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[188331_s_at] collagen

Description C39E9.3 /REP_DB=WormBase Gene ID /WP=CE05386 /TR=Q18537 /GB=CAA94329.1 /SUBMIT=HINXTON /CHR=4 /FEA=Sanger Annotation /DEF=collagen
Cluster 6grp_total > 82      4grp_total > 49      6grp_cgc > 97      4grp_rule_based > L2      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 260
1 2 3 4 range
A 4.2
(-3)
A 		263
(3)
P 		187.5
(1.2)
P 		13.4
(-2.8)
A 		259
B 2.6
(-3)
A 		207.3
(2.7)
P 		216.7
(3)
P 		6.3
(-2.9)
A 		214
C 3
(-3)
A 		239.1
(3)
P 		190.4
(1.8)
P 		6
(-2.9)
A 		236
avr 3.3
(-3) 		236.5
(3) 		198.2
(2) 		8.6
(-2.9) 		233

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 319
1 2 3 4 5 6 range
A 39.9
(-3)
A 		158.4
(-0.1)
P 		114
(-1.2)
P 		282.4
(3)
P 		239.7
(1.9)
P 		64.8
(-2.4)
A 		243
B 21.3
(-3)
A 		155.1
(-0.4)
P 		125.2
(-1)
P 		250
(1.4)
P 		335.6
(3)
P 		71.7
(-2)
M 		314
C 16.2
(-3)
A 		217.3
(1.6)
P 		95.4
(-1.2)
A 		241.6
(2.2)
P 		277.9
(3)
P 		86.4
(-1.4)
P 		262
avr 25.8
(-3) 		176.9
(0.5) 		111.5
(-1) 		258
(2.4) 		284.4
(3) 		74.3
(-1.9) 		259
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 68
1 2 3 4 range
A 1.5
(-3)
A 		57.1
(3)
P 		49
(2.1)
P 		2
(-2.9)
A 		56
B 0.8
(-3)
A 		51.2
(3)
P 		50.2
(2.9)
P 		1.3
(-2.9)
A 		50
C 1
(-3)
A 		68.7
(3)
P 		66.4
(2.8)
P 		1
(-3)
A 		68
avr 1.1
(-3) 		59
(3) 		55.2
(2.6) 		1.4
(-3) 		58

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 130
1 2 3 4 5 6 range
A 7.4
(-3)
A 		56.3
(1.5)
P 		24.8
(-1.4)
P 		71.6
(2.9)
P 		72.3
(3)
P 		15.8
(-2.2)
A 		65
B 7.4
(-3)
A 		51.6
(-0.9)
P 		30.4
(-1.9)
P 		66.2
(-0.3)
P 		136.4
(3)
P 		26.7
(-2.1)
M 		129
C 6
(-3)
A 		66.3
(1.3)
P 		24.3
(-1.7)
A 		48.6
(0)
P 		89.9
(3)
P 		28.9
(-1.4)
P 		84
avr 6.9
(-3) 		58.1
(0.3) 		26.5
(-1.7) 		62.1
(0.6) 		99.5
(3) 		23.8
(-1.9) 		93
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 188331_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.9410
Sequence Type Exemplar sequence
Representative Public ID C39E9.3 NCBI
Target Description C39E9.3 /REP_DB=WormBase Gene ID /WP=CE05386 /TR=Q18537 /GB=CAA94329.1 /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_070106(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_070106 NCBI Caenorhabditis elegans C39E9.3 (collagen) mRNA, complete cds. 11/11 A 
SNAP00000026301 ENSEMBL cdna:SNAP chromosome:CEL140:IV:13065736:13067258:-1 11/11 None
GENEFINDER00000026316 ENSEMBL cdna:GeneFinder chromosome:CEL140:IV:13065736:13067258:-1 11/11 None
C39E9.3 ENSEMBL cdna:known chromosome:CEL140:IV:13065736:13067258:-1 gene:C39E9.3 11/11 A 
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:13065741-13067264(-) 100.0 100.0
Public Domain and Genome References
Gene Title collagen
Gene Symbol col-131
Ensembl C39E9.3
Entrez Gene 178254 Entrez gene
SwissProt Q18537 EMBL-EBI
WormBase CE05386 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 CAA94329 Hypothetical protein C39E9.3 [Caenorhabditis elegans] ref|NP_502507.1| C39E9.3 [Caenorhabditis elegans] 1.0E-116
blast CAE61621 Hypothetical protein CBG05547 [Caenorhabditis briggsae] 2.0E-92
Protein Domains
Database ID Description E-Value
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 7.5E-5
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 1.3E-8
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 4.2E-7
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_502507.1 1 5-23
C39E9.3 1 5-23
SNAP00000026301 1 5-23
GENEFINDER00000026316 1 5-23
Sequence
Target Sequence 
>C. ELEGANS:188331_S_AT
tgctccaggacccgttggtcctgttggaatggaaggagatcgaggaaatcgtggaggtct
tggtgtggatggaccgttgggttctattggtcttcaaggtccccctggaagaactggatc
tacaggagatgttggagaatctggacccattgggccgaatggtcaagatgcattgtattg
tccat

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
TGCTCCAGGACCCGTTGGTCCTGTT 551 567 696 Antisense
GACCCGTTGGTCCTGTTGGAATGGA 95 381 704 Antisense
GAAATCGTGGAGGTCTTGGTGTGGA 91 363 740 Antisense
GGTGTGGATGGACCGTTGGGTTCTA 388 307 757 Antisense
TGGGTTCTATTGGTCTTCAAGGTCC 368 553 773 Antisense
TTCAAGGTCCCCCTGGAAGAACTGG 695 679 788 Antisense
GTCCCCCTGGAAGAACTGGATCTAC 224 469 794 Antisense
GAACTGGATCTACAGGAGATGTTGG 59 349 806 Antisense
TGGAGAATCTGGACCCATTGGGCCG 111 545 828 Antisense
TCTGGACCCATTGGGCCGAATGGTC 90 607 835 Antisense
GGTCAAGATGCATTGTATTGTCCAT 666 503 856 Antisense
Sequence Source Affymetrix Proprietary Database