Antisense
CCAGGACGTGACGGACTTGCTGGAC 489 271 484 Antisense
GGACCAGCAGGACAACTTGGACCAC 320 523 568 Antisense
GGAGGATCAAACGTTGCACCATCTC 141 517 595 Antisense
GGAGCCCCAGGAAAATCTGGTTCCG 397 519 742 Antisense
Sequence Source Affymetrix Proprietary Database