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[188375_at] collagen

Description F17C11.3 /REP_DB=WormBase Gene ID /WP=CE05650 /TR=Q19514 /GB=CAA96625.1 /SUBMIT=HINXTON /CHR=5 /FEA=Sanger Annotation /DEF=collagen
Cluster 6grp_total > 20      4grp_total > 41      6grp_cgc > 73      6grp_cgc_sub > 02_03      6grp_total_sub > Hat      6grp_rule_based > S2      4grp_rule_based > L2      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 161
1 2 3 4 range
A 14.6
(-3)
A 		175.7
(3)
A 		170.2
(2.8)
A 		94.8
(-0)
A 		161
B 27
(-3)
A 		169.7
(3)
A 		147.3
(2.1)
A 		86.3
(-0.5)
A 		143
C 45.6
(-3)
A 		128.2
(1.8)
A 		148.8
(3)
A 		133.4
(2.1)
A 		103
avr 29.1
(-3) 		157.9
(3) 		155.4
(2.9) 		104.8
(0.5) 		129

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 114
1 2 3 4 5 6 range
A 59.1
(-1.7)
A 		142.3
(3)
A 		110.7
(1.2)
A 		105.3
(0.9)
A 		85.6
(-0.2)
A 		35.5
(-3)
A 		107
B 78.3
(-1.7)
A 		132
(3)
A 		115.9
(1.6)
A 		62.9
(-3)
A 		98.5
(0.1)
A 		74.5
(-2)
A 		69
C 36.8
(-3)
A 		117.9
(1.3)
A 		149.8
(3)
A 		85.4
(-0.4)
A 		75.4
(-1)
A 		38.3
(-2.9)
A 		113
avr 58.1
(-2.4) 		130.7
(3) 		125.5
(2.6) 		84.5
(-0.4) 		86.5
(-0.3) 		49.4
(-3) 		81
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 47
1 2 3 4 range
A 5.3
(-3)
A 		38.1
(2)
A 		44.5
(3)
A 		13.9
(-1.7)
A 		39
B 8.6
(-3)
A 		41.9
(3)
A 		34.1
(1.6)
A 		18.4
(-1.2)
A 		33
C 15.1
(-3)
A 		36.9
(0.6)
A 		51.9
(3)
A 		22.5
(-1.8)
A 		37
avr 9.7
(-3) 		39
(2.2) 		43.5
(3) 		18.3
(-1.5) 		34

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 42
1 2 3 4 5 6 range
A 10.9
(-2.7)
A 		50.6
(3)
A 		24.1
(-0.8)
A 		26.7
(-0.4)
A 		25.8
(-0.5)
A 		8.6
(-3)
A 		42
B 27.3
(-0.7)
A 		43.9
(3)
A 		28.2
(-0.5)
A 		16.7
(-3)
A 		40
(2.1)
A 		27.8
(-0.6)
A 		27
C 13.6
(-2.8)
A 		36
(2.5)
A 		38.1
(3)
A 		17.2
(-2)
A 		24.4
(-0.2)
A 		12.8
(-3)
A 		25
avr 17.3
(-2.8) 		43.5
(3) 		30.1
(0) 		20.2
(-2.2) 		30.1
(0) 		16.4
(-3) 		27
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 188375_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.14465
Sequence Type Exemplar sequence
Representative Public ID F17C11.3 NCBI
Target Description F17C11.3 /REP_DB=WormBase Gene ID /WP=CE05650 /TR=Q19514 /GB=CAA96625.1 /SUBMIT=HINXTON /CHR=5 /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_073392(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_073392 NCBI Caenorhabditis elegans F17C11.3 (collagen) mRNA, complete cds. 11/11 None
SNAP00000033896 ENSEMBL cdna:SNAP chromosome:CEL140:V:10952600:10954283:1 11/11 None
GENEFINDER00000033917 ENSEMBL cdna:GeneFinder chromosome:CEL140:V:10952600:10954517:1 9/11 None
F17C11.3 ENSEMBL cdna:known chromosome:CEL140:V:10952524:10954283:1 gene:F17C11.3 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
chrV:10952599-10954283(+) 97.14 100.0
Public Domain and Genome References
Gene Title collagen
Gene Symbol col-153
Ensembl F17C11.3
Entrez Gene 179517 Entrez gene
SwissProt Q19514 EMBL-EBI
WormBase CE05650 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 CAA96625 Hypothetical protein F17C11.3 [Caenorhabditis elegans] ref|NP_505793.1| F17C11.3 [Caenorhabditis elegans] 1.0E-145
blast CAA96625 Hypothetical protein F17C11.3 [Caenorhabditis elegans] ref|NP_505793.1| F17C11.3 [Caenorhabditis elegans] 1.0E-128
blast CAE75130 Hypothetical protein CBG23058 [Caenorhabditis briggsae] 1.0E-106
blast CAE75130 Hypothetical protein CBG23058 [Caenorhabditis briggsae] 3.0E-97
blast CAB01588 Hypothetical protein ZK836.1 [Caenorhabditis elegans] ref|NP_506061.1| ZK836.1 [Caenorhabditis elegans] gb|AAL08218.1| cuticle collagen protein LON-3 [Caenorhabditis elegans] gb|AAL76993.1| cuticle collagen LON-3 [Caenorhabditis elegans] sp|Q23628|LON3_CAEEL Cuticle collagen lon-3 precursor 7.0E-20
Protein Domains
Database ID Description E-Value
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 1.2E-12
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 6.3E-8
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_505793.1 1 9-31
F17C11.3 1 9-31
SNAP00000033896 1 9-31
GENEFINDER00000033917 1 9-31
Sequence
Target Sequence 
>C. ELEGANS:188375_AT
ctctggacctgctggtccacttggtgaccagggaattgatggaattgatggaattgatgg
tgtagatggatatgatggatttgatgcttatccaagtcctccagcaaaacactcaaaggc
tccattcacttgtccccgtggtccaccaggagacataggatcagatggtccacgtggtaa
aagaggtcttcgtggaccacggggtcgccctggtagaccaggaattaatggaaatccagg
attcccaggagatatgggtgcacctggtcaaccaggagtagatggaatagttggtgaacg
aggtgttaatggtattgatggagtgacatatattccacggcaaggtgtgaaaggggcaat
ggggcaaccaggaaatgagggtcaacctggaaagaaaggaaggcctggtctaccaggaac
tgaaggaatcagaggatacgaaggaatgagtggattaagaggaattgaaggtgttggcgg
gccaccaggaccacctggaccacaaggaacaataggaggagatgcggcgtattgtcaatg
tccaaaccgtggtgacaa

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
CTCTGGACCTGCTGGTCCACTTGGT 518 229 414 Antisense
GATTTGATGCTTATCCAAGTCCTCC 14 429 491 Antisense
CAAGTCCTCCAGCAAAACACTCAAA 71 185 506 Antisense
ACACTCAAAGGCTCCATTCACTTGT 117 111 522 Antisense
GACATAGGATCAGATGGTCCACGTG 695 369 565 Antisense
GGGGTCGCCCTGGTAGACCAGGAAT 179 487 614 Antisense
GAGATATGGGTGCACCTGGTCAACC 513 395 662 Antisense
GGAGTGACATATATTCCACGGCAAG 217 517 733 Antisense
TTGAAGGTGTTGGCGGGCCACCAGG 320 651 878 Antisense
GGAGGAGATGCGGCGTATTGTCAAT 691 515 928 Antisense
GTCAATGTCCAAACCGTGGTGACAA 648 463 947 Antisense
Sequence Source Affymetrix Proprietary Database