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[190093_at] cuticular collagen

Description W05G11.3 /REP_DB=WormBase Gene ID /WP=CE14628 /TR=O44904 /GB=AAC71147.1 /SUBMIT=ST.LOUIS /CHR=3 /FEA=Sanger Annotation /DEF=cuticular collagen
Cluster 6grp_total > 99      4grp_total > 43      6grp_cgc > 79      6grp_cgc_sub > Da      6grp_total_sub > Increase      6grp_rule_based > S5      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 229
1 2 3 4 range
A 20
(-3)
A 		248.7
(3)
A 		77.9
(-1.5)
A 		35.9
(-2.6)
A 		229
B 103.5
(3)
A 		73.3
(0.1)
A 		48.9
(-2.3)
A 		41.3
(-3)
A 		62
C 54.5
(-2.9)
A 		124.9
(3)
A 		63.6
(-2.2)
A 		53.5
(-3)
A 		71
avr 59.3
(-2.1) 		149
(3) 		63.5
(-1.9) 		43.6
(-3) 		105

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 1688
1 2 3 4 5 6 range
A 34.3
(-3)
A 		31.1
(-3)
A 		29.9
(-3)
A 		178
(-2.4)
P 		1502.7
(2.6)
P 		1615.1
(3)
P 		1585
B 48.3
(-3)
A 		91.2
(-2.8)
A 		64.2
(-2.9)
A 		156.8
(-2.6)
P 		1698.4
(3)
P 		1158.7
(1)
P 		1650
C 48.2
(-2.8)
A 		10
(-3)
A 		67
(-2.8)
A 		213
(-2.2)
P 		1515.6
(3)
P 		934.6
(0.7)
P 		1506
avr 43.6
(-3) 		44.1
(-3) 		53.7
(-3) 		182.6
(-2.5) 		1572.2
(3) 		1236.1
(1.7) 		1529
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 49
1 2 3 4 range
A 7.3
(-2.8)
A 		54
(3)
A 		20.4
(-1.1)
A 		5.3
(-3)
A 		49
B 33
(3)
A 		18.1
(-0.7)
A 		11.3
(-2.4)
A 		8.8
(-3)
A 		24
C 18
(-1)
A 		35.9
(3)
A 		22.2
(-0.1)
A 		9
(-3)
A 		27
avr 19.4
(-0.5) 		36
(3) 		18
(-0.8) 		7.7
(-3) 		28

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 687
1 2 3 4 5 6 range
A 6.3
(-3)
A 		11
(-2.9)
A 		6.5
(-3)
A 		45.2
(-2.5)
P 		453.4
(3)
P 		393.2
(2.2)
P 		447
B 16.8
(-3)
A 		30.4
(-2.9)
A 		15.6
(-3)
A 		41.5
(-2.8)
P 		690.1
(3)
P 		432.1
(0.7)
P 		675
C 17.9
(-2.8)
A 		3.1
(-3)
A 		17.1
(-2.8)
A 		42.8
(-2.5)
P 		490.4
(3)
P 		312.9
(0.8)
P 		487
avr 13.7
(-3) 		14.8
(-3) 		13.1
(-3) 		43.2
(-2.7) 		544.6
(3) 		379.4
(1.1) 		532
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 190093_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.8296
Sequence Type Exemplar sequence
Representative Public ID W05G11.3 NCBI
Target Description W05G11.3 /REP_DB=WormBase Gene ID /WP=CE14628 /TR=O44904 /GB=AAC71147.1 /SUBMIT=ST.LOUIS /CHR=3 /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_064730(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_064730 NCBI Caenorhabditis elegans COLlagen family member (col-88) (col-88) mRNA, complete cds. 11/11 None
SNAP00000017782 ENSEMBL cdna:SNAP chromosome:CEL140:III:41062:41970:1 11/11 None
GENEFINDER00000017792 ENSEMBL cdna:GeneFinder chromosome:CEL140:III:41062:42979:1 11/11 None
W05G11.3.1 ENSEMBL cdna:known chromosome:CEL140:III:41060:41970:1 gene:W05G11.3 11/11 None
W05G11.3.2 ENSEMBL cdna:known chromosome:CEL140:III:41061:41970:1 gene:W05G11.3 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
chrIII:41061-41970(+) 100.0 100.0
Public Domain and Genome References
Gene Title cuticular collagen
Gene Symbol col-88
Ensembl W05G11.3
Entrez Gene 175170 Entrez gene
SwissProt O44904 EMBL-EBI
WormBase CE14628 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 AAC71147 Collagen protein 88 [Caenorhabditis elegans] ref|NP_497131.1| COLlagen family member (col-88) [Caenorhabditis elegans] 3.0E-85
blast AAC71147 Collagen protein 88 [Caenorhabditis elegans] ref|NP_497131.1| COLlagen family member (col-88) [Caenorhabditis elegans] 8.0E-82
blast CAE69191 Hypothetical protein CBG15226 [Caenorhabditis briggsae] 4.0E-31
blast CAE69191 Hypothetical protein CBG15226 [Caenorhabditis briggsae] 7.0E-31
Protein Domains
Database ID Description E-Value
Pfam IPR002486 EMBL-EBI Nematode cuticle collagen, N-terminal 1.1E-22
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 2.5E-4
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 6.1E-12
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 7.0E-12
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_497131.1 1 7-29
W05G11.3.1 1 7-29
W05G11.3.2 1 7-29
SNAP00000017782 1 7-29
GENEFINDER00000017792 1 7-29
Sequence
Target Sequence 
>C. ELEGANS:190093_AT
atggagctggtcagggatcatcccaacagccaagtgaatgcattacctgcccagctggag
ccccaggaccacaaggaccagacggaccagccggtgccccaggagctgatggacaagccg
gatccccaggtgctccaggacaggatggacagccaggaggcccaggagcacagggagacg
ctggagccccaggaaatgacggtaccccaggacaagacggagctccaggacagaacggac
agcgtggaaacggagccgccggggcaccaggaccacaaggaccagcaggaaacgcaggac
aagctggacaaccaggagccgacggacagccaggagctcaaggatccgccggaatcgccg
gagcaccaggacagccaggaaaagccggagaagacggagaggctggagagaacggtaccg
atggagagccaggaactgatgccgagtactgccagtgcccaccgagaactggtgccatcg
aggtcgagccagccacccaggaggagggata

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
ATGGAGCTGGTCAGGGATCATCCCA 604 51 380 Antisense
CAGGGATCATCCCAACAGCCAAGTG 162 209 391 Antisense
AAGTGAATGCATTACCTGCCCAGCT 127 159 411 Antisense
GAGGCCCAGGAGCACAGGGAGACGC 265 405 536 Antisense
AGCTCCAGGACAGAACGGACAGCGT 540 79 600 Antisense
GGACAGCGTGGAAACGGAGCCGCCG 313 525 616 Antisense
TCAAGGATCCGCCGGAATCGCCGGA 568 631 717 Antisense
GAGGCTGGAGAGAACGGTACCGATG 690 403 778 Antisense
AGTGCCCACCGAGAACTGGTGCCAT 330 57 833 Antisense
CTGGTGCCATCGAGGTCGAGCCAGC 23 241 848 Antisense
AGCCAGCCACCCAGGAGGAGGGATA 674 81 866 Antisense
Sequence Source Affymetrix Proprietary Database