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[189812_s_at] cuticular collagen

Description K02D7.3 /REP_DB=WormBase Gene ID /WP=CE17996 /TR=O45105 /GB=AAC02608.1 /SUBMIT=ST.LOUIS /CHR=4 /FEA=Sanger Annotation /DEF=cuticular collagen
Cluster 6grp_total > 93      4grp_total > 61      6grp_cgc > 98      6grp_total_sub > Hat      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 14
1 2 3 4 range
A 10.7
(-2.1)
A 		14.5
(-0.3)
A 		21.8
(3)
A 		8.7
(-3)
A 		13
B 20.5
(3)
A 		11.5
(-1.3)
A 		7.9
(-3)
A 		7.9
(-3)
A 		13
C 14.1
(-0.6)
A 		15.6
(3)
A 		13.1
(-3)
A 		13.6
(-1.8)
A 		3
avr 15.1
(3) 		13.9
(1.6) 		14.3
(2) 		10.1
(-3) 		5

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 457
1 2 3 4 5 6 range
A 31
(-2.9)
A 		26.6
(-3)
A 		172.6
(-0.2)
A 		106.6
(-1.4)
A 		335.6
(3)
A 		52
(-2.5)
A 		309
B 12.1
(-3)
A 		21.1
(-2.8)
A 		77.8
(-1.9)
A 		58
(-2.2)
A 		359.6
(3)
P 		15.7
(-2.9)
A 		348
C 26.3
(-2.8)
A 		16.4
(-2.9)
A 		294
(0.7)
A 		93.2
(-1.9)
A 		467.6
(3)
P 		10.6
(-3)
A 		457
avr 23.1
(-3) 		21.4
(-3) 		181.5
(-0.4) 		85.9
(-1.9) 		387.6
(3) 		26.1
(-2.9) 		366
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 5
1 2 3 4 range
A 3.9
(0.5)
A 		3.2
(-0.4)
A 		5.7
(3)
A 		1.3
(-3)
A 		4
B 6.5
(3)
A 		2.8
(-1.6)
A 		1.8
(-2.9)
A 		1.7
(-3)
A 		5
C 4.7
(3)
A 		4.5
(2.5)
A 		4.6
(2.8)
A 		2.3
(-3)
A 		2
avr 5
(3) 		3.5
(0.2) 		4
(1.1) 		1.8
(-3) 		3

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 148
1 2 3 4 5 6 range
A 5.7
(-3)
A 		9.5
(-2.8)
A 		37.6
(-1)
A 		27
(-1.7)
A 		101.3
(3)
A 		12.7
(-2.6)
A 		96
B 4.2
(-3)
A 		7
(-2.9)
A 		18.9
(-2.4)
A 		15.4
(-2.5)
A 		146.1
(3)
P 		5.8
(-2.9)
A 		142
C 9.8
(-2.7)
A 		5
(-2.9)
A 		74.8
(-0.1)
A 		18.7
(-2.4)
A 		151.3
(3)
P 		3.5
(-3)
A 		148
avr 6.6
(-3) 		7.2
(-3) 		43.8
(-1.2) 		20.4
(-2.3) 		132.9
(3) 		7.3
(-3) 		126
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 189812_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.10916
Sequence Type Exemplar sequence
Representative Public ID K02D7.3 NCBI
Target Description K02D7.3 /REP_DB=WormBase Gene ID /WP=CE17996 /TR=O45105 /GB=AAC02608.1 /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_067504(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_067504 NCBI Caenorhabditis elegans COLlagen family member (col-101) (col-101) mRNA, complete cds. 11/11 None
SNAP00000015232 ENSEMBL cdna:SNAP chromosome:CEL140:IV:325519:326529:-1 11/11 None
GENEFINDER00000015234 ENSEMBL cdna:GeneFinder chromosome:CEL140:IV:325519:326529:-1 11/11 None
K02D7.3 ENSEMBL cdna:known chromosome:CEL140:IV:325437:326529:-1 gene:K02D7.3 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
chrIV:325518-326529(-) 92.49 100.0
Public Domain and Genome References
Gene Title cuticular collagen
Gene Symbol col-101
Ensembl K02D7.3
Entrez Gene 176854 Entrez gene
SwissProt O45105 EMBL-EBI
WormBase CE17996 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 AAC02608 Collagen protein 101 [Caenorhabditis elegans] ref|NP_499905.1| COLlagen family member (col-101) [Caenorhabditis elegans] 1.0E-55
blast CAE74724 Hypothetical protein CBG22542 [Caenorhabditis briggsae] 6.0E-45
blast CAB01509 Hypothetical protein F57B1.3 [Caenorhabditis elegans] ref|NP_506283.1| F57B1.3 [Caenorhabditis elegans] 2.0E-42
Protein Domains
Database ID Description E-Value
Pfam IPR002486 EMBL-EBI Nematode cuticle collagen, N-terminal 2.2E-12
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 4.5E-4
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 1.1E-10
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 4.7E-4
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_499905.1 1 20-42
K02D7.3 1 20-42
SNAP00000015232 1 20-42
GENEFINDER00000015234 1 20-42
Sequence
Target Sequence 
>C. ELEGANS:189812_S_AT
gcttccggaggattctcatcagggggaagtggaggaggatcttgttgctcttgtggagtt
ggaagcgcagggccagccggatctccgggacaagacggagcaccaggaaacgatggagct
ccaggagccccaggaaacccaggacaagatgctcaagacaaccagccagccgggccagac
tcattctgttttgactgcccagctggaccaccaggaccatcgggcgctccaggacaaaag
ggtccatcgggtgctccaggacagccaggccgtagtggaggagcgtctcttccaggacca
ccaggaccagctggaccaccaggaccatccggacagccaggatccaacggaaacgctgga
gccccaggtgctccaggacacgttgttgatgttccaggaactccaggaccagctggacca
ccaggaccagctggaccagccggagctccaggacagccaggtcaagccggacacgctcaa
ccaggacaaccaggaccacaaggagatgctggagctccaggagcgccaggacagccagga
tcagcaggacaaccaggaaacgatggaggggatggaggacaaggagcctgcgatcattgc

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GCTTCCGGAGGATTCTCATCAGGGG 72 307 328 Antisense
AAGTGGAGGAGGATCTTGTTGCTCT 507 159 354 Antisense
GTGGAGTTGGAAGCGCAGGGCCAGC 655 489 380 Antisense
GCCAGCCGGATCTCCGGGACAAGAC 431 277 399 Antisense
AAGATGCTCAAGACAACCAGCCAGC 231 155 473 Antisense
CGGGCCAGACTCATTCTGTTTTGAC 705 243 498 Antisense
TCCAGGACAGCCAGGCCGTAGTGGA 557 279 582 Antisense
GCCAGGCCGTAGTGGAGGAGCGTCT 627 275 591 Antisense
TAGTGGAGGAGCGTCTCTTCCAGGA 1 653 600 Antisense
AGGTGCTCCAGGACACGTTGTTGAT 392 57 693 Antisense
AGGACAAGGAGCCTGCGATCATTGC 691 53 903 Antisense
Sequence Source Affymetrix Proprietary Database