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[188293_at] collagen

Description C30F2.1 /REP_DB=WormBase Gene ID /WP=CE17480 /TR=Q18327 /GB=CAA94580.1 /SUBMIT=HINXTON /CHR=X /FEA=Sanger Annotation /DEF=collagen
Cluster 6grp_high1_10_10 > 22      4grp_high_8_8 > 37      6grp_total > 02      4grp_total > 42      6grp_cgc > 52      6grp_high1_sub > De      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 106
1 2 3 4 range
A 111.6
(-3)
P 		163
(3)
P 		154
(1.9)
P 		115.2
(-2.6)
A 		51
B 120.5
(0.2)
A 		170.6
(3)
P 		123.4
(0.3)
P 		64.6
(-3)
A 		106
C 83.8
(-3)
A 		113.2
(0.1)
M 		110.8
(-0.1)
P 		139.9
(3)
P 		56
avr 105.3
(-3) 		148.9
(3) 		129.4
(0.3) 		106.6
(-2.8) 		44

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 96
1 2 3 4 5 6 range
A 113.2
(0.7)
A 		81.8
(-3)
A 		132.4
(3)
P 		84
(-2.7)
A 		125.4
(2.2)
P 		97.4
(-1.2)
P 		51
B 123.5
(1)
P 		155.1
(3)
P 		76.4
(-1.9)
A 		105
(-0.1)
P 		129.1
(1.4)
P 		59.2
(-3)
P 		96
C 86
(-1.7)
M 		125.6
(3)
P 		93.1
(-0.9)
A 		122.6
(2.6)
P 		112.5
(1.4)
P 		75
(-3)
P 		51
avr 107.6
(1) 		120.8
(2.8) 		100.6
(0.1) 		103.9
(0.6) 		122.3
(3) 		77.2
(-3) 		45
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 28
1 2 3 4 range
A 40.6
(3)
P 		35.4
(1.7)
P 		40.3
(2.9)
P 		16.9
(-3)
A 		24
B 38.4
(2.2)
A 		42.1
(3)
P 		28.6
(0.1)
P 		13.8
(-3)
A 		28
C 27.8
(-1.3)
A 		32.6
(0.6)
M 		38.6
(3)
P 		23.6
(-3)
P 		15
avr 35.6
(2.6) 		36.7
(3) 		35.8
(2.7) 		18.1
(-3) 		19

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 34
1 2 3 4 5 6 range
A 20.9
(-3)
A 		29.1
(-0.1)
A 		28.8
(-0.2)
P 		21.3
(-2.9)
A 		37.8
(3)
P 		23.7
(-2)
P 		17
B 43
(1.3)
P 		51.6
(2.8)
P 		18.5
(-3)
A 		27.8
(-1.4)
P 		52.5
(3)
P 		22.1
(-2.4)
P 		34
C 31.9
(0.4)
M 		38.3
(3)
P 		23.7
(-3)
A 		24.7
(-2.6)
P 		36.4
(2.2)
P 		25.1
(-2.4)
P 		15
avr 31.9
(-0.3) 		39.7
(2.2) 		23.7
(-3) 		24.6
(-2.7) 		42.2
(3) 		23.6
(-3) 		19
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 188293_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.17382
Sequence Type Exemplar sequence
Representative Public ID C30F2.1 NCBI
Target Description C30F2.1 /REP_DB=WormBase Gene ID /WP=CE17480 /TR=Q18327 /GB=CAA94580.1 /SUBMIT=HINXTON /CHR=X /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_078229(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_078229 NCBI Caenorhabditis elegans C30F2.1 (collagen) mRNA, complete cds. 11/11 None
SNAP00000029821 ENSEMBL cdna:SNAP chromosome:CEL140:X:16072817:16074766:1 11/11 None
GENEFINDER00000029828 ENSEMBL cdna:GeneFinder chromosome:CEL140:X:16072817:16074766:1 11/11 None
C30F2.1 ENSEMBL cdna:known chromosome:CEL140:X:16072817:16074766:1 gene:C30F2.1 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
chrX:16072816-16074766(+) 100.0 100.0
Public Domain and Genome References
Gene Title collagen
Gene Symbol col-187
Ensembl C30F2.1
Entrez Gene 181685 Entrez gene
SwissProt Q18327 EMBL-EBI
WormBase CE17480 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 CAA94580 Hypothetical protein C30F2.1 [Caenorhabditis elegans] ref|NP_510630.1| C30F2.1 [Caenorhabditis elegans] 1.0E-109
blast CAE69999 Hypothetical protein CBG16406 [Caenorhabditis briggsae] 9.0E-64
blast CAE67061 Hypothetical protein CBG12469 [Caenorhabditis briggsae] 3.0E-13
Protein Domains
Database ID Description E-Value
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 5.0E-4
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 7.3E-5
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 7.9E-9
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_510630.1 1 7-29
C30F2.1 1 7-29
SNAP00000029821 1 7-29
GENEFINDER00000029828 1 7-29
Sequence
Target Sequence 
>C. ELEGANS:188293_AT
ggacctcccggctgtagaggagaaccaggaccttcaggcctacccggaaggcgtggaatc
aacaattatgagactttgccattaaagaagtgtatttggagggaaagattggcgtgtatc
atgtgcccaagagggccgccgggaagaagagggcgaatgggagatgatggggaaccaggg
gcgccgggcaggcgtggattgtcaggaactttcttgacaggaatcaaaaagttgagagga
ccaccgggggaacccggggaacctggtagacctggaacccctgggacaccgggaaacgat
ggcaaagatgggcgtaatggctaccggcttagaccggacaaaataactagaggcccgcct
ggacccatgggcgctcgaggtgaaccgggccatcgaggtcttccaggagataatggaatg
ccagggccaatggggccgccgggttaccgaggagacaacggaagacgtggggcgccgggg
ctgcccggtagaactggaagacatggaaaacccggtggagattcatcatattgtccgtgt
cct

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GGACCTCCCGGCTGTAGAGGAGAAC 455 379 355 Antisense
AGAGGAGAACCAGGACCTTCAGGCC 287 67 370 Antisense
TTCAGGCCTACCCGGAAGGCGTGGA 100 685 387 Antisense
GCGTGTATCATGTGCCCAAGAGGGC 102 293 466 Antisense
CGCCGGGCAGGCGTGGATTGTCAGG 496 255 536 Antisense
AAGATGGGCGTAATGGCTACCGGCT 492 153 659 Antisense
ACAAAATAACTAGAGGCCCGCCTGG 156 113 692 Antisense
GCTCGAGGTGAACCGGGCCATCGAG 227 297 727 Antisense
GAATGCCAGGGCCAATGGGGCCGCC 10 331 770 Antisense
GGGCTGCCCGGTAGAACTGGAAGAC 688 491 832 Antisense
AGATTCATCATATTGTCCGTGTCCT 599 65 873 Antisense
Sequence Source Affymetrix Proprietary Database