[Home] | [Total List]

[189463_at] cuticle collagen

Description K12D12.3 /REP_DB=WormBase Gene ID /WP=CE02272 /TR=Q21437 /GB=CAA88865.1 /SUBMIT=HINXTON /CHR=2 /FEA=Sanger Annotation /DEF=cuticle collagen
Cluster 6grp_total > 83      4grp_total > 50      6grp_cgc > 87      6grp_cgc_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.
4 395
1 2 3 4 range
A 159.9
(1.4)
A 		203.2
(3)
A 		183.9
(2.3)
P 		41.7
(-3)
A 		162
B 155
(-1)
A 		373.4
(3)
A 		364.1
(2.8)
A 		45.2
(-3)
A 		328
C 140.7
(-1.8)
A 		436.4
(3)
A 		282.2
(0.5)
A 		66.9
(-3)
A 		370
avr 151.9
(-0.9) 		337.7
(3) 		276.7
(1.7) 		51.3
(-3) 		286

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 18593
1 2 3 4 5 6 range
A 54.9
(-3)
A 		221
(-2.9)
A 		450.9
(-2.8)
P 		14448.3
(3)
P 		14146.2
(2.9)
P 		3183.7
(-1.7)
P 		14393
B 149.5
(-3)
A 		149.6
(-3)
A 		415.3
(-2.9)
P 		12647.8
(2)
P 		15191.3
(3)
P 		2961.6
(-1.9)
P 		15042
C 143.9
(-3)
A 		105
(-3)
A 		624.6
(-2.8)
P 		12079.8
(0.9)
P 		18648.2
(3)
P 		2183.9
(-2.3)
P 		18543
avr 116.1
(-3) 		158.5
(-3) 		496.9
(-2.9) 		13058.6
(1.9) 		15995.2
(3) 		2776.4
(-2) 		15879
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 119
1 2 3 4 range
A 58.2
(3)
A 		44.1
(1.4)
A 		48.1
(1.8)
P 		6.1
(-3)
A 		52
B 49.4
(-0.1)
A 		92.2
(3)
A 		84.4
(2.4)
A 		9.6
(-3)
A 		83
C 46.6
(-1.1)
A 		125.5
(3)
A 		98.3
(1.6)
A 		11.3
(-3)
A 		114
avr 51.4
(0.2) 		87.3
(3) 		76.9
(2.2) 		9
(-3) 		78

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 6162
1 2 3 4 5 6 range
A 10.1
(-3)
A 		78.6
(-2.9)
A 		98.2
(-2.9)
P 		3664.4
(2.1)
P 		4268.7
(3)
P 		775.1
(-1.9)
P 		4259
B 52
(-3)
A 		49.8
(-3)
A 		100.8
(-3)
P 		3350
(0.2)
P 		6172
(3)
P 		1104.4
(-2)
P 		6122
C 53.3
(-3)
A 		32
(-3)
A 		159
(-2.9)
P 		2429.3
(-0.6)
P 		6034.3
(3)
P 		731.1
(-2.3)
P 		6002
avr 38.5
(-3) 		53.5
(-3) 		119.3
(-2.9) 		3147.9
(0.4) 		5491.7
(3) 		870.2
(-2.1) 		5453
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 189463_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.3164
Sequence Type Exemplar sequence
Representative Public ID K12D12.3 NCBI
Target Description K12D12.3 /REP_DB=WormBase Gene ID /WP=CE02272 /TR=Q21437 /GB=CAA88865.1 /SUBMIT=HINXTON /CHR=2 /FEA=Sanger Annotation /DEF=cuticle 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_064134(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_064134 NCBI Caenorhabditis elegans COLlagen family member (col-84) (col-84) mRNA, complete cds. 11/11 None
SNAP00000036845 ENSEMBL cdna:SNAP chromosome:CEL140:II:11868449:11871405:1 11/11 None
GENEFINDER00000036849 ENSEMBL cdna:GeneFinder chromosome:CEL140:II:11868449:11869547:1 11/11 None
K12D12.3 ENSEMBL cdna:known chromosome:CEL140:II:11868449:11869592:1 gene:K12D12.3 11/11 None
Annotation Notes
Cross Hybridizing mRNA Matched Probes Nature of Assignment Related Probesets by Grade
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrII:11868445-11869544(+) 100.0 100.0
Public Domain and Genome References
Gene Title cuticle collagen
Gene Symbol col-84
Ensembl K12D12.3
Entrez Gene 174824 Entrez gene
SwissProt Q21437 EMBL-EBI
WormBase CE02272 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 CAA88865 Hypothetical protein K12D12.3 [Caenorhabditis elegans] ref|NP_496535.1| COLlagen family member (col-84) [Caenorhabditis elegans] 6.0E-83
blast CAE59388 Hypothetical protein CBG02745 [Caenorhabditis briggsae] 1.0E-67
blast CAE59983 Hypothetical protein CBG03475 [Caenorhabditis briggsae] 9.0E-33
Protein Domains
Database ID Description E-Value
Pfam IPR002486 EMBL-EBI Nematode cuticle collagen, N-terminal 1.3E-21
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 8.5E-12
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 3.1E-8
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_496535.1 1 7-29
K12D12.3 1 7-29
SNAP00000036845 1 7-29
GENEFINDER00000036849 1 7-29
Sequence
Target Sequence 
>C. ELEGANS:189463_AT
tccaggatctccgggaccaaacggagtgccaggagtcgacggaaagccaggacacgattc
tttggacgtcaccccagaaccacaagacactggactctgctactattgcccaggtggacc
accaggagctccagggccaaacggaagaccaggacttcgtggaatgaagggagccgatgg
aggactcggtcgcaccggacacgatggaaatccaggacatccaggagagatgggagctcc
aggaccacaaggaaagcaaggaccagatggtcgccaaggagagaagggagccgacggacg
caagccaatcggacgtccaggaccaaagggacaacgtggaccacaaggagaacaaggacc
agtcggagacaacggaagaaacggaccagttggaggagctggaccagctggaccacaagg
aggatccggaggaccaggagagaagggactcgatggaggaccaggatccgaaggaaaggt
cggaagaccaggaaaggatgccgaatactgcccatgcccagctcgtgaatcccacggtgg
aa

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
TCCAGGATCTCCGGGACCAAACGGA 481 589 420 Antisense
CAAACGGAGTGCCAGGAGTCGACGG 645 191 437 Antisense
AGCCAGGACACGATTCTTTGGACGT 28 85 464 Antisense
CCACAAGACACTGGACTCTGCTACT 538 275 499 Antisense
CTGGACTCTGCTACTATTGCCCAGG 417 241 509 Antisense
ACGGAAGACCAGGACTTCGTGGAAT 375 95 560 Antisense
GGAGCCGATGGAGGACTCGGTCGCA 481 521 589 Antisense
CGGTCGCACCGGACACGATGGAAAT 134 245 606 Antisense
GCCGACGGACGCAAGCCAATCGGAC 76 283 709 Antisense
GGGACTCGATGGAGGACCAGGATCC 9 495 864 Antisense
CCAGCTCGTGAATCCCACGGTGGAA 216 271 937 Antisense
Sequence Source Affymetrix Proprietary Database