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[189717_at] cuticular collagen

Description T28F2.6 /REP_DB=WormBase Gene ID /WP=CE14361 /TR=O01662 /GB=AAB53052.1 /SUBMIT=ST.LOUIS /CHR=1 /FEA=Sanger Annotation /DEF=cuticular collagen
Cluster 6grp_total > 83      4grp_total > 09      6grp_cgc > 87      6grp_cgc_sub > 05      6grp_total_sub > Hat      6grp_rule_based > S5      4grp_rule_based > L4      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 434
1 2 3 4 range
A 31.5
(-3)
A 		78.8
(-2.2)
A 		56.1
(-2.6)
A 		392.6
(3)
P 		361
B 21.2
(-3)
A 		40.1
(-2.7)
A 		136.5
(-1)
A 		374.8
(3)
P 		354
C 16.2
(-3)
A 		82.6
(-2.1)
A 		43.1
(-2.6)
A 		450.3
(3)
P 		434
avr 23
(-3) 		67.2
(-2.3) 		78.6
(-2.1) 		405.9
(3) 		383

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 7401
1 2 3 4 5 6 range
A 22.7
(-3)
A 		38.4
(-3)
A 		28.6
(-3)
A 		4491.9
(2.2)
P 		5160.3
(3)
P 		907.2
(-2)
P 		5138
B 18
(-3)
A 		20.8
(-3)
A 		130.5
(-2.9)
A 		3307.1
(0.3)
P 		6084.2
(3)
P 		902.1
(-2.1)
P 		6066
C 7.8
(-3)
A 		33.1
(-3)
A 		48.5
(-3)
A 		3000.6
(-0.6)
P 		7409.1
(3)
P 		709.7
(-2.4)
P 		7401
avr 16.2
(-3) 		30.8
(-3) 		69.2
(-2.9) 		3599.9
(0.5) 		6217.9
(3) 		839.7
(-2.2) 		6202
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 75
1 2 3 4 range
A 11.5
(-3)
A 		17.1
(-2.3)
A 		14.7
(-2.6)
A 		57.5
(3)
P 		46
B 6.8
(-3)
A 		9.9
(-2.7)
A 		31.6
(-1)
A 		79.9
(3)
P 		73
C 5.4
(-3)
A 		23.7
(-1.4)
A 		15
(-2.2)
A 		75.9
(3)
P 		71
avr 7.9
(-3) 		16.9
(-2.1) 		20.4
(-1.8) 		71.1
(3) 		63

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 2469
1 2 3 4 5 6 range
A 4.2
(-3)
A 		13.6
(-3)
A 		6.2
(-3)
A 		1139.3
(1.4)
P 		1557.2
(3)
P 		220.9
(-2.2)
P 		1553
B 6.3
(-3)
A 		6.9
(-3)
A 		31.7
(-2.9)
A 		875.9
(-0.9)
P 		2471.9
(3)
P 		336.4
(-2.2)
P 		2466
C 2.9
(-3)
A 		10.1
(-3)
A 		12.3
(-3)
A 		603.4
(-1.5)
P 		2397.5
(3)
P 		237.6
(-2.4)
P 		2395
avr 4.5
(-3) 		10.2
(-3) 		16.7
(-3) 		872.9
(-0.6) 		2142.2
(3) 		265
(-2.3) 		2138
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 189717_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.319
Sequence Type Exemplar sequence
Representative Public ID T28F2.6 NCBI
Target Description T28F2.6 /REP_DB=WormBase Gene ID /WP=CE14361 /TR=O01662 /GB=AAB53052.1 /SUBMIT=ST.LOUIS /CHR=1 /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_058793(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_058793 NCBI Caenorhabditis elegans COLlagen family member (col-50) (col-50) mRNA, complete cds. 11/11 None
SNAP00000038906 ENSEMBL cdna:SNAP chromosome:CEL140:I:3651298:3652601:-1 11/11 None
GENEFINDER00000038915 ENSEMBL cdna:GeneFinder chromosome:CEL140:I:3651298:3652601:-1 11/11 None
T28F2.6 ENSEMBL cdna:known chromosome:CEL140:I:3651298:3652601:-1 gene:T28F2.6 11/11 None
Annotation Notes
Cross Hybridizing mRNA Matched Probes Nature of Assignment Related Probesets by Grade
NM_001028853 1/11 Cross Hyb Matching Probes None
SNAP00000039259 1/11 Cross Hyb Matching Probes None
GENEFINDER00000039267 1/11 Cross Hyb Matching Probes None
K02E11.10 1/11 Cross Hyb Matching Probes None
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrI:3651297-3652601(-) 83.45 100.0
Public Domain and Genome References
Gene Title cuticular collagen
Gene Symbol col-50
Ensembl T28F2.6
Entrez Gene 189050 Entrez gene
SwissProt O01662 EMBL-EBI
WormBase CE14361 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 AAB53052 Collagen protein 50 [Caenorhabditis elegans] ref|NP_491194.1| COLlagen family member (col-50) [Caenorhabditis elegans] 3.0E-41
blast CAE66648 Hypothetical protein CBG11985 [Caenorhabditis briggsae] 3.0E-34
blast AAP68908 Collagen protein 51 [Caenorhabditis elegans] ref|NP_491195.1| COLlagen family member (col-51) [Caenorhabditis elegans] pir||T15143 hypothetical protein T28F2.8 - Caenorhabditis elegans 9.0E-23
Protein Domains
Database ID Description E-Value
Pfam IPR002486 EMBL-EBI Nematode cuticle collagen, N-terminal 3.7E-19
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 1.9E-4
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 0.0017
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 2.3E-4
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_491194.1 1 7-29
T28F2.6 1 7-29
SNAP00000038906 1 7-29
GENEFINDER00000038915 1 7-29
Sequence
Target Sequence 
>C. ELEGANS:189717_AT
gacagccaggagccggtggaactaccagcaccaaccaacctggacctccaggaccagcag
gaccacctgggccagccggaccagcaggagaggacgcgtatgctcaaccatcaccagccg
gaacaccaggaccaccaggaccaccaggaaaagatggagaagctggaccagacggaccag
ctggagcaccaggaaccgatggagctccaggaccagatgctgcctattgtccatgcccac
caagaaccttgggagccggagcttatcctgaaggaggagatgcagctgcagcagcccctg
ctggaggatacgatggaggtgccggtgctgcccctgaagcagctccagccgctgctgccg
cccctcaaccggctccagctccagccgctgctgctgccccagccggaggttaccaaggag
gagctgctgccggtgcagccgcaccaccacctgctccagccgctgctgccgcccctgaac
cggctccagctccagcagccgccccaccaccagctccagccgctggtggctccccaaccg
gaggataccgccgcaagaaggt

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GACAGCCAGGAGCCGGTGGAACTAC 115 369 677 Antisense
AGGAGCCGGTGGAACTACCAGCACC 667 55 684 Antisense
AGGAGAGGACGCGTATGCTCAACCA 112 57 762 Antisense
TGCCCACCAAGAACCTTGGGAGCCG 630 581 910 Antisense
AGAACCTTGGGAGCCGGAGCTTATC 696 57 919 Antisense
GAGCCGGAGCTTATCCTGAAGGAGG 427 385 929 Antisense
AGGAGATGCAGCTGCAGCAGCCCCT 72 55 951 Antisense
GCTGGAGGATACGATGGAGGTGCCG 558 293 976 Antisense
CCAGCCGGAGGTTACCAAGGAGGAG 295 271 1075 Antisense
CAAGGAGGAGCTGCTGCCGGTGCAG 28 185 1090 Antisense
CCGGAGGATACCGCCGCAAGAAGGT 248 263 1214 Antisense
Sequence Source Affymetrix Proprietary Database