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[192029_at] cuticular collagen

Description F36A4.6 /REP_DB=WormBase Gene ID /WP=CE07182 /GEN=col-33 /TR=Q20091 /GB=AAA96159.1 /SUBMIT=ST.LOUIS /CHR=4 /FEA=Sanger Annotation /DEF=cuticular collagen
Cluster 6grp_total > 83      4grp_total > 42      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.
4 105
1 2 3 4 range
A 8.4
(-3)
A 		102.4
(2.6)
A 		109.3
(3)
A 		54.5
(-0.3)
A 		101
B 5.4
(-3)
A 		105.7
(3)
A 		11
(-2.7)
A 		5.2
(-3)
A 		101
C 4.8
(-3)
A 		99.8
(3)
A 		72.8
(1.3)
A 		19.4
(-2.1)
A 		95
avr 6.2
(-3) 		102.6
(3) 		64.4
(0.6) 		26.4
(-1.7) 		96

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 2737
1 2 3 4 5 6 range
A 13.7
(-3)
A 		40.5
(-2.9)
A 		13.6
(-3)
A 		1600.3
(3)
P 		1441.9
(2.4)
P 		463.6
(-1.3)
P 		1587
B 7.8
(-3)
A 		65.1
(-2.8)
A 		7
(-3)
A 		1095.6
(0.5)
P 		1848.2
(3)
P 		354.7
(-1.9)
P 		1841
C 6.1
(-3)
A 		42.9
(-2.9)
A 		38.1
(-2.9)
A 		910.7
(-1)
P 		2742.8
(3)
P 		303.7
(-2.3)
P 		2737
avr 9.2
(-3) 		49.5
(-2.9) 		19.6
(-3) 		1202.2
(0.6) 		2011
(3) 		374
(-1.9) 		2002
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 28
1 2 3 4 range
A 3.1
(-3)
A 		22.2
(1.5)
A 		28.6
(3)
A 		8
(-1.8)
A 		26
B 1.7
(-2.9)
A 		26.1
(3)
A 		2.5
(-2.7)
A 		1.1
(-3)
A 		25
C 1.6
(-3)
A 		28.7
(3)
A 		25.4
(2.3)
A 		3.3
(-2.6)
A 		27
avr 2.1
(-3) 		25.7
(3) 		18.8
(1.2) 		4.1
(-2.5) 		24

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 886
1 2 3 4 5 6 range
A 2.5
(-3)
A 		14.4
(-2.8)
A 		3
(-3)
A 		405.9
(2.6)
P 		435.1
(3)
P 		112.9
(-1.5)
P 		433
B 2.7
(-3)
A 		21.7
(-2.8)
A 		1.7
(-3)
A 		290.2
(-0.7)
P 		750.9
(3)
P 		132.3
(-2)
P 		749
C 2.3
(-3)
A 		13.1
(-2.9)
A 		9.7
(-2.9)
A 		183.1
(-1.8)
P 		887.5
(3)
P 		101.7
(-2.3)
P 		885
avr 2.5
(-3) 		16.4
(-2.9) 		4.8
(-3) 		293.1
(-0.5) 		691.2
(3) 		115.6
(-2) 		689
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 192029_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.10969
Sequence Type Exemplar sequence
Representative Public ID F36A4.6 NCBI
Target Description F36A4.6 /REP_DB=WormBase Gene ID /WP=CE07182 /GEN=col-33 /TR=Q20091 /GB=AAA96159.1 /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_068123(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_068123 NCBI Caenorhabditis elegans COLlagen family member (col-33) (col-33) mRNA, complete cds. 11/11 None
SNAP00000033263 ENSEMBL cdna:SNAP chromosome:CEL140:IV:4263334:4265168:1 11/11 None
GENEFINDER00000033284 ENSEMBL cdna:GeneFinder chromosome:CEL140:IV:4263912:4265168:1 11/11 None
F36A4.6 ENSEMBL cdna:known chromosome:CEL140:IV:4263334:4265168:1 gene:F36A4.6 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:4263916-4265174(+) 97.27 97.27
Public Domain and Genome References
Gene Title cuticular collagen
Gene Symbol col-33
Ensembl F36A4.6
Entrez Gene 177191 Entrez gene
SwissProt Q20091 EMBL-EBI
WormBase CE34548 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 AAA96159 Collagen protein 33 [Caenorhabditis elegans] ref|NP_500524.2| COLlagen family member (col-33) [Caenorhabditis elegans] 4.0E-39
blast AAA96159 Collagen protein 33 [Caenorhabditis elegans] ref|NP_500524.2| COLlagen family member (col-33) [Caenorhabditis elegans] 5.0E-34
blast CAE61462 Hypothetical protein CBG05354 [Caenorhabditis briggsae] 8.0E-23
blast AAA27985 alpha-collagen 8.0E-23
Protein Domains
Database ID Description E-Value
Pfam IPR002486 EMBL-EBI Nematode cuticle collagen, N-terminal 2.4E-11
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 1.6E-10
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 7.1E-12
Pfam IPR002486 EMBL-EBI Nematode cuticle collagen, N-terminal 2.4E-11
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 1.6E-10
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 7.1E-12
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_500524.2 1 20-42
F36A4.6 1 20-42
SNAP00000033263 1 20-42
GENEFINDER00000033284 1 7-29
Sequence
Target Sequence 
>C. ELEGANS:192029_AT
aggcggaaactgtgaggcctgctgccttccaggacccgctggacccgccggtgccccagg
aaaccctgggagaccgggtaaacctggagctccaggacttccaggaaaccctggaaagcc
accagttcagccttgtgagccaattactccaccaccatgcaaaccatgtccagatggacc
cgcgggaccaccaggaccacctggagcacctggagatgctggaacaaacggagctccggg
agcgcctggaggtgatgctccacccggtgaggcaggaccgaaaggaccaccaggaccacc
aggatcccccggagcacccggagagccaggaagacctggagacgacgcaccaagtgagcc
actcatcccaggggagccaggaccacaaggaccaccgggaccacctggacaagccggacc
agacggacaacctggagcacccggaggacccggaactcctggatcaaaag

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
AGGCGGAAACTGTGAGGCCTGCTGC 406 53 342 Antisense
GAGACCGGGTAAACCTGGAGCTCCA 82 393 411 Antisense
GAAACCCTGGAAAGCCACCAGTTCA 46 357 446 Antisense
CACCAGTTCAGCCTTGTGAGCCAAT 340 201 461 Antisense
AAACCATGTCCAGATGGACCCGCGG 7 127 502 Antisense
CAAACGGAGCTCCGGGAGCGCCTGG 644 191 566 Antisense
GGAGCGCCTGGAGGTGATGCTCCAC 536 521 580 Antisense
TGAGGCAGGACCGAAAGGACCACCA 618 567 609 Antisense
CAGGAAGACCTGGAGACGACGCACC 654 207 668 Antisense
TGGAGACGACGCACCAAGTGAGCCA 222 547 678 Antisense
GGACCCGGAACTCCTGGATCAAAAG 487 519 787 Antisense
Sequence Source Affymetrix Proprietary Database