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[189723_s_at] cuticular collagen

Description EGAP7.1 /REP_DB=WormBase Gene ID /WP=CE07013 /TR=Q19079 /GB=AAB00598.1 /SUBMIT=ST.LOUIS /CHR=X /FEA=Sanger Annotation /DEF=cuticular collagen
Cluster 6grp_high1_10_10 > 09      6grp_total > 03      4grp_total > 50      6grp_cgc > 51      4grp_rule_based > L2      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 4015
1 2 3 4 range
A 35.8
(-3)
A 		3599.9
(3)
P 		2411.5
(1)
P 		124.1
(-2.9)
A 		3564
B 19.8
(-3)
A 		4015.9
(3)
P 		3316.4
(2)
P 		13.7
(-3)
A 		4002
C 30.8
(-3)
A 		4022.4
(3)
P 		3230.4
(1.8)
P 		7.6
(-3)
A 		4015
avr 28.8
(-3) 		3879.4
(3) 		2986.1
(1.6) 		48.5
(-3) 		3851

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 2505
1 2 3 4 5 6 range
A 2122.3
(2.8)
P 		1511.3
(0.7)
P 		2126.5
(2.9)
P 		2161
(3)
P 		2168.6
(3)
P 		481.7
(-3)
A 		1687
B 2986.3
(3)
P 		2328.4
(1.2)
P 		1808.2
(-0.2)
P 		2159.1
(0.8)
P 		1784.9
(-0.3)
P 		772.8
(-3)
P 		2214
C 2105.2
(2)
P 		2365.9
(2.8)
P 		1493.5
(0.1)
P 		1454
(-0)
P 		2426.9
(3)
P 		488.9
(-3)
A 		1938
avr 2404.6
(3) 		2068.5
(1.9) 		1809.4
(1) 		1924.7
(1.4) 		2126.8
(2.1) 		581.1
(-3) 		1824
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 1155
1 2 3 4 range
A 13
(-3)
A 		781.4
(3)
P 		630.4
(1.8)
P 		18.2
(-3)
A 		768
B 6.3
(-3)
A 		991.8
(3)
P 		768.5
(1.6)
P 		2.9
(-3)
A 		989
C 10.2
(-3)
A 		1156.5
(3)
P 		1125.9
(2.8)
P 		1.3
(-3)
A 		1155
avr 9.8
(-3) 		976.6
(3) 		841.6
(2.2) 		7.5
(-3) 		969

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 922
1 2 3 4 5 6 range
A 391.2
(0.1)
P 		537.5
(1.7)
P 		463.1
(0.9)
P 		548.1
(1.8)
P 		654.4
(3)
P 		117.3
(-3)
A 		537
B 1039.1
(3)
P 		775
(0.9)
P 		439.1
(-1.8)
P 		571.9
(-0.7)
P 		725.2
(0.5)
P 		288.2
(-3)
P 		751
C 780.3
(3)
P 		721.9
(2.4)
P 		380.1
(-0.9)
P 		292.4
(-1.8)
P 		785.3
(3)
P 		163.6
(-3)
A 		622
avr 736.9
(3) 		678.1
(2.4) 		427.4
(-0.4) 		470.8
(0.1) 		721.6
(2.8) 		189.7
(-3) 		547
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 189723_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.18082
Sequence Type Exemplar sequence
Representative Public ID EGAP7.1 NCBI
Target Description EGAP7.1 /REP_DB=WormBase Gene ID /WP=CE07013 /TR=Q19079 /GB=AAB00598.1 /SUBMIT=ST.LOUIS /CHR=X /FEA=Sanger Annotation /DEF=cuticular 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_075994(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_075994 NCBI Caenorhabditis elegans DumPY : shorter than wild-type family member (dpy-3) (dpy-3) mRNA, complete cds. 11/11 None
SNAP00000008502 ENSEMBL cdna:SNAP chromosome:CEL140:X:2144649:2145639:-1 11/11 None
GENEFINDER00000008503 ENSEMBL cdna:GeneFinder chromosome:CEL140:X:2144649:2145639:-1 11/11 None
EGAP7.1.1 ENSEMBL cdna:known chromosome:CEL140:X:2144607:2145641:-1 gene:EGAP7.1 11/11 None
EGAP7.1.2 ENSEMBL cdna:known chromosome:CEL140:X:2144607:2145643:-1 gene:EGAP7.1 11/11 None
Annotation Notes
Cross Hybridizing mRNA Matched Probes Nature of Assignment Related Probesets by Grade
GENEFINDER00000006409 1/11 Cross Hyb Matching Probes None
M110.1 1/11 Cross Hyb Matching Probes A 
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrX:2144648-2145639(-) 85.92 100.0
Public Domain and Genome References
Gene Title cuticular collagen
Gene Symbol dpy-3
Ensembl EGAP7.1
Entrez Gene 180529 Entrez gene
SwissProt Q19079 EMBL-EBI
WormBase CE07013 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 AAB00598 Dumpy : shorter than wild-type protein 3 [Caenorhabditis elegans] ref|NP_508395.1| DumPY : shorter than wild-type family member (dpy-3) [Caenorhabditis elegans] 3.0E-56
blast CAE68347 Hypothetical protein CBG14077 [Caenorhabditis briggsae] 7.0E-50
Protein Domains
Database ID Description E-Value
Pfam IPR002486 EMBL-EBI Nematode cuticle collagen, N-terminal 1.9E-19
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 2.3E-4
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 5.4E-11
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 2.3E-11
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_508395.1 1 13-35
EGAP7.1.1 1 13-35
EGAP7.1.2 1 13-35
SNAP00000008502 1 13-35
GENEFINDER00000008503 1 13-35
Sequence
Target Sequence 
>C. ELEGANS:189723_S_AT
tgctggatcttgctgtacttgtcaagttggaccaccaggaccaccaggaccacctggaag
agacggacgtccgggagcaccaggaagaccaggaaacccaggaccaccaggaagagacgg
agcacttcttccgggacccccaccgaagccaccatgccagaagtgtccaccaggaccacc
aggaccagccgggccaccaggaccaaaaggccttccaggaccacaaggagatgccggtac
atcaggacaagatggcgttccaggacttccaggaccaccaggaccatcaggaccacaagg
agcaccgggagttccaggagaaaaaggaccaactggagagccaggaaaggttatcaatgg
agctccaccaggacctccaggaccaccaggaccaccgggaccacaaggaccaccaggacc
accaggaaaggatggacaacctggaaaggccggaccaccaggattgccaggagatcctgg
agagaagggatctgacggacttccaggaccacacggaggaactggaccacgtggaccacc
aggacaacctggatcctgtgatcatt

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
TGCTGGATCTTGCTGTACTTGTCAA 401 581 315 Antisense
CCAGGACCACCTGGAAGAGACGGAC 289 271 358 Antisense
AAGAGACGGAGCACTTCTTCCGGGA 671 149 426 Antisense
ACCGAAGCCACCATGCCAGAAGTGT 645 87 456 Antisense
ATGCCAGAAGTGTCCACCAGGACCA 389 41 468 Antisense
GGAGATGCCGGTACATCAGGACAAG 212 519 541 Antisense
CAAGGAGCACCGGGAGTTCCAGGAG 660 181 610 Antisense
TGGACAACCTGGAAAGGCCGGACCA 679 545 747 Antisense
AGAAGGGATCTGACGGACTTCCAGG 276 75 797 Antisense
GGACCACACGGAGGAACTGGACCAC 404 521 820 Antisense
GGACAACCTGGATCCTGTGATCATT 298 527 856 Antisense
Sequence Source Affymetrix Proprietary Database