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[183666_at] cuticular collagen

Description C52D10.13 /REP_DB=WormBase Gene ID /WP=CE17596 /SUBMIT=ST.LOUIS /CHR=4 /FEA=Sanger Annotation /DEF=cuticular collagen
Cluster 6grp_total > 94      4grp_total > 58      6grp_cgc > 89      6grp_total_sub > Hat      6grp_rule_based > S5      4grp_rule_based > L2      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 270
1 2 3 4 range
A 84.4
(-1.3)
A 		278.7
(3)
A 		260.1
(2.6)
A 		8.6
(-3)
A 		270
B 105
(-0.9)
A 		252.8
(3)
A 		247.5
(2.9)
A 		22.6
(-3)
A 		230
C 84.8
(-1.6)
A 		236.3
(3)
A 		235.5
(3)
A 		39.4
(-3)
A 		197
avr 91.4
(-1.2) 		255.9
(3) 		247.7
(2.8) 		23.5
(-3) 		232

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 2880
1 2 3 4 5 6 range
A 109.3
(-3)
A 		219.5
(-2.6)
A 		100.1
(-3)
A 		777.4
(-0.7)
P 		1864.4
(3)
P 		1447
(1.6)
P 		1764
B 117.9
(-3)
A 		196.2
(-2.8)
A 		132.6
(-3)
A 		714.6
(-1.4)
P 		2308
(3)
P 		1682.2
(1.3)
P 		2190
C 85.8
(-3)
A 		184.6
(-2.8)
A 		153.3
(-2.9)
A 		596
(-1.9)
P 		2965.7
(3)
P 		1289.5
(-0.5)
P 		2880
avr 104.3
(-3) 		200.1
(-2.7) 		128.7
(-2.9) 		696
(-1.4) 		2379.4
(3) 		1472.9
(0.6) 		2275
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 81
1 2 3 4 range
A 30.7
(-0.4)
A 		60.5
(2.3)
A 		68
(3)
A 		1.3
(-3)
A 		67
B 33.5
(-0)
A 		62.4
(3)
A 		57.4
(2.5)
A 		4.8
(-3)
A 		58
C 28.1
(-1.3)
A 		67.9
(1.9)
A 		82.1
(3)
A 		6.7
(-3)
A 		75
avr 30.8
(-0.6) 		63.6
(2.5) 		69.2
(3) 		4.3
(-3) 		65

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 940
1 2 3 4 5 6 range
A 20.1
(-3)
A 		78.1
(-2.4)
A 		21.8
(-3)
A 		197.2
(-1)
P 		562.6
(3)
P 		352.3
(0.7)
P 		543
B 41
(-2.9)
A 		65.3
(-2.8)
A 		32.2
(-3)
A 		189.3
(-2)
P 		937.7
(3)
P 		627.3
(0.9)
P 		906
C 31.8
(-3)
A 		56.3
(-2.8)
A 		39
(-3)
A 		119.9
(-2.4)
P 		959.7
(3)
P 		431.7
(-0.4)
P 		928
avr 31
(-3) 		66.6
(-2.7) 		31
(-3) 		168.8
(-2) 		820
(3) 		470.4
(0.3) 		789
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 183666_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.8952
Sequence Type Exemplar sequence
Representative Public ID C52D10.13 NCBI
Target Description C52D10.13 /REP_DB=WormBase Gene ID /WP=CE17596 /SUBMIT=ST.LOUIS /CHR=4 /FEA=Sanger Annotation /DEF=cuticular 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_070647(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_070647 NCBI Caenorhabditis elegans COLlagen family member (col-138) (col-138) mRNA, complete cds. 11/11 None
SNAP00000030648 ENSEMBL cdna:SNAP chromosome:CEL140:IV:17182840:17183685:-1 11/11 None
GENEFINDER00000030664 ENSEMBL cdna:GeneFinder chromosome:CEL140:IV:17182840:17183685:-1 11/11 None
C52D10.13 ENSEMBL cdna:known chromosome:CEL140:IV:17182840:17183685:-1 gene:C52D10.13 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
chrIV:17182845-17183691(-) 96.45 100.0
Public Domain and Genome References
Gene Title cuticular collagen
Gene Symbol col-138
Ensembl C52D10.13
Entrez Gene 183722 Entrez gene
SwissProt Q966N5 EMBL-EBI
WormBase CE17596 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 NP_503048 COLlagen family member (col-138) [Caenorhabditis elegans] gb|AAK77204.1| Collagen protein 138 [Caenorhabditis elegans] 3.0E-55
blast CAE57403 Hypothetical protein CBG00356 [Caenorhabditis briggsae] 3.0E-52
blast NP_494880 F11G11.12 [Caenorhabditis elegans] gb|AAB37843.1| Collagen protein 73 [Caenorhabditis elegans] 6.0E-27
Protein Domains
Database ID Description E-Value
Pfam IPR002486 EMBL-EBI Nematode cuticle collagen, N-terminal 5.1E-7
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 9.1E-4
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 1.3E-10
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 9.9E-14
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_503048.1 1 13-35
C52D10.13 1 13-35
SNAP00000030648 1 13-35
GENEFINDER00000030664 1 13-35
Sequence
Target Sequence 
>C. ELEGANS:183666_AT
ccagaagcgttccaccaacgagaagtgctgctcttgcggaactggaaccgccggaccagt
tggagcaccgggagatgatggagctccaggatccgacggaaaggctggaaagcctggagt
caacggaaaggatgccgatgcccagcagatcccaaccgccgacgatttctgctttgagtg
tgagccatctccagttggaccaccaggaccaccaggaccaaagggaccagacggagagtc
cggagcaccaggagagccagggccagccggccgtccaggaaacaagggagctccaggacc
agccggaccagtcggagccgatggagagccaggagagcttggagcaccaggagcaccagg
agttcagcgtaccgtcgcatcgccagtcggagagccaggagagccaggagagcaaggacc
aaagggagaagccggacaagatggacgtccaggacagccaggaagacaaggaccacaagg
agagccaggacaaaacggaaaggatggagagccaggaaaggacggagtcgacggagagcc
aggaaagccaggagaggacggaccaaagggatcctgcgatc

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
CCAGAAGCGTTCCACCAACGAGAAG 198 271 243 Antisense
CCAACGAGAAGTGCTGCTCTTGCGG 156 277 257 Antisense
TTGCGGAACTGGAACCGCCGGACCA 395 701 276 Antisense
GGCTGGAAAGCCTGGAGTCAACGGA 149 539 345 Antisense
GCCGACGATTTCTGCTTTGAGTGTG 690 283 400 Antisense
GCTTTGAGTGTGAGCCATCTCCAGT 606 303 413 Antisense
GGGACCAGACGGAGAGTCCGGAGCA 440 493 465 Antisense
CCGGACCAGTCGGAGCCGATGGAGA 85 265 545 Antisense
GAAGCCGGACAAGATGGACGTCCAG 277 345 670 Antisense
AAGGACGGAGTCGACGGAGAGCCAG 297 161 760 Antisense
GACGGACCAAAGGGATCCTGCGATC 257 377 799 Antisense
Sequence Source Affymetrix Proprietary Database