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[190360_s_at] cuticular collagen

Description F27C1.8 /REP_DB=WormBase Gene ID /WP=CE09720 /TR=SW:P91285 /GB=AAB37656.1 /SUBMIT=ST.LOUIS /CHR=1 /FEA=Sanger Annotation /DEF=cuticular collagen
Cluster 6grp_highest_10_10 > 08      6grp_high1_10_10 > 43      6grp_highest_nonorm > 27      6grp_total > 10      4grp_total > 49      6grp_cgc > 74      6grp_high1_sub > 02      6grp_cgc_sub > 02_03_04_05      6grp_total_sub > Hat      6grp_rule_based > S2      4grp_rule_based > L3      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 21384
1 2 3 4 range
A 98.8
(-3)
P 		19198.6
(2.9)
P 		19371.3
(3)
P 		29.8
(-3)
A 		19342
B 85
(-3)
P 		18000.6
(2)
P 		21404.2
(3)
P 		19.9
(-3)
A 		21384
C 82.4
(-3)
P 		16057.9
(2.2)
P 		18427.6
(3)
P 		65.3
(-3)
M 		18362
avr 88.7
(-3) 		17752.4
(2.4) 		19734.4
(3) 		38.3
(-3) 		19696

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 12169
1 2 3 4 5 6 range
A 555.2
(-3)
P 		12667.6
(3)
P 		9167.6
(1.3)
P 		8333.4
(0.9)
P 		7016
(0.2)
P 		3938.1
(-1.3)
P 		12112
B 499
(-3)
P 		12115
(3)
P 		8280.7
(1)
P 		8723.5
(1.2)
P 		7182.5
(0.5)
P 		3920
(-1.2)
P 		11616
C 695.8
(-3)
P 		11390.9
(3)
P 		10386.5
(2.4)
P 		8221.7
(1.2)
P 		8128.2
(1.2)
P 		3262.1
(-1.6)
P 		10695
avr 583.3
(-3) 		12057.8
(3) 		9278.3
(1.5) 		8426.2
(1.1) 		7442.2
(0.6) 		3706.7
(-1.4) 		11475
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 6418
1 2 3 4 range
A 36
(-3)
P 		4167.5
(1.9)
P 		5064
(3)
P 		4.4
(-3)
A 		5060
B 27.1
(-3)
P 		4445.7
(2.4)
P 		4959.9
(3)
P 		4.2
(-3)
A 		4956
C 27.3
(-3)
P 		4616.8
(1.3)
P 		6422.6
(3)
P 		11
(-3)
M 		6412
avr 30.1
(-3) 		4410
(1.8) 		5482.2
(3) 		6.5
(-3) 		5476

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 4403
1 2 3 4 5 6 range
A 102.4
(-3)
P 		4505.2
(3)
P 		1996.5
(-0.4)
P 		2113.6
(-0.3)
P 		2117.1
(-0.3)
P 		958.8
(-1.8)
P 		4403
B 173.6
(-3)
P 		4032.6
(3)
P 		2010.8
(-0.1)
P 		2310.6
(0.3)
P 		2918.2
(1.3)
P 		1461.7
(-1)
P 		3859
C 257.9
(-3)
P 		3475.7
(3)
P 		2643.6
(1.4)
P 		1653.4
(-0.4)
P 		2630.2
(1.4)
P 		1092
(-1.4)
P 		3218
avr 178
(-3) 		4004.5
(3) 		2217
(0.2) 		2025.9
(-0.1) 		2555.2
(0.7) 		1170.8
(-1.4) 		3827
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 190360_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.1637
Sequence Type Exemplar sequence
Representative Public ID F27C1.8 NCBI
Target Description F27C1.8 /REP_DB=WormBase Gene ID /WP=CE09720 /TR=SW:P91285 /GB=AAB37656.1 /SUBMIT=ST.LOUIS /CHR=1 /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_059194(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_059194 NCBI Caenorhabditis elegans DumPY : shorter than wild-type family member (dpy-5) (dpy-5) mRNA, complete cds. 11/11 None
SNAP00000014505 ENSEMBL cdna:SNAP chromosome:CEL140:I:5432200:5433054:-1 11/11 None
GENEFINDER00000014522 ENSEMBL cdna:GeneFinder chromosome:CEL140:I:5432200:5433054:-1 11/11 None
F27C1.8 ENSEMBL cdna:known chromosome:CEL140:I:5432200:5433054:-1 gene:F27C1.8 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
chrI:5432199-5433054(-) 100.0 100.0
Public Domain and Genome References
Gene Title cuticular collagen
Gene Symbol dpy-5
Ensembl F27C1.8
Entrez Gene 172197 Entrez gene
SwissProt P91285 EMBL-EBI
WormBase CE09720 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 AAB37656 Dumpy : shorter than wild-type protein 5 [Caenorhabditis elegans] ref|NP_491595.1| DumPY : shorter than wild-type family member (dpy-5) [Caenorhabditis elegans] sp|P91285|DPY5_CAEEL Cuticle collagen dpy-5 (Dumpy-5 protein) 1.0E-100
blast CAE67065 Hypothetical protein CBG12473 [Caenorhabditis briggsae] 2.0E-98
blast CAB04587 Hypothetical protein K08C9.4 [Caenorhabditis elegans] ref|NP_492936.1| COLlagen family member (col-65) [Caenorhabditis elegans] 2.0E-19
Protein Domains
Database ID Description E-Value
Pfam IPR002486 EMBL-EBI Nematode cuticle collagen, N-terminal 9.8E-22
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 9.7E-11
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 2.6E-13
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_491595.1 1 4-26
F27C1.8 1 4-26
SNAP00000014505 1 4-26
GENEFINDER00000014522 1 4-26
Sequence
Target Sequence 
>C. ELEGANS:190360_S_AT
cgttccaacagccaatgctcttgcggacttccatctcaaggatgcccagccggagctcca
ggaaacccaggagccccaggagagccaggaggcactggaccagacggaaagaacggacca
actggacttccaggacttaacattccaattccaaatgacttccctaaggagtgcatcaag
tgcccagctggaccaccaggacaagatggacttccaggacaagaaggattccaaggactt
ccaggagacgctggaaagcgtggaaccccaggaaaggacggagagccaggacgtgttgga
gatattggagatcaaggaactccaggacaagacggacaaccaggacttgctggaccacca
ggacgcgatggacttaccggaaagggacaaccaggagtcgctggacgcccaggaatgcca
ggaccacgtggagagccaggaaacaacggaaatccaggagaggaaggacaaactggagcc
cagggaccaactggacagccaggaaaggacggattcaacggaaacgacggaactccagga
caagctggaccacaaggagccgttggagccgatgccgaatactgc

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
CGTTCCAACAGCCAATGCTCTTGCG 115 247 250 Antisense
CTCTTGCGGACTTCCATCTCAAGGA 7 231 267 Antisense
GAGCCAGGAGGCACTGGACCAGACG 277 383 331 Antisense
AGAACGGACCAACTGGACTTCCAGG 83 73 359 Antisense
GGACTTCCAGGACTTAACATTCCAA 640 525 373 Antisense
ATTCCAATTCCAAATGACTTCCCTA 353 7 391 Antisense
ATGACTTCCCTAAGGAGTGCATCAA 427 45 404 Antisense
CAGGACGCGATGGACTTACCGGAAA 220 201 608 Antisense
GAGGAAGGACAAACTGGAGCCCAGG 470 405 709 Antisense
GAGCCCAGGGACCAACTGGACAGCC 634 385 725 Antisense
CGTTGGAGCCGATGCCGAATACTGC 497 245 810 Antisense
Sequence Source Affymetrix Proprietary Database