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[189835_at] cuticular collagen

Description C50D2.4 /REP_DB=WormBase Gene ID /WP=CE08889 /TR=O44796 /GB=AAB94952.1 /SUBMIT=ST.LOUIS /CHR=2 /FEA=Sanger Annotation /DEF=cuticular collagen
Cluster 6grp_high1_10_10 > 91      6grp_total > 83      4grp_total > 50      6grp_cgc > 98      6grp_high1_sub > 05      6grp_total_sub > Hat      6grp_rule_based > S5      4grp_rule_based > L2      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 411
1 2 3 4 range
A 86.8
(-1.9)
A 		420.1
(3)
A 		344.2
(1.9)
M 		9.4
(-3)
A 		411
B 114.7
(-2)
A 		371.1
(3)
A 		331.5
(2.2)
A 		61.6
(-3)
A 		310
C 181.8
(-0.7)
A 		399.2
(3)
A 		247.9
(0.4)
P 		48.7
(-3)
A 		351
avr 127.8
(-1.5) 		396.8
(3) 		307.9
(1.5) 		39.9
(-3) 		357

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 405
1 2 3 4 5 6 range
A 192.7
(-3)
A 		315
(-0.2)
P 		299.8
(-0.5)
P 		385.4
(1.4)
P 		454.1
(3)
P 		261.9
(-1.4)
P 		261
B 108.7
(-3)
P 		206.3
(-1.4)
P 		243.8
(-0.8)
A 		310.6
(0.2)
P 		482.5
(3)
P 		215.6
(-1.3)
P 		374
C 206.1
(-2.1)
P 		153.9
(-3)
P 		286.8
(-0.8)
A 		267.3
(-1.1)
P 		513.2
(3)
P 		186.4
(-2.5)
A 		359
avr 169.2
(-3) 		225.1
(-1.9) 		276.8
(-0.9) 		321.1
(-0.1) 		483.3
(3) 		221.3
(-2) 		314
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 113
1 2 3 4 range
A 31.6
(-1)
A 		91.2
(3)
A 		90
(2.9)
M 		1.4
(-3)
A 		90
B 36.6
(-1.2)
A 		91.7
(3)
A 		76.8
(1.9)
A 		13.1
(-3)
A 		79
C 60.2
(-0.1)
A 		114.8
(3)
A 		86.4
(1.4)
P 		8.2
(-3)
A 		107
avr 42.8
(-0.7) 		99.2
(3) 		84.4
(2) 		7.6
(-3) 		92

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 161
1 2 3 4 5 6 range
A 35.5
(-3)
A 		112
(1.5)
P 		65.3
(-1.2)
P 		97.8
(0.7)
P 		137
(3)
P 		63.8
(-1.3)
P 		102
B 37.8
(-3)
P 		68.7
(-1.8)
P 		59.2
(-2.2)
A 		82.3
(-1.3)
P 		196
(3)
P 		80.4
(-1.4)
P 		158
C 76.4
(-1.5)
P 		46.9
(-3)
P 		73
(-1.7)
A 		53.8
(-2.7)
P 		166.1
(3)
P 		62.4
(-2.2)
A 		119
avr 49.9
(-3) 		75.9
(-1.7) 		65.8
(-2.2) 		78
(-1.6) 		166.4
(3) 		68.9
(-2) 		117
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 189835_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.4836
Sequence Type Exemplar sequence
Representative Public ID C50D2.4 NCBI
Target Description C50D2.4 /REP_DB=WormBase Gene ID /WP=CE08889 /TR=O44796 /GB=AAB94952.1 /SUBMIT=ST.LOUIS /CHR=2 /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_061259(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_061259 NCBI Caenorhabditis elegans COLlagen family member (col-68) (col-68) mRNA, complete cds. 11/11 None
SNAP00000026473 ENSEMBL cdna:SNAP chromosome:CEL140:II:104543:105722:1 11/11 None
GENEFINDER00000026484 ENSEMBL cdna:GeneFinder chromosome:CEL140:II:104543:105722:1 11/11 None
C50D2.4 ENSEMBL cdna:known chromosome:CEL140:II:104543:105819:1 gene:C50D2.4 11/11 None
Annotation Notes
Cross Hybridizing mRNA Matched Probes Nature of Assignment Related Probesets by Grade
NM_063181 1/11 Cross Hyb Matching Probes B 
SNAP00000002676 1/11 Cross Hyb Matching Probes None
GENEFINDER00000002691 1/11 Cross Hyb Matching Probes None
ZK1290.3a 1/11 Cross Hyb Matching Probes A B 
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrII:104542-105722(+) 100.0 100.0
Public Domain and Genome References
Gene Title cuticular collagen
Gene Symbol col-68
Ensembl C50D2.4
Entrez Gene 173395 Entrez gene
SwissProt O44796 EMBL-EBI
WormBase CE08889 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_493660 COLlagen family member (col-68) [Caenorhabditis elegans] gb|AAB94952.1| Collagen protein 68 [Caenorhabditis elegans] 2.0E-70
blast CAE62810 Hypothetical protein CBG06986 [Caenorhabditis briggsae] 4.0E-66
blast CAE64818 Hypothetical protein CBG09612 [Caenorhabditis briggsae] gb|AAB41793.1| cuticle collagen [Caenorhabditis briggsae] 1.0E-33
Protein Domains
Database ID Description E-Value
Pfam IPR002486 EMBL-EBI Nematode cuticle collagen, N-terminal 8.3E-14
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 1.8E-4
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 4.1E-12
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 4.0E-5
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_493660.1 1 24-46
C50D2.4 1 24-46
SNAP00000026473 1 24-46
GENEFINDER00000026484 1 24-46
Sequence
Target Sequence 
>C. ELEGANS:189835_AT
ggtggaggagcatgctgctcttgtggagttggcccacctggtccatcaggagctccagga
acagacgggaatcctggaaatgatgggtctccaggaaatcctggaacacccggacaagat
gcagtaggagacgaatccccgactgctgcagatttctgtttcgactgcccaacaggacca
ccgggaccacctggaaagcaaggacctaaaggaccaaatggagaaccaggcgctccagga
actccaggaggaaatgcacttccaggaccaccaggtccccctggacctcaaggtccaccg
ggagccgatggattaccaggtaaccccggggctccaggtgttccaggccaagttatcgaa
gtaccaggtactccagggccagctggtccaccaggtcctccaggcccaatcggcccacca
ggacagccaggagctccaggaagttcccaaccaggaccacaagggccaccaggagaccca
ggaattgatggagctccaggaaatcctggatctccaggagagcctggaccacca

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GGTGGAGGAGCATGCTGCTCTTGTG 286 499 403 Antisense
AATGATGGGTCTCCAGGAAATCCTG 83 165 481 Antisense
GGAACACCCGGACAAGATGCAGTAG 351 527 505 Antisense
TGCAGTAGGAGACGAATCCCCGACT 599 543 522 Antisense
ATCCCCGACTGCTGCAGATTTCTGT 214 39 537 Antisense
TCTGTTTCGACTGCCCAACAGGACC 141 609 557 Antisense
TGGACCTCAAGGTCCACCGGGAGCC 199 537 684 Antisense
CACCGGGAGCCGATGGATTACCAGG 604 199 698 Antisense
GGCCAAGTTATCGAAGTACCAGGTA 518 541 748 Antisense
GCTCCAGGAAGTTCCCAACCAGGAC 201 299 835 Antisense
ATCTCCAGGAGAGCCTGGACCACCA 245 33 912 Antisense
Sequence Source Affymetrix Proprietary Database