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[173607_s_at] collagen

Description C43978 /REP_DB=TREMBL Accession /5_PRIME_EXT_ID=F59F3.2 /5_PRIME_EXT_DB=WormBase Gene ID /GB=C43978 /WB_GENE_ID=F59F3.2 /WP=CE18797 /CHR=X /FEA=Genomic Cluster /DEF=collagen; C.elegans cDNA clone yk337f11 : 5prime end, single read.
Cluster 6grp_total > 24      4grp_total > 51      6grp_cgc > 33      6grp_cgc_sub > De      6grp_total_sub > Decrease      6grp_rule_based > S2      4grp_rule_based > L2      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 180
1 2 3 4 range
A 48.1
(-2)
A 		187.1
(3)
A 		41.2
(-2.2)
A 		18.7
(-3)
A 		168
B 69.6
(-0.1)
A 		109.7
(2)
A 		127.8
(3)
A 		13.9
(-3)
A 		114
C 95.8
(-2.7)
A 		194.3
(3)
A 		123.9
(-1.1)
A 		90.5
(-3)
A 		104
avr 71.2
(-1.5) 		163.7
(3) 		97.6
(-0.2) 		41
(-3) 		123

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 134
1 2 3 4 5 6 range
A 97.7
(0.4)
A 		138.5
(2.6)
A 		145
(3)
A 		79.9
(-0.6)
A 		36.6
(-3)
A 		49.4
(-2.3)
A 		108
B 114.9
(1.9)
A 		138.7
(3)
A 		97.4
(1.1)
A 		61.3
(-0.6)
A 		16.4
(-2.7)
A 		10.6
(-3)
A 		128
C 112.2
(1.5)
A 		136.2
(3)
A 		69.5
(-1.1)
A 		38.3
(-3)
A 		45.8
(-2.5)
A 		62.8
(-1.5)
A 		98
avr 108.3
(1.3) 		137.8
(3) 		104
(1.1) 		59.8
(-1.5) 		32.9
(-3) 		40.9
(-2.5) 		105
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 53
1 2 3 4 range
A 17.5
(-0.7)
A 		40.6
(3)
A 		10.8
(-1.7)
A 		2.7
(-3)
A 		38
B 22.2
(1.3)
A 		27.1
(2.4)
A 		29.6
(3)
A 		3
(-3)
A 		27
C 31.7
(-0.6)
A 		55.9
(3)
A 		43.2
(1.1)
A 		15.3
(-3)
A 		41
avr 23.8
(-0.1) 		41.2
(3) 		27.9
(0.7) 		7
(-3) 		34

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 45
1 2 3 4 5 6 range
A 18
(-1.9)
A 		49.3
(3)
A 		31.6
(0.2)
A 		20.3
(-1.6)
A 		11.1
(-3)
A 		12
(-2.9)
A 		38
B 40
(2.1)
A 		46.2
(3)
A 		23.7
(-0.2)
A 		16.2
(-1.3)
A 		6.7
(-2.6)
A 		4
(-3)
A 		42
C 41.6
(3)
A 		41.6
(3)
A 		17.7
(-1.2)
A 		7.7
(-3)
A 		14.8
(-1.7)
A 		21
(-0.6)
A 		34
avr 33.2
(0.8) 		45.7
(3) 		24.3
(-0.7) 		14.7
(-2.3) 		10.9
(-3) 		12.3
(-2.8) 		35
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 173607_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.25963
Sequence Type Exemplar sequence
Representative Public ID C43978 NCBI
Target Description C43978 /REP_DB=TREMBL Accession /5_PRIME_EXT_ID=F59F3.2 /5_PRIME_EXT_DB=WormBase Gene ID /GB=C43978 /WB_GENE_ID=F59F3.2 /WP=CE18797 /CHR=X /FEA=Genomic Cluster /DEF=collagen; C.elegans cDNA clone yk337f11 : 5prime end, single read.
Cluster Evidence This cluster is supported by a Genomic Cluster.
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_077436(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_077436 NCBI Caenorhabditis elegans F59F3.2 (collagen) mRNA, complete cds. 11/11 None
SNAP00000038682 ENSEMBL cdna:SNAP chromosome:CEL140:X:10999762:11001732:-1 11/11 None
F59F3.2 ENSEMBL cdna:known chromosome:CEL140:X:10999664:11001772:-1 gene:F59F3.2 11/11 None
Annotation Notes
Cross Hybridizing mRNA Matched Probes Nature of Assignment Related Probesets by Grade
GENEFINDER00000038685 8/11 Cross Hyb Matching Probes None
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrX:10999762-11001509(-) 100.0 100.0
Public Domain and Genome References
Gene Title collagen
Gene Symbol col-177
Ensembl F59F3.2
Entrez Gene 181290 Entrez gene
SwissProt Q21039 EMBL-EBI
WormBase CE37384 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
Protein Similarities
Method ID Description E-Value
blast CAA91992 Hypothetical protein F59F3.2 [Caenorhabditis elegans] ref|NP_509837.2| F59F3.2 [Caenorhabditis elegans] 1.0E-148
blast CAA91992 Hypothetical protein F59F3.2 [Caenorhabditis elegans] ref|NP_509837.2| F59F3.2 [Caenorhabditis elegans] 1.0E-115
blast CAE70777 Hypothetical protein CBG17531 [Caenorhabditis briggsae] 1.0E-88
blast CAE70777 Hypothetical protein CBG17531 [Caenorhabditis briggsae] 5.0E-88
Protein Domains
Database ID Description E-Value
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 9.4E-5
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 6.5E-10
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 9.4E-5
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 6.5E-10
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_509837.2 1 21-38
F59F3.2 1 21-38
Sequence
Target Sequence 
>C. ELEGANS:173607_S_AT
gctaaatggtcttcctgggccaaagggtcttccaggatcagttggattgccaggagccag
aggagatccaggcaacaatggaaaacctgcaccaccgggtccagaagggttcccaggtcc
tgttggagatttgggcgatgcaggagaatatggccttcgtggagtgcctgggagaagagg
aagtccaggaaaagacggtggatattgtcagtgtccaccacgagaaggttcatcattctc
ttcgtccacttcaacattgaatcgtcaaagtgtcaaagtttccacatctagaaacaggtt
aacatcaaataacaatgatgctgtagacgattatgaagccgaagtagaacggcatgtgac
tcccaggcagcagcaacagcagcaacaaccattccaaagaagacgatggcagaaagctaa
ccaacaaaaccaacgtgacatgtacgttaacctacgaaaaaacacacactcggatttgat
tgatgtcggagaatccagcatgaggagatctccaatggcgccatt

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GCTAAATGGTCTTCCTGGGCCAAAG 332 301 400 Antisense
GGATCAGTTGGATTGCCAGGAGCCA 337 511 434 Antisense
AACAATGGAAAACCTGCACCACCGG 334 135 473 Antisense
CCAGAAGGGTTCCCAGGTCCTGTTG 517 261 500 Antisense
TATGGCCTTCGTGGAGTGCCTGGGA 676 653 548 Antisense
GATATTGTCAGTGTCCACCACGAGA 405 427 600 Antisense
AGAAGGTTCATCATTCTCTTCGTCC 489 75 622 Antisense
GAAGTAGAACGGCATGTGACTCCCA 522 335 740 Antisense
AGCAGCAACAACCATTCCAAAGAAG 367 77 777 Antisense
AACACACACTCGGATTTGATTGATG 307 135 860 Antisense
TGAGGAGATCTCCAATGGCGCCATT 400 567 900 Antisense
Sequence Source Affymetrix Proprietary Database