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[190584_at] collagen

Description C09G5.4 /REP_DB=WormBase Gene ID /WP=CE01484 /GEN=col-39 /TR=SW:Q09455 /GB=CAA86757.1 /SUBMIT=HINXTON /CHR=2 /FEA=Sanger Annotation /DEF=collagen
Cluster 6grp_highest_10_10 > 44      6grp_high1_10_10 > 43      6grp_highest_nonorm > 25      6grp_total > 10      4grp_total > 49      6grp_highest_sub > 02      6grp_cgc > 63      6grp_high1_sub > 02      6grp_cgc_sub > 02      6grp_total_sub > Hat      6grp_rule_based > S2      4grp_rule_based > L2      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 12199
1 2 3 4 range
A 1219
(-2.4)
P 		12255.9
(3)
P 		11409.5
(2.6)
P 		56.6
(-3)
A 		12199
B 1037.9
(-2.5)
P 		10621.2
(3)
P 		10571.3
(3)
P 		80.3
(-3)
A 		10541
C 1054
(-2.5)
P 		10269.5
(3)
P 		9739.6
(2.7)
P 		132.4
(-3)
A 		10137
avr 1103.6
(-2.4) 		11048.9
(3) 		10573.5
(2.7) 		89.8
(-3) 		10959

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 7924
1 2 3 4 5 6 range
A 1123
(-3)
P 		7882.9
(3)
P 		5200.5
(0.6)
P 		4028.2
(-0.4)
P 		3321
(-1)
P 		2229.1
(-2)
P 		6760
B 1329.3
(-3)
P 		8824.5
(3)
P 		6374.6
(1)
P 		4062.1
(-0.8)
P 		3365.1
(-1.4)
P 		2296.4
(-2.2)
P 		7495
C 1026.6
(-3)
P 		8950.1
(3)
P 		4946.6
(-0)
P 		4185
(-0.6)
P 		3829.2
(-0.9)
P 		1591
(-2.6)
P 		7924
avr 1159.6
(-3) 		8552.5
(3) 		5507.2
(0.5) 		4091.8
(-0.6) 		3505.1
(-1.1) 		2038.8
(-2.3) 		7393
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 3386
1 2 3 4 range
A 443.8
(-2.1)
P 		2660.4
(2.3)
P 		2982.7
(3)
P 		8.3
(-3)
A 		2974
B 331
(-2.3)
P 		2623.2
(3)
P 		2449.6
(2.6)
P 		17.1
(-3)
A 		2606
C 348.9
(-2.4)
P 		2952.5
(2.2)
P 		3394.6
(3)
P 		22.3
(-3)
A 		3372
avr 374.6
(-2.3) 		2745.4
(2.6) 		2942.3
(3) 		15.9
(-3) 		2926

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 2730
1 2 3 4 5 6 range
A 207
(-3)
P 		2803.5
(3)
P 		1132.6
(-0.9)
P 		1021.7
(-1.1)
P 		1002.1
(-1.2)
P 		542.7
(-2.2)
P 		2597
B 462.5
(-3)
P 		2937.3
(3)
P 		1548
(-0.4)
P 		1075.9
(-1.5)
P 		1367.2
(-0.8)
P 		856.3
(-2)
P 		2475
C 380.5
(-3)
P 		2730.9
(3)
P 		1259
(-0.8)
P 		841.6
(-1.8)
P 		1239.1
(-0.8)
P 		532.6
(-2.6)
P 		2350
avr 350
(-3) 		2823.9
(3) 		1313.2
(-0.7) 		979.7
(-1.5) 		1202.8
(-0.9) 		643.9
(-2.3) 		2474
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 190584_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.2995
Sequence Type Exemplar sequence
Representative Public ID C09G5.4 NCBI
Target Description C09G5.4 /REP_DB=WormBase Gene ID /WP=CE01484 /GEN=col-39 /TR=SW:Q09455 /GB=CAA86757.1 /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_063908(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_063908 NCBI Caenorhabditis elegans C09G5.4 (collagen) mRNA, complete cds. 11/11 None
SNAP00000014220 ENSEMBL cdna:SNAP chromosome:CEL140:II:10704833:10705871:1 11/11 None
GENEFINDER00000014231 ENSEMBL cdna:GeneFinder chromosome:CEL140:II:10704833:10705871:1 11/11 None
C09G5.4 ENSEMBL cdna:known chromosome:CEL140:II:10704814:10705921:1 gene:C09G5.4 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
chrII:10704829-10705868(+) 100.0 100.0
Public Domain and Genome References
Gene Title collagen
Gene Symbol col-39
Ensembl C09G5.4
Entrez Gene 174651 Entrez gene
SwissProt Q09455 EMBL-EBI
WormBase CE01484 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 CAA86757 Hypothetical protein C09G5.4 [Caenorhabditis elegans] ref|NP_496309.1| C09G5.4 [Caenorhabditis elegans] sp|Q09455|COL39_CAEEL Cuticle collagen 39 precursor 2.0E-53
blast CAE59619 Hypothetical protein CBG03028 [Caenorhabditis briggsae] 2.0E-46
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-37
Protein Domains
Database ID Description E-Value
Pfam IPR002486 EMBL-EBI Nematode cuticle collagen, N-terminal 3.7E-23
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 7.1E-4
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 3.4E-11
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 2.8E-13
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_496309.1 1 7-29
C09G5.4 1 7-29
SNAP00000014220 1 7-29
GENEFINDER00000014231 1 7-29
Sequence
Target Sequence 
>C. ELEGANS:190584_AT
gagttgctggaccaaagagccatgaacaacaagagtgcatcaagtgcccagccggatccc
caggaccagcaggagctccaggagcaccaggaccacaaggaccaaatggacagccaggac
acccaggacaaggaggaagccaaggaccagcaggaccacgaggaccagctggagatgctg
gagcaccaggacaagtcggtgccccaggaaacccaggacaagccggaagaggaggacaac
gttcccacggacttccaggaccatctggagccccaggaccacaaggaccatcaggagccc
caggccagccaggacaatctggaggtcaaggacaacaaggaccagcaggaccagccggac
cagacggacaaccaggacagccaggtcaagatggacaagccggagcaccaggaaacgatg
gagccccaggagccgatgctgcttactgcccatgcccatcccgcagtggatcttcctcag
cagttgaaactggagctgccgagcagggataccgtcaccgtgctgttgctgctcgccacc
gcaacgtcattcgtcgccgtgtcgccaagaagcgcgtcgtcaag

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GAGTTGCTGGACCAAAGAGCCATGA 540 397 371 Antisense
GAGCCATGAACAACAAGAGTGCATC 179 385 387 Antisense
CAAGGAGGAAGCCAAGGACCAGCAG 597 183 499 Antisense
GCACCAGGACAAGTCGGTGCCCCAG 104 313 553 Antisense
GAAGAGGAGGACAACGTTCCCACGG 252 339 596 Antisense
GGACAATCTGGAGGTCAAGGACAAC 658 525 682 Antisense
CAGTGGATCTTCCTCAGCAGTTGAA 625 207 834 Antisense
GGATCTTCCTCAGCAGTTGAAACTG 584 509 838 Antisense
GTTGAAACTGGAGCTGCCGAGCAGG 184 439 853 Antisense
AAACTGGAGCTGCCGAGCAGGGATA 185 127 857 Antisense
TGTCGCCAAGAAGCGCGTCGTCAAG 523 557 930 Antisense
Sequence Source Affymetrix Proprietary Database