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[188675_at] collagen

Description C09G5.3 /REP_DB=WormBase Gene ID /WP=CE01483 /TR=SW:Q09233 /GB=CAA86756.1 /SUBMIT=HINXTON /CHR=2 /FEA=Sanger Annotation /DEF=collagen
Cluster 6grp_total > 93      4grp_total > 49      6grp_cgc > 98      6grp_total_sub > Hat      6grp_rule_based > S5      4grp_rule_based > L2      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 27
1 2 3 4 range
A 7.9
(-3)
A 		31
(3)
A 		28.2
(2.3)
A 		20.5
(0.3)
A 		23
B 6.1
(-2.2)
A 		20.5
(3)
A 		18.1
(2.1)
A 		3.9
(-3)
A 		17
C 6.2
(-3)
A 		21.3
(1.7)
A 		25.5
(3)
A 		9.5
(-2)
A 		19
avr 6.7
(-3) 		24.3
(3) 		23.9
(2.9) 		11.3
(-1.4) 		18

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 197
1 2 3 4 5 6 range
A 6.1
(-3)
A 		22.5
(-2.2)
A 		32.5
(-1.8)
A 		134.6
(3)
A 		135.3
(3)
A 		26.8
(-2)
A 		129
B 3.1
(-3)
A 		27.6
(-2.3)
A 		21.4
(-2.4)
A 		106
(0.1)
A 		199.6
(3)
A 		19.6
(-2.5)
A 		197
C 13.1
(-2.8)
A 		20.6
(-2.6)
A 		12.5
(-2.8)
A 		25.5
(-2.4)
A 		194.5
(3)
A 		7.1
(-3)
A 		187
avr 7.4
(-3) 		23.6
(-2.4) 		22.1
(-2.5) 		88.7
(-0.1) 		176.5
(3) 		17.8
(-2.6) 		169
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 8
1 2 3 4 range
A 2.9
(-3)
A 		6.7
(2.1)
A 		7.4
(3)
A 		3
(-2.9)
A 		5
B 1.9
(-1.5)
A 		5.1
(3)
A 		4.2
(1.7)
A 		0.8
(-3)
A 		4
C 2
(-2.7)
A 		6.1
(0.7)
A 		8.9
(3)
A 		1.6
(-3)
A 		7
avr 2.3
(-2.4) 		6
(2) 		6.8
(3) 		1.8
(-3) 		5

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 80
1 2 3 4 5 6 range
A 1.1
(-3)
A 		8
(-2)
A 		7.1
(-2.1)
A 		34.1
(2)
A 		40.8
(3)
A 		6.5
(-2.2)
A 		40
B 1.1
(-3)
A 		9.2
(-2.4)
A 		5.2
(-2.7)
A 		28.1
(-1)
A 		81.1
(3)
A 		7.3
(-2.5)
A 		80
C 4.9
(-2.8)
A 		6.3
(-2.6)
A 		3.2
(-2.9)
A 		5.1
(-2.7)
A 		62.9
(3)
A 		2.4
(-3)
A 		61
avr 2.4
(-3) 		7.8
(-2.5) 		5.2
(-2.7) 		22.4
(-1) 		61.6
(3) 		5.4
(-2.7) 		59
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 188675_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.2859
Sequence Type Exemplar sequence
Representative Public ID C09G5.3 NCBI
Target Description C09G5.3 /REP_DB=WormBase Gene ID /WP=CE01483 /TR=SW:Q09233 /GB=CAA86756.1 /SUBMIT=HINXTON /CHR=2 /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_063907(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_063907 NCBI Caenorhabditis elegans C09G5.3 (collagen) mRNA, complete cds. 11/11 None
SNAP00000014218 ENSEMBL cdna:SNAP chromosome:CEL140:II:10699981:10704435:1 11/11 None
GENEFINDER00000014228 ENSEMBL cdna:GeneFinder chromosome:CEL140:II:10703529:10704435:1 11/11 None
C09G5.3 ENSEMBL cdna:known chromosome:CEL140:II:10703529:10704435:1 gene:C09G5.3 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
chrII:10703525-10704432(+) 100.0 100.0
Public Domain and Genome References
Gene Title collagen
Gene Symbol col-79
Ensembl C09G5.3
Entrez Gene 174650 Entrez gene
SwissProt Q09233 EMBL-EBI
WormBase CE01483 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 CAA86760 Hypothetical protein C09G5.1 [Caenorhabditis elegans] ref|NP_496306.2| GABA/Glycine Receptor family (see gbr) family member (ggr-1) [Caenorhabditis elegans] sp|Q09453|GLRB4_CAEEL Glycine receptor beta-type chain 4 precursor 1.0E-167
blast CAE59621 Hypothetical protein CBG03030 [Caenorhabditis briggsae] 1.0E-158
blast CAA86756 Hypothetical protein C09G5.3 [Caenorhabditis elegans] ref|NP_496308.1| C09G5.3 [Caenorhabditis elegans] sp|Q09233|YQ33_CAEEL Putative cuticle collagen C09G5.3 1.0E-89
blast CAA86756 Hypothetical protein C09G5.3 [Caenorhabditis elegans] ref|NP_496308.1| C09G5.3 [Caenorhabditis elegans] sp|Q09233|YQ33_CAEEL Putative cuticle collagen C09G5.3 3.0E-89
blast CAE59620 Hypothetical protein CBG03029 [Caenorhabditis briggsae] 5.0E-71
blast CAB04587 Hypothetical protein K08C9.4 [Caenorhabditis elegans] ref|NP_492936.1| COLlagen family member (col-65) [Caenorhabditis elegans] 4.0E-18
Protein Domains
Database ID Description E-Value
Pfam IPR006029 EMBL-EBI Neurotransmitter-gated ion-channel transmembrane region 2.2E-30
Pfam IPR002486 EMBL-EBI Nematode cuticle collagen, N-terminal 9.7E-20
Pfam IPR006202 EMBL-EBI Neurotransmitter-gated ion-channel ligand binding domain 9.2E-15
Pfam IPR006202 EMBL-EBI Neurotransmitter-gated ion-channel ligand binding domain 0.0013
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 0.0019
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 7.5E-10
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 1.0E-10
Pfam IPR002486 EMBL-EBI Nematode cuticle collagen, N-terminal 9.7E-20
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 0.0019
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 7.5E-10
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 1.0E-10
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_496308.1 1 7-29
C09G5.3 1 7-29
SNAP00000014218 3 159-178,220-242,341-363
GENEFINDER00000014228 1 7-29
Sequence
Target Sequence 
>C. ELEGANS:188675_AT
aagagccatcaaactgtccaggagggcctccaggaccaccaggagaaaagggaaatgatg
gggtcgatggagtggatggtattccaggattcccaggtgaaaatggaggagctgcactgg
atcagccagctgatgggacatgcatcaagtgtccaccagggccccgtggaccacctggac
cacaaggagaggagggaccatctggagatgtcggagaggatggagagccaggagttccag
ggaatgacggagcagatggaacaccaggaaaatctggagctccaggagggaaaggacccc
aaggtccaccgggaacaccaggaagaccaggtcagccaggaagaaaggctattggagagg
cagggccaaagggtccaccaggagcaccaggaaccgatggacgccgtggagagaatggaa
ctgatggggatgatggtgtagatggacaaccaggagatgaaggtgatgctggaaaagatg
gaacaccgggagaaccaggaccacaaggagaacaaggaaccgaaggccagcctggaaccg
acggcgcgtattgtcc

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
AAGAGCCATCAAACTGTCCAGGAGG 555 153 269 Antisense
ACTGTCCAGGAGGGCCTCCAGGACC 480 95 281 Antisense
GGGGTCGATGGAGTGGATGGTATTC 24 497 328 Antisense
GGAGGAGCTGCACTGGATCAGCCAG 631 515 373 Antisense
ATCAGCCAGCTGATGGGACATGCAT 199 29 389 Antisense
AGGAGAGGAGGGACCATCTGGAGAT 51 57 453 Antisense
GCTCCAGGAGGGAAAGGACCCCAAG 705 293 547 Antisense
GAGAGGCAGGGCCAAAGGGTCCACC 60 395 623 Antisense
GAACCGATGGACGCCGTGGAGAGAA 103 347 659 Antisense
ACAAGGAACCGAAGGCCAGCCTGGA 522 111 780 Antisense
CTGGAACCGACGGCGCGTATTGTCC 634 239 800 Antisense
Sequence Source Affymetrix Proprietary Database