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[188622_at] collagen

Description C09G5.5 /REP_DB=WormBase Gene ID /WP=CE01485 /TR=SW:Q09456 /GB=CAA86758.1 /SUBMIT=HINXTON /CHR=2 /FEA=Sanger Annotation /DEF=collagen
Cluster 6grp_highest_10_10 > 09      6grp_high1_10_10 > 91      6grp_highest_nonorm > 48      6grp_total > 93      4grp_total > 61      6grp_cgc > 99      6grp_high1_sub > 05      6grp_total_sub > Hat      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 3682
1 2 3 4 range
A 3294.2
(3)
P 		2348.7
(1.3)
P 		2675.4
(1.9)
P 		16.9
(-3)
A 		3277
B 3696.9
(3)
P 		1634.2
(-0.4)
P 		2826.8
(1.6)
P 		14.9
(-3)
A 		3682
C 3151.5
(3)
P 		1992.8
(0.7)
P 		2777.2
(2.3)
P 		64.1
(-3)
A 		3087
avr 3380.9
(3) 		1991.9
(0.5) 		2759.8
(1.9) 		32
(-3) 		3349

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 7279
1 2 3 4 5 6 range
A 3599.4
(-2.4)
P 		5012.2
(-0.4)
P 		4072
(-1.7)
P 		3149.7
(-3)
P 		7408.4
(3)
P 		3208.5
(-2.9)
P 		4259
B 3563.8
(-2.4)
P 		3885.8
(-2)
P 		5677
(0.4)
P 		3132
(-3)
P 		7619.8
(3)
P 		3535.6
(-2.5)
P 		4488
C 3529.9
(-2)
P 		3600.3
(-2)
P 		4659.9
(-1.1)
P 		2342.2
(-3)
P 		9621.6
(3)
P 		3001.6
(-2.5)
P 		7279
avr 3564.4
(-2.2) 		4166.1
(-1.5) 		4803
(-0.8) 		2874.6
(-3) 		8216.6
(3) 		3248.6
(-2.6) 		5342
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 1197
1 2 3 4 range
A 1199.4
(3)
P 		509.8
(-0.5)
P 		699.4
(0.5)
P 		2.5
(-3)
A 		1197
B 1178.9
(3)
P 		403.6
(-1)
P 		655
(0.3)
P 		3.2
(-3)
A 		1176
C 1043.2
(3)
P 		572.9
(0.3)
P 		967.9
(2.6)
P 		10.8
(-3)
A 		1032
avr 1140.5
(3) 		495.4
(-0.4) 		774.1
(1.1) 		5.5
(-3) 		1135

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 2642
1 2 3 4 5 6 range
A 663.5
(-3)
P 		1782.6
(1.3)
P 		886.8
(-2.1)
P 		798.8
(-2.5)
P 		2235.5
(3)
P 		781.2
(-2.6)
P 		1572
B 1240
(-1.9)
P 		1293.4
(-1.8)
P 		1378.6
(-1.5)
P 		829.6
(-3)
P 		3095.8
(3)
P 		1318.4
(-1.7)
P 		2266
C 1308.4
(-1.1)
P 		1098.6
(-1.6)
P 		1186
(-1.4)
P 		471
(-3)
P 		3113.4
(3)
P 		1004.8
(-1.8)
P 		2642
avr 1070.6
(-1.9) 		1391.5
(-1) 		1150.5
(-1.7) 		699.8
(-3) 		2814.9
(3) 		1034.8
(-2) 		2115
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 188622_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.3140
Sequence Type Exemplar sequence
Representative Public ID C09G5.5 NCBI
Target Description C09G5.5 /REP_DB=WormBase Gene ID /WP=CE01485 /TR=SW:Q09456 /GB=CAA86758.1 /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_063909(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_063909 NCBI Caenorhabditis elegans C09G5.5 (collagen) mRNA, complete cds. 11/11 None
SNAP00000014221 ENSEMBL cdna:SNAP chromosome:CEL140:II:10707157:10708133:1 11/11 None
GENEFINDER00000014237 ENSEMBL cdna:GeneFinder chromosome:CEL140:II:10707133:10708133:1 11/11 None
C09G5.5 ENSEMBL cdna:known chromosome:CEL140:II:10707131:10708417:1 gene:C09G5.5 11/11 None
Annotation Notes
Cross Hybridizing mRNA Matched Probes Nature of Assignment Related Probesets by Grade
NM_069896 1/11 Cross Hyb Matching Probes A 
SNAP00000023282 1/11 Cross Hyb Matching Probes None
GENEFINDER00000023293 1/11 Cross Hyb Matching Probes None
M18.1 1/11 Cross Hyb Matching Probes A 
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrII:10707129-10708130(+) 89.2 100.0
Public Domain and Genome References
Gene Title collagen
Gene Symbol col-80
Ensembl C09G5.5
Entrez Gene 174652 Entrez gene
SwissProt Q09456 EMBL-EBI
WormBase CE01485 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 CAA86758 Hypothetical protein C09G5.5 [Caenorhabditis elegans] ref|NP_496310.1| C09G5.5 [Caenorhabditis elegans] sp|Q09456|YQ35_CAEEL Putative cuticle collagen C09G5.5 3.0E-45
blast CAE59618 Hypothetical protein CBG03027 [Caenorhabditis briggsae] 8.0E-44
blast CAA86758 Hypothetical protein C09G5.5 [Caenorhabditis elegans] ref|NP_496310.1| C09G5.5 [Caenorhabditis elegans] sp|Q09456|YQ35_CAEEL Putative cuticle collagen C09G5.5 6.0E-41
blast CAE59618 Hypothetical protein CBG03027 [Caenorhabditis briggsae] 4.0E-40
blast CAB01961 Hypothetical protein C15A11.5 [Caenorhabditis elegans] ref|NP_492090.1| C15A11.5 [Caenorhabditis elegans] sp|P18832|COL7_CAEEL Cuticle collagen 7 precursor 6.0E-36
Protein Domains
Database ID Description E-Value
Pfam IPR002486 EMBL-EBI Nematode cuticle collagen, N-terminal 9.0E-24
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 1.1E-4
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 8.3E-9
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 1.1E-9
Pfam IPR002486 EMBL-EBI Nematode cuticle collagen, N-terminal 9.0E-24
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 1.1E-4
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 8.3E-9
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 1.1E-9
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_496310.1 1 5-27
C09G5.5 1 5-27
GENEFINDER00000014237 1 5-27
Sequence
Target Sequence 
>C. ELEGANS:188622_AT
cagctcaccaccaacagcaagagtgcatcaagtgcccacaaggagcaccaggaccagccg
gagcaccaggaaacccaggaccacaaggaccaaacggaaacccaggagcaccagcccacg
gaggaggccaaggaccaccaggaccaccaggaccagctggagacgctggatctccaggac
aagccggagccccaggaaacccaggacgcccaggacaatctggacagcgttcccgcggac
tcccaggaccatccggacgtccaggaccacaaggaccaccaggagccccaggacaaccag
gaagcggaagcactccaggaccagccggaccaccaggaccaccaggaccaaacggacaac
caggacacccaggacaagacggacaaccaggagccccaggaaacgatggagccccaggat
ctgacgccgcttattgtccatgcccagctcgcagtgccgcagttttccgtcaccgtaatg
ttgctgtcaaccgtcaccgtgctgttgccaagaagcgcgttgtcgccaagaagcgtgttg
tcgccagaaagcgcgtc

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
CAGCTCACCACCAACAGCAAGAGTG 179 203 380 Antisense
ACCACCAACAGCAAGAGTGCATCAA 610 85 386 Antisense
ACCAGCCCACGGAGGAGGCCAAGGA 31 83 489 Antisense
CCAGCTGGAGACGCTGGATCTCCAG 206 273 532 Antisense
CAGGAAGCGGAAGCACTCCAGGACC 505 207 677 Antisense
CAGTTTTCCGTCACCGTAATGTTGC 364 189 839 Antisense
TTCCGTCACCGTAATGTTGCTGTCA 677 697 844 Antisense
GTAATGTTGCTGTCAACCGTCACCG 184 463 854 Antisense
GCTGTTGCCAAGAAGCGCGTTGTCG 177 295 880 Antisense
GCGCGTTGTCGCCAAGAAGCGTGTT 3 289 894 Antisense
GCGTGTTGTCGCCAGAAAGCGCGTC 183 293 912 Antisense
Sequence Source Affymetrix Proprietary Database