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[188481_at] collagen

Description F52F12.2 /REP_DB=WormBase Gene ID /WP=CE10842 /TR=O02271 /GB=CAB05733.1 /SUBMIT=HINXTON /CHR=1 /FEA=Sanger Annotation /DEF=collagen
Cluster 6grp_total > 03      4grp_total > 06      6grp_cgc > 50      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 67
1 2 3 4 range
A 73.5
(-1)
P 		55.9
(-3)
M 		84.5
(0.2)
M 		109
(3)
P 		53
B 52.8
(-1.6)
P 		42.1
(-3)
A 		51.7
(-1.7)
A 		87.8
(3)
P 		46
C 81.9
(3)
P 		56
(-2.7)
P 		54.5
(-3)
A 		74.8
(1.4)
P 		27
avr 69.4
(-0.2) 		51.3
(-3) 		63.6
(-1.1) 		90.5
(3) 		39

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 55
1 2 3 4 5 6 range
A 46.3
(1.5)
A 		33.3
(-1.6)
A 		50.8
(2.6)
A 		49
(2.1)
A 		52.6
(3)
A 		27.3
(-3)
A 		25
B 34.8
(-1.6)
P 		63.1
(3)
A 		26.2
(-3)
A 		38.4
(-1)
A 		41.1
(-0.6)
A 		30.9
(-2.2)
P 		37
C 55.3
(0.7)
P 		52.3
(0.4)
A 		38.4
(-1.1)
A 		76.4
(3)
A 		22.9
(-2.8)
A 		21
(-3)
A 		55
avr 45.5
(1.1) 		49.6
(1.9) 		38.5
(-0.4) 		54.6
(3) 		38.9
(-0.3) 		26.4
(-3) 		28
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 17
1 2 3 4 range
A 26.8
(3)
P 		12.1
(-3)
M 		22.1
(1.1)
M 		16
(-1.4)
P 		15
B 16.9
(1.7)
P 		10.4
(-3)
A 		12
(-1.8)
A 		18.7
(3)
P 		8
C 27.1
(3)
P 		16.1
(-1.6)
P 		19
(-0.4)
A 		12.6
(-3)
P 		15
avr 23.6
(3) 		12.9
(-3) 		17.7
(-0.3) 		15.8
(-1.4) 		11

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 15
1 2 3 4 5 6 range
A 8.5
(-1.8)
A 		11.8
(0.4)
A 		11.1
(-0.1)
A 		12.4
(0.7)
A 		15.9
(3)
A 		6.6
(-3)
A 		9
B 12.1
(-0.7)
P 		21
(3)
A 		6.4
(-3)
A 		10.2
(-1.4)
A 		16.7
(1.2)
A 		11.5
(-0.9)
P 		15
C 20.5
(3)
P 		15.9
(1)
A 		9.8
(-1.8)
A 		15.4
(0.7)
A 		7.4
(-2.8)
A 		7
(-3)
A 		14
avr 13.7
(1.1) 		16.2
(3) 		9.1
(-2.5) 		12.7
(0.3) 		13.3
(0.8) 		8.4
(-3) 		8
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 188481_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.1243
Sequence Type Exemplar sequence
Representative Public ID F52F12.2 NCBI
Target Description F52F12.2 /REP_DB=WormBase Gene ID /WP=CE10842 /TR=O02271 /GB=CAB05733.1 /SUBMIT=HINXTON /CHR=1 /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_060218(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_060218 NCBI Caenorhabditis elegans F52F12.2 (collagen) mRNA, complete cds. 11/11 None
GENEFINDER00000038790 ENSEMBL cdna:GeneFinder chromosome:CEL140:I:9900638:9903717:-1 11/11 None
SNAP00000038775 ENSEMBL cdna:SNAP chromosome:CEL140:I:9901819:9903717:-1 11/11 None
F52F12.2 ENSEMBL cdna:known chromosome:CEL140:I:9901819:9903717:-1 gene:F52F12.2 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
chrI:9901749-9903648(-) 100.0 100.0
Public Domain and Genome References
Gene Title collagen
Gene Symbol col-64
Ensembl F52F12.2
Entrez Gene 186127 Entrez gene
SwissProt O02271 EMBL-EBI
WormBase CE10842 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 CAB05733 Hypothetical protein F52F12.2 [Caenorhabditis elegans] ref|NP_492619.1| F52F12.2 [Caenorhabditis elegans] 1.0E-106
blast CAE60272 Hypothetical protein CBG03851 [Caenorhabditis briggsae] 9.0E-78
blast CAE59859 Hypothetical protein CBG03334 [Caenorhabditis briggsae] 8.0E-17
Protein Domains
Database ID Description E-Value
Pfam IPR002486 EMBL-EBI Nematode cuticle collagen, N-terminal 2.9E-19
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 1.1E-12
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 3.0E-8
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_492619.1 1 7-29
F52F12.2 1 7-29
GENEFINDER00000038790 1 7-29
SNAP00000038775 1 7-29
Sequence
Target Sequence 
>C. ELEGANS:188481_AT
ggattcatcggattccctggattcccaggtgcacctggtgagaatggagaacaaggaaac
aatgcaactcgtggagttggaattcctggaccagcaggaccaccgggtcctccaggagaa
gtcggaatgcctggagtaacaggtgaaactggagaagacggacatgatggacctgaagga
ccagaaggaccagctggaaatataggagatatagctgaagaaggaccagatggtattcca
ggcgagcaaggagttcctgggttcgattccggctattgtccatgtcctcgtcgatcatct
tcaagagtttcaccttccggtggatcttctccaatctcagatacattcattgcatctcca
acacttcttccaccatcaactacactttcatcaacccctccaactatatctccatctgct
ccaactcttctaccaactagatctccaaaatctcgtgaagaaactccgacaagaagagaa
gaacaacaagtaccaccgaatcct

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GGATTCATCGGATTCCCTGGATTCC 384 509 541 Antisense
TTCCCTGGATTCCCAGGTGCACCTG 241 697 553 Antisense
CCACCGGGTCCTCCAGGAGAAGTCG 251 271 640 Antisense
GACCAGATGGTATTCCAGGCGAGCA 392 381 764 Antisense
GGCGAGCAAGGAGTTCCTGGGTTCG 396 531 781 Antisense
TGTCCTCGTCGATCATCTTCAAGAG 483 557 823 Antisense
GAGTTTCACCTTCCGGTGGATCTTC 211 399 845 Antisense
GTGGATCTTCTCCAATCTCAGATAC 592 489 860 Antisense
AGATACATTCATTGCATCTCCAACA 2 67 879 Antisense
AACTCTTCTACCAACTAGATCTCCA 421 141 963 Antisense
AGAACAACAAGTACCACCGAATCCT 335 73 1020 Antisense
Sequence Source Affymetrix Proprietary Database