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[188365_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 > 92      4grp_total > 49      6grp_cgc > 97      4grp_rule_based > L3      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 134
1 2 3 4 range
A 3.5
(-3)
A 		83.4
(1.6)
A 		107.5
(3)
A 		8.2
(-2.7)
A 		104
B 2
(-3)
A 		121.7
(2.4)
A 		136.2
(3)
A 		24.9
(-2)
A 		134
C 1.8
(-3)
A 		106.8
(2.3)
A 		121.3
(3)
A 		4.1
(-2.9)
A 		120
avr 2.4
(-3) 		104
(2.1) 		121.7
(3) 		12.4
(-2.5) 		119

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 196
1 2 3 4 5 6 range
A 4.2
(-3)
A 		71.6
(-0.9)
A 		72.5
(-0.9)
A 		195.9
(3)
A 		171.4
(2.2)
A 		4
(-3)
A 		192
B 20.2
(-2.8)
A 		56.7
(-1.6)
A 		13.1
(-3)
A 		127.6
(0.7)
A 		199.1
(3)
A 		36.6
(-2.2)
A 		186
C 9.1
(-2.8)
A 		76
(-0.4)
A 		23.4
(-2.3)
A 		110.2
(0.8)
A 		172.4
(3)
A 		2.8
(-3)
A 		170
avr 11.2
(-3) 		68.1
(-1) 		36.3
(-2.1) 		144.6
(1.7) 		181
(3) 		14.5
(-2.9) 		170
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 42
1 2 3 4 range
A 1.3
(-3)
A 		18.1
(0.8)
A 		28.1
(3)
A 		1.2
(-3)
A 		27
B 0.6
(-3)
A 		30.1
(2.7)
A 		31.6
(3)
A 		5.3
(-2.1)
A 		31
C 0.6
(-3)
A 		30.7
(1.3)
A 		42.3
(3)
A 		0.7
(-3)
A 		42
avr 0.8
(-3) 		26.3
(1.6) 		34
(3) 		2.4
(-2.7) 		33

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 80
1 2 3 4 5 6 range
A 0.8
(-3)
A 		25.5
(-0.1)
A 		15.8
(-1.2)
A 		49.7
(2.8)
A 		51.7
(3)
A 		1
(-3)
A 		51
B 7
(-2.7)
A 		18.9
(-1.8)
A 		3.2
(-3)
A 		33.8
(-0.6)
A 		80.9
(3)
A 		13.7
(-2.2)
A 		78
C 3.4
(-2.7)
A 		23.2
(-0.6)
A 		6
(-2.4)
A 		22.2
(-0.7)
A 		55.8
(3)
A 		0.9
(-3)
A 		55
avr 3.7
(-3) 		22.5
(-1.1) 		8.3
(-2.5) 		35.2
(0.2) 		62.8
(3) 		5.2
(-2.8) 		59
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 188365_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:188365_AT
gggccatctggaccaaaaggtctgccagggcaggatggtgcaccgggagagccaggacct
gctgggaaaatgggacaaaacacgggtgatgttcaaacaatgcatgtagatccaggatgt
cagtattgtccagccggagaaatggggcccccaggtgcgcctggaaagatcggaccacga
ggtcaacgtggacaatctggcggcgcaggaactcccggtaacaacggagcaccgggacat
aatggagaactgggaccttgtggtcaagcgggacctcccggaccagctggtgcaatcggt
agacgtggtatggataccgttcgcgaaaaaggagtacgaggacctattggtgctcca

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GGGCCATCTGGACCAAAAGGTCTGC 119 493 346 Antisense
TCTGCCAGGGCAGGATGGTGCACCG 55 611 366 Antisense
AGGATGTCAGTATTGTCCAGCCGGA 686 55 459 Antisense
CGGAGAAATGGGGCCCCCAGGTGCG 292 243 480 Antisense
GGTGCGCCTGGAAAGATCGGACCAC 341 501 499 Antisense
GACAATCTGGCGGCGCAGGAACTCC 264 365 536 Antisense
GGTAACAACGGAGCACCGGGACATA 333 487 562 Antisense
GACCTTGTGGTCAAGCGGGACCTCC 320 383 599 Antisense
CCAGCTGGTGCAATCGGTAGACGTG 131 273 628 Antisense
GACGTGGTATGGATACCGTTCGCGA 660 377 647 Antisense
AGTACGAGGACCTATTGGTGCTCCA 82 61 678 Antisense
Sequence Source Affymetrix Proprietary Database