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[188361_at] collagen

Description C39E9.9 /REP_DB=WormBase Gene ID /WP=CE05392 /TR=Q18536 /GB=CAA94328.1 /SUBMIT=HINXTON /CHR=4 /FEA=Sanger Annotation /DEF=collagen
Cluster 6grp_total > 93      4grp_total > 50      6grp_cgc > 98      6grp_total_sub > Hat      4grp_rule_based > L2      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 80
1 2 3 4 range
A 29
(-2.6)
A 		81.4
(2.1)
A 		91.2
(3)
A 		24.2
(-3)
A 		67
B 40.4
(-1.1)
A 		82
(2.9)
A 		82.9
(3)
A 		20.3
(-3)
A 		63
C 29.5
(-2.7)
A 		99.8
(3)
A 		65
(0.2)
A 		26.3
(-3)
A 		74
avr 33
(-2.1) 		87.7
(3) 		79.7
(2.3) 		23.6
(-3) 		64

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 39
1 2 3 4 5 6 range
A 37.4
(-3)
A 		56.3
(0.4)
A 		70.2
(3)
A 		66
(2.2)
A 		70.3
(3)
A 		52.8
(-0.2)
A 		33
B 38.8
(-2.1)
A 		58.5
(2.9)
A 		35.4
(-3)
A 		47.2
(0)
A 		58.8
(3)
A 		44.3
(-0.7)
A 		23
C 36.4
(-3)
A 		68.3
(2.1)
A 		41.9
(-2.1)
A 		49.3
(-0.9)
A 		73.9
(3)
A 		43
(-1.9)
A 		38
avr 37.5
(-3) 		61
(1.7) 		49.2
(-0.7) 		54.2
(0.3) 		67.7
(3) 		46.7
(-1.2) 		30
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 25
1 2 3 4 range
A 10.6
(-0.9)
A 		17.7
(1.2)
A 		23.9
(3)
A 		3.5
(-3)
A 		20
B 12.9
(0.2)
A 		20.2
(3)
A 		19.2
(2.6)
A 		4.3
(-3)
A 		16
C 9.8
(-1.7)
A 		28.7
(3)
A 		22.7
(1.5)
A 		4.4
(-3)
A 		24
avr 11.1
(-0.7) 		22.2
(3) 		21.9
(2.9) 		4.1
(-3) 		18

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 17
1 2 3 4 5 6 range
A 6.9
(-3)
A 		20
(2.5)
A 		15.3
(0.5)
A 		16.7
(1.1)
A 		21.2
(3)
A 		12.9
(-0.5)
A 		14
B 13.5
(-1.1)
A 		19.5
(1.3)
A 		8.6
(-3)
A 		12.5
(-1.5)
A 		23.9
(3)
A 		16.5
(0.1)
A 		15
C 13.5
(-1.5)
A 		20.8
(1.7)
A 		10.7
(-2.7)
A 		9.9
(-3)
A 		23.9
(3)
A 		14.4
(-1.1)
A 		14
avr 11.3
(-3) 		20.1
(1.5) 		11.5
(-2.9) 		13
(-2.1) 		23
(3) 		14.6
(-1.3) 		12
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 188361_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.9158
Sequence Type Exemplar sequence
Representative Public ID C39E9.9 NCBI
Target Description C39E9.9 /REP_DB=WormBase Gene ID /WP=CE05392 /TR=Q18536 /GB=CAA94328.1 /SUBMIT=HINXTON /CHR=4 /FEA=Sanger Annotation /DEF=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_070113(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_070113 NCBI Caenorhabditis elegans C39E9.9 (collagen) mRNA, complete cds. 11/11 None
SNAP00000026309 ENSEMBL cdna:SNAP chromosome:CEL140:IV:13089613:13091037:-1 11/11 None
GENEFINDER00000026317 ENSEMBL cdna:GeneFinder chromosome:CEL140:IV:13089613:13091037:-1 11/11 None
C39E9.9 ENSEMBL cdna:known chromosome:CEL140:IV:13089613:13091037:-1 gene:C39E9.9 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
chrIV:13089618-13091043(-) 100.0 100.0
Public Domain and Genome References
Gene Title collagen
Gene Symbol col-132
Ensembl C39E9.9
Entrez Gene 183347 Entrez gene
SwissProt Q18536 EMBL-EBI
WormBase CE05392 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 CAA94328 Hypothetical protein C39E9.9 [Caenorhabditis elegans] ref|NP_502514.1| C39E9.9 [Caenorhabditis elegans] 1.0E-67
blast CAE58661 Hypothetical protein CBG01830 [Caenorhabditis briggsae] 7.0E-62
Protein Domains
Database ID Description E-Value
Pfam IPR002486 EMBL-EBI Nematode cuticle collagen, N-terminal 7.9E-16
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 2.6E-4
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 3.4E-11
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_502514.1 1 7-29
C39E9.9 1 7-29
SNAP00000026309 1 7-29
GENEFINDER00000026317 1 7-29
Sequence
Target Sequence 
>C. ELEGANS:188361_AT
aataaggtcaataactgcccacccggacctgcaggaccaccaggagagccaggagcccct
ggagatgacggatggaatggagacgcaggacaacccggaccagactttccactctttgat
caatccctcatctatcaaagacccccatgcattcgctgcccagtcggagagccaggacct
ccaggtccagacggagagccaggagagcagggaccaccaggaccaccgggagttgacaac
tttgaagttggacatgatggaccaccaggtgtcgagggagaacctggagatgctggagat
caaggagaagacggggagccaggtgtcgatggaagaccaggcgccagtggaatcagagag
ataggaatgccaggagcaccaggggcaccgggtgttgcaggagctgaaggactcccaggc
aaggatggagagccaggaattcctgggccagaaggggaagagggaccacctggagcagca
ggattggatggagagcggggagacgaaggggagccaggacctgaaggaccacctggaatc
ccaggacctgatgcagcct

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
AATAAGGTCAATAACTGCCCACCCG 515 169 244 Antisense
GAGCCCCTGGAGATGACGGATGGAA 431 385 296 Antisense
CAGACTTTCCACTCTTTGATCAATC 602 205 344 Antisense
GGACCTCCAGGTCCAGACGGAGAGC 402 523 418 Antisense
GGACCACCAGGTGTCGAGGGAGAAC 557 521 502 Antisense
AGACGGGGAGCCAGGTGTCGATGGA 200 1 552 Antisense
GGAAGACCAGGCGCCAGTGGAATCA 425 531 574 Antisense
GCACCGGGTGTTGCAGGAGCTGAAG 570 313 628 Antisense
AGCTGAAGGACTCCCAGGCAAGGAT 63 79 645 Antisense
GAGCCAGGACCTGAAGGACCACCTG 541 385 754 Antisense
GGAATCCCAGGACCTGATGCAGCCT 484 531 778 Antisense
Sequence Source Affymetrix Proprietary Database