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[172801_x_at] cuticualr collagen

Description ZC513.8 /REP_DB=WormBase Gene ID /WP=CE07615 /TR=Q23364 /GB=AAC48270.1 /SUBMIT=ST.LOUIS /CHR=5 /FEA=Sanger Annotation /DEF=cuticualr collagen
Cluster 6grp_highest_10_10 > 29      6grp_high1_10_10 > 81      4grp_highest_8_8 > 09      4grp_high_8_8 > 53      6grp_highest_nonorm > 09      6grp_total > 81      4grp_total > 58      6grp_highest_sub > 04_05      6grp_cgc > 86      6grp_high1_sub > 04      6grp_cgc_sub > 04      6grp_total_sub > Hat      6grp_rule_based > S4      4grp_rule_based > L3      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 27225
1 2 3 4 range
A 11786.2
(-0.7)
P 		28306
(3)
P 		27949.7
(2.9)
P 		1464.3
(-3)
P 		26842
B 12952.9
(-0.4)
P 		23250.9
(1.8)
P 		28484.1
(3)
P 		1258.8
(-3)
P 		27225
C 9373.5
(-0.7)
P 		22508.6
(3)
P 		21924.6
(2.8)
P 		1309
(-3)
P 		21200
avr 11370.9
(-0.6) 		24688.5
(2.7) 		26119.5
(3) 		1344
(-3) 		24776

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 27831
1 2 3 4 5 6 range
A 10324.8
(-3)
P 		22130
(-0.5)
P 		22385.3
(-0.4)
P 		38156.2
(3)
P 		32838.1
(1.9)
P 		20719.7
(-0.8)
P 		27831
B 14399.4
(-3)
P 		21462
(-0.8)
P 		30022.6
(1.9)
P 		33437
(3)
P 		27949.5
(1.3)
P 		16637.4
(-2.3)
P 		19038
C 15551.7
(-2.7)
P 		19057.8
(-1.7)
P 		19562.8
(-1.6)
P 		36894.7
(3)
P 		35865.3
(2.7)
P 		14296.2
(-3)
P 		22599
avr 13425.3
(-3) 		20883.3
(-1) 		23990.2
(-0.2) 		36162.6
(3) 		32217.6
(2) 		17217.8
(-2) 		22737
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 7427
1 2 3 4 range
A 4291.4
(0.4)
P 		6144.5
(2)
P 		7306.6
(3)
P 		214.3
(-3)
P 		7092
B 4130.6
(0.7)
P 		5742.4
(2.2)
P 		6600.4
(3)
P 		268.3
(-3)
P 		6332
C 3102.9
(-0.7)
P 		6471.4
(2.1)
P 		7641.4
(3)
P 		220.7
(-3)
P 		7421
avr 3841.6
(0.1) 		6119.4
(2.1) 		7182.8
(3) 		234.4
(-3) 		6948

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 9702
1 2 3 4 5 6 range
A 1903.3
(-3)
P 		7870.5
(1.5)
P 		4875
(-0.8)
P 		9677.3
(2.8)
P 		9909.1
(3)
P 		5044.6
(-0.6)
P 		8006
B 5010.3
(-3)
P 		7143.8
(-1)
P 		7290.4
(-0.8)
P 		8856.3
(0.6)
P 		11355.5
(3)
P 		6204
(-1.9)
P 		6345
C 5764.3
(-2.1)
P 		5815.1
(-2.1)
P 		4979.1
(-2.8)
P 		7419.5
(-0.7)
P 		11605.5
(3)
P 		4785.8
(-3)
P 		6820
avr 4226
(-3) 		6943.1
(-0.6) 		5714.8
(-1.7) 		8651
(0.9) 		10956.7
(3) 		5344.8
(-2) 		6731
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 172801_x_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.12466
Sequence Type Exemplar sequence
Representative Public ID ZC513.8 NCBI
Target Description ZC513.8 /REP_DB=WormBase Gene ID /WP=CE07615 /TR=Q23364 /GB=AAC48270.1 /SUBMIT=ST.LOUIS /CHR=5 /FEA=Sanger Annotation /DEF=cuticualr 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_072673(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_072673 NCBI Caenorhabditis elegans COLlagen family member (col-43) (col-43) mRNA, complete cds. 11/11 None
SNAP00000025313 ENSEMBL cdna:SNAP chromosome:CEL140:V:8052416:8053455:-1 11/11 None
GENEFINDER00000025319 ENSEMBL cdna:GeneFinder chromosome:CEL140:V:8052416:8053455:-1 11/11 None
ZC513.8 ENSEMBL cdna:known chromosome:CEL140:V:8052337:8053484:-1 gene:ZC513.8 11/11 None
Annotation Notes
Cross Hybridizing mRNA Matched Probes Nature of Assignment Related Probesets by Grade
NM_059685 1/11 Cross Hyb Matching Probes A 
NM_069160 1/11 Cross Hyb Matching Probes A 
NM_069706 1/11 Cross Hyb Matching Probes A 
NM_063086 1/11 Cross Hyb Matching Probes A 
NM_064134 1/11 Cross Hyb Matching Probes A 
NM_063181 1/11 Cross Hyb Matching Probes B 
SNAP00000007964 1/11 Cross Hyb Matching Probes None
GENEFINDER00000007975 1/11 Cross Hyb Matching Probes None
SNAP00000002676 1/11 Cross Hyb Matching Probes None
GENEFINDER00000002691 1/11 Cross Hyb Matching Probes None
SNAP00000006114 1/11 Cross Hyb Matching Probes None
GENEFINDER00000006126 1/11 Cross Hyb Matching Probes None
SNAP00000036845 1/11 Cross Hyb Matching Probes None
GENEFINDER00000036849 1/11 Cross Hyb Matching Probes None
SNAP00000003708 1/11 Cross Hyb Matching Probes None
GENEFINDER00000003712 1/11 Cross Hyb Matching Probes None
SNAP00000005654 1/11 Cross Hyb Matching Probes None
SNAP00000005655 1/11 Cross Hyb Matching Probes None
GENEFINDER00000005663 1/11 Cross Hyb Matching Probes None
GENEFINDER00000005664 1/11 Cross Hyb Matching Probes None
SNAP00000037122 1/11 Cross Hyb Matching Probes None
GENEFINDER00000037126 1/11 Cross Hyb Matching Probes None
C15A11.1 1/11 Cross Hyb Matching Probes A 
C27H5.5 1/11 Cross Hyb Matching Probes A 
ZK1290.3a 1/11 Cross Hyb Matching Probes A B 
K12D12.3 1/11 Cross Hyb Matching Probes A 
C53B4.5 1/11 Cross Hyb Matching Probes A 
C29F4.1.2 1/11 Cross Hyb Matching Probes None
C29F4.1.1 1/11 Cross Hyb Matching Probes None
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrV:8052416-8053456(-) 92.54 100.0
Public Domain and Genome References
Gene Title cuticualr collagen
Gene Symbol col-43
Ensembl ZC513.8
Entrez Gene 179187 Entrez gene
SwissProt Q23364 EMBL-EBI
WormBase CE07615 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 AAC48270 Collagen protein 43 [Caenorhabditis elegans] ref|NP_505074.1| COLlagen family member (col-43) [Caenorhabditis elegans] dbj|BAB69889.1| collagen [Caenorhabditis elegans] 8.0E-55
blast CAE66150 Hypothetical protein CBG11380 [Caenorhabditis briggsae] 8.0E-55
blast CAE75463 Hypothetical protein CBG23461 [Caenorhabditis briggsae] 1.0E-40
Protein Domains
Database ID Description E-Value
Pfam IPR002486 EMBL-EBI Nematode cuticle collagen, N-terminal 1.3E-9
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 4.8E-10
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 6.1E-13
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_505074.1 1 13-35
ZC513.8 1 13-35
SNAP00000025313 1 13-35
GENEFINDER00000025319 1 13-35
Sequence
Target Sequence 
>C. ELEGANS:172801_X_AT
aatgcgagggatgctgtcttccaggaccaccaggaccagccggagtcccaggaaagccag
gaaagccagggcgtccaggagcaccaggacaaccaggagtcccaggaaaaccaccaactg
ctccatgtgagccaactactccaccaccatgcaagccatgcccacaaggaccacccggac
caccaggacccccaggagccccaggagacccaggagaggctggaaccccaggacgcccag
gaaccgacgccaccccaggacttccaggaccacgtggaccaccaggaccaccaggagagg
ccggacaaccaggaccacaaggagatgctggaactccagctcaatccgaaccacttaccc
caggagcaccaggagaggcaggagatgctggaccagccggaccaccaggaccaccaggag
ctccaggaaacgacggaccaccaggaccaccaggaccaaagggatctccaggaccagacg
gaccagcaggagtcgatggacaagctggaccaccaggaccaccaggacaagccggaactc
caggagagaagggaatctgtccaaagtactgcgctc

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
AATGCGAGGGATGCTGTCTTCCAGG 53 167 308 Antisense
GCCAGGAAAGCCAGGGCGTCCAGGA 252 277 363 Antisense
AACCACCAACTGCTCCATGTGAGCC 264 143 416 Antisense
GCTGGAACTCCAGCTCAATCCGAAC 315 295 634 Antisense
TACCCCAGGAGCACCAGGAGAGGCA 652 645 663 Antisense
GGAGATGCTGGACCAGCCGGACCAC 240 519 688 Antisense
GGAGCTCCAGGAAACGACGGACCAC 319 521 724 Antisense
GGACCACCAGGACCAAAGGGATCTC 559 521 751 Antisense
GGACCAGACGGACCAGCAGGAGTCG 453 523 778 Antisense
GTCGATGGACAAGCTGGACCACCAG 178 473 799 Antisense
GGAATCTGTCCAAAGTACTGCGCTC 65 531 859 Antisense
Sequence Source Affymetrix Proprietary Database