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[189713_at] cuticular collagen

Description T28F2.8 /REP_DB=WormBase Gene ID /WP=CE14365 /TR=O01663 /GB=AAB53059.1 /SUBMIT=ST.LOUIS /CHR=1 /FEA=Sanger Annotation /DEF=cuticular collagen
Cluster 6grp_total > 93      4grp_total > 42      6grp_cgc > 88      6grp_total_sub > Hat      6grp_rule_based > S5      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 164
1 2 3 4 range
A 56.2
(-2.1)
A 		179.3
(3)
A 		131.4
(1)
A 		34.6
(-3)
A 		145
B 20.7
(-3)
A 		69.5
(0.5)
A 		30
(-2.3)
A 		104
(3)
A 		83
C 16.7
(-2.6)
A 		28
(0.7)
A 		15.4
(-3)
A 		35.9
(3)
A 		21
avr 31.2
(-3) 		92.3
(3) 		58.9
(-0.3) 		58.2
(-0.3) 		61

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 4665
1 2 3 4 5 6 range
A 54
(-2.9)
A 		28.8
(-3)
A 		13.6
(-3)
A 		1779.7
(0.8)
P 		2785.3
(3)
P 		423.9
(-2.1)
P 		2772
B 38.6
(-3)
A 		61.2
(-2.9)
A 		22
(-3)
A 		1092.2
(-1.3)
P 		3717
(3)
P 		371.1
(-2.4)
P 		3695
C 75.5
(-3)
A 		68.2
(-3)
A 		132
(-2.9)
A 		1166.6
(-1.6)
P 		4678.2
(3)
P 		334.5
(-2.7)
P 		4610
avr 56
(-3) 		52.7
(-3) 		55.9
(-3) 		1346.2
(-0.9) 		3726.8
(3) 		376.5
(-2.5) 		3674
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 34
1 2 3 4 range
A 20.5
(-0.3)
A 		38.9
(3)
A 		34.4
(2.2)
A 		5.1
(-3)
A 		34
B 6.6
(-3)
A 		17.2
(1.1)
A 		7
(-2.8)
A 		22.2
(3)
A 		16
C 5.5
(-2.8)
A 		8.1
(3)
A 		5.4
(-3)
A 		6
(-1.7)
A 		3
avr 10.9
(-3) 		21.4
(3) 		15.6
(-0.3) 		11.1
(-2.9) 		11

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 1511
1 2 3 4 5 6 range
A 10
(-2.9)
A 		10.2
(-2.9)
A 		3
(-3)
A 		451.4
(0.2)
P 		840.5
(3)
P 		103.2
(-2.3)
P 		838
B 13.4
(-3)
A 		20.4
(-2.9)
A 		5.3
(-3)
A 		289.3
(-1.9)
P 		1510.2
(3)
P 		138.4
(-2.5)
P 		1505
C 28
(-3)
A 		20.8
(-3)
A 		33.6
(-2.9)
A 		234.6
(-2.1)
P 		1513.8
(3)
P 		112
(-2.6)
P 		1493
avr 17.1
(-3) 		17.1
(-3) 		14
(-3) 		325.1
(-1.5) 		1288.2
(3) 		117.9
(-2.5) 		1274
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 189713_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.136
Sequence Type Exemplar sequence
Representative Public ID T28F2.8 NCBI
Target Description T28F2.8 /REP_DB=WormBase Gene ID /WP=CE14365 /TR=O01663 /GB=AAB53059.1 /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_058794(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_058794 NCBI Caenorhabditis elegans COLlagen family member (col-51) (col-51) mRNA, complete cds. 11/11 None
SNAP00000038907 ENSEMBL cdna:SNAP chromosome:CEL140:I:3653999:3655267:1 11/11 None
GENEFINDER00000038912 ENSEMBL cdna:GeneFinder chromosome:CEL140:I:3653999:3655267:1 11/11 None
T28F2.8 ENSEMBL cdna:known chromosome:CEL140:I:3653960:3655267:1 gene:T28F2.8 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
chrI:3653959-3655267(+) 67.13 100.0
Public Domain and Genome References
Gene Title cuticular collagen
Gene Symbol col-51
Ensembl T28F2.8
Entrez Gene 189052 Entrez gene
SwissProt Q7Z152 EMBL-EBI
WormBase CE14365 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 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 7.0E-40
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 7.0E-32
blast CAE66647 Hypothetical protein CBG11984 [Caenorhabditis briggsae] 1.0E-26
blast AAB53052 Collagen protein 50 [Caenorhabditis elegans] ref|NP_491194.1| COLlagen family member (col-50) [Caenorhabditis elegans] 2.0E-18
Protein Domains
Database ID Description E-Value
Pfam IPR002486 EMBL-EBI Nematode cuticle collagen, N-terminal 3.4E-15
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 0.0012
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 2.3E-9
Pfam IPR002486 EMBL-EBI Nematode cuticle collagen, N-terminal 3.4E-15
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 0.0012
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 2.3E-9
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_491195.1 1 20-42
T28F2.8 1 20-42
SNAP00000038907 1 7-29
GENEFINDER00000038912 1 7-29
Sequence
Target Sequence 
>C. ELEGANS:189713_AT
gagcaccaggacaggatggtcaaccaggagcaccaggaaccaatacagtcaactcaccag
gaggaccaggtccagctggaccaccgggaccaccaggaccaccaggacaagatggatccg
gcggagctgctcaaccaggacctccaggaccaccaggaccaccaggaaacgatggacaac
caggaggtccaggacaaccaggaggaccaggacaagacggaggaccaggaaccgatgctg
cctattgcccatgcccaccacgtactccagcaggaggaggtggaggtggtgacttcccag
ccggaggtggaggtggaggttattctacaggaggtggaggaggaagagcagattctggag
gagctgctggaggagccggaggagccggagggtactctggaggcggcggaggcggaggtg
gaggcgccgcagctggcggaggatacaatgccggaggcggaggcggaggagctccacaag
ctgctccagctccacaagcagctccagctcctgcagcccctgctggaggtggatacaacg
ccggaggtggtggagg

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GAGCACCAGGACAGGATGGTCAACC 656 389 698 Antisense
GCACCAGGAACCAATACAGTCAACT 188 315 727 Antisense
ACAGTCAACTCACCAGGAGGACCAG 256 107 742 Antisense
AAGATGGATCCGGCGGAGCTGCTCA 271 155 806 Antisense
CACCACGTACTCCAGCAGGAGGAGG 276 201 953 Antisense
GTGGAGGTGGAGGTTATTCTACAGG 275 491 1004 Antisense
GCCGGAGGAGCCGGAGGGTACTCTG 461 263 1072 Antisense
GCCGGAGGGTACTCTGGAGGCGGCG 521 257 1081 Antisense
GGATACAATGCCGGAGGCGGAGGCG 636 509 1138 Antisense
GCTGGAGGTGGATACAACGCCGGAG 153 291 1219 Antisense
GATACAACGCCGGAGGTGGTGGAGG 553 423 1229 Antisense
Sequence Source Affymetrix Proprietary Database