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[188552_at] collagen

Description Y81G3A.5 /REP_DB=WormBase Gene ID /WP=CE23120 /TR=Q9XVY1 /GB=CAA22518.1 /SUBMIT=HINXTON /CHR=2 /FEA=Sanger Annotation /DEF=collagen
Cluster 6grp_total > 48      4grp_total > 03      6grp_cgc > 26      6grp_total_sub > Cup      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 70
1 2 3 4 range
A 11.7
(-1.8)
A 		5.6
(-3)
A 		6.4
(-2.8)
A 		35.2
(3)
A 		30
B 12.5
(3)
A 		5.5
(-2.9)
A 		5.4
(-3)
A 		11.5
(2.2)
A 		7
C 8.7
(-2.9)
A 		10
(-2.8)
A 		7.9
(-3)
A 		74.9
(3)
A 		67
avr 11
(-2.2) 		7
(-2.9) 		6.6
(-3) 		40.5
(3) 		34

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 9
1 2 3 4 5 6 range
A 4.7
(-2.3)
A 		9.7
(0.9)
A 		3.6
(-3)
A 		11.6
(2.2)
A 		4.4
(-2.5)
A 		12.9
(3)
A 		9
B 11.8
(3)
A 		5.3
(-2.3)
A 		4.4
(-3)
A 		5.4
(-2.2)
A 		5.7
(-1.9)
A 		5.9
(-1.8)
A 		7
C 6.5
(-1.6)
A 		9.1
(3)
A 		5.7
(-3)
A 		5.9
(-2.6)
A 		7.6
(0.4)
A 		6.6
(-1.4)
A 		3
avr 7.7
(1.8) 		8
(2.2) 		4.6
(-3) 		7.6
(1.6) 		5.9
(-1) 		8.5
(3) 		4
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 11
1 2 3 4 range
A 4.3
(1.8)
A 		1.2
(-3)
A 		1.7
(-2.2)
A 		5.1
(3)
A 		4
B 4
(3)
A 		1.3
(-2.8)
A 		1.2
(-3)
A 		2.4
(-0.4)
A 		3
C 2.9
(-2.9)
A 		2.9
(-2.9)
A 		2.7
(-3)
A 		12.6
(3)
A 		10
avr 3.7
(-0.7) 		1.8
(-3) 		1.9
(-2.9) 		6.7
(3) 		5

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 3
1 2 3 4 5 6 range
A 0.9
(-2.8)
A 		3.5
(3)
A 		0.8
(-3)
A 		2.9
(1.7)
A 		1.3
(-1.9)
A 		3.1
(2.1)
A 		3
B 4.1
(3)
A 		1.8
(-1.6)
A 		1.1
(-3)
A 		1.4
(-2.4)
A 		2.3
(-0.6)
A 		2.2
(-0.8)
A 		3
C 2.4
(1.5)
A 		2.8
(3)
A 		1.5
(-1.9)
A 		1.2
(-3)
A 		2.4
(1.5)
A 		2.2
(0.8)
A 		2
avr 2.5
(2.3) 		2.7
(3) 		1.1
(-3) 		1.8
(-0.4) 		2
(0.4) 		2.5
(2.3) 		2
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 188552_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.3590
Sequence Type Exemplar sequence
Representative Public ID Y81G3A.5 NCBI
Target Description Y81G3A.5 /REP_DB=WormBase Gene ID /WP=CE23120 /TR=Q9XVY1 /GB=CAA22518.1 /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_064382(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_064382 NCBI Caenorhabditis elegans Y81G3A.5 (collagen) mRNA, complete cds. 11/11 None
SNAP00000006875 ENSEMBL cdna:SNAP chromosome:CEL140:II:13095583:13098171:-1 11/11 None
GENEFINDER00000006880 ENSEMBL cdna:GeneFinder chromosome:CEL140:II:13095583:13098171:-1 11/11 None
Y81G3A.5 ENSEMBL cdna:known chromosome:CEL140:II:13095905:13098171:-1 gene:Y81G3A.5 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:13095901-13098168(-) 100.0 100.0
Public Domain and Genome References
Gene Title collagen
Gene Symbol col-86
Ensembl Y81G3A.5
Entrez Gene 190749 Entrez gene
SwissProt Q9XVY1 EMBL-EBI
WormBase CE23120 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 CAA22518 Hypothetical protein Y81G3A.5 [Caenorhabditis elegans] ref|NP_496783.1| Y81G3A.5 [Caenorhabditis elegans] 2.0E-86
blast CAE59420 Hypothetical protein CBG02789 [Caenorhabditis briggsae] 1.0E-31
blast CAE75407 Hypothetical protein CBG23397 [Caenorhabditis briggsae] 1.0E-17
Protein Domains
Database ID Description E-Value
Pfam IPR002486 EMBL-EBI Nematode cuticle collagen, N-terminal 2.6E-12
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 1.4E-4
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 9.3E-5
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 7.8E-4
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_496783.1 1 7-29
Y81G3A.5 1 7-29
SNAP00000006875 1 7-29
GENEFINDER00000006880 1 7-29
Sequence
Target Sequence 
>C. ELEGANS:188552_AT
caagtgggtgtatcacttgccccgcgggaccaatgggatctcctggaccagatggacctc
caggagttcctggtgctactggaaatcctggcagcttgggagaatcaagcttgggagcag
gttcaccgggaccaccaggaggtgtaggtcccccaggtccgaatggaactcccggagcac
ctggagacgaaggcatacctggagttcctggagcaaacgtcatttgcccgcctggaccgg
caggatcaatgggatctgtcggacttcctggaccacctggaaatgatttgggaaatagta
atggacctccaggccctcctggtcaaatgggacaacctgggaaaccaggatctatgggag
gtcttggccaatctggaccaacaggatctgatggtattcctggaatcgatgggcaatact
gtcattgtccacaacgtacacataatttgggtatgaacagataccatgacgaaccaattc
cagt

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
CAAGTGGGTGTATCACTTGCCCCGC 693 183 416 Antisense
GGTGCTACTGGAAATCCTGGCAGCT 453 501 487 Antisense
CAAGCTTGGGAGCAGGTTCACCGGG 631 185 521 Antisense
GGTCCGAATGGAACTCCCGGAGCAC 418 501 571 Antisense
AAGGCATACCTGGAGTTCCTGGAGC 60 159 605 Antisense
CCGCCTGGACCGGCAGGATCAATGG 622 261 643 Antisense
CAATGGGATCTGTCGGACTTCCTGG 26 183 662 Antisense
CAGGCCCTCCTGGTCAAATGGGACA 543 207 725 Antisense
AGGTCTTGGCCAATCTGGACCAACA 394 53 774 Antisense
GGGCAATACTGTCATTGTCCACAAC 1 495 826 Antisense
GATACCATGACGAACCAATTCCAGT 96 425 875 Antisense
Sequence Source Affymetrix Proprietary Database