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[192163_at] cuticular collagen

Description ZK1193.1 /REP_DB=WormBase Gene ID /WP=CE05126 /GEN=col-19 /TR=Q23411 /GB=AAA83293.1 /SUBMIT=ST.LOUIS /CHR=X /FEA=Sanger Annotation /DEF=cuticular collagen
Cluster 6grp_total > 93      4grp_total > 50      6grp_cgc > 99      6grp_total_sub > Hat      6grp_rule_based > S5      4grp_rule_based > L2      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 14
1 2 3 4 range
A 8
(-1.5)
A 		17.3
(3)
A 		14.3
(1.6)
A 		4.8
(-3)
A 		13
B 5.6
(-3)
A 		15.3
(2.8)
A 		15.7
(3)
A 		6.5
(-2.5)
A 		10
C 5.9
(-1.7)
A 		14.9
(3)
A 		11.9
(1.4)
A 		3.4
(-3)
A 		12
avr 6.5
(-2.1) 		15.8
(3) 		14
(2) 		4.9
(-3) 		11

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 3858
1 2 3 4 5 6 range
A 5.3
(-3)
A 		12.1
(-3)
A 		20.4
(-3)
A 		35
(-2.9)
A 		2958
(3)
P 		582.3
(-1.8)
A 		2953
B 13.4
(-3)
A 		8.3
(-3)
A 		15.4
(-3)
A 		25.2
(-3)
A 		3646.3
(3)
P 		793.9
(-1.7)
P 		3638
C 5.5
(-3)
A 		13.3
(-3)
A 		18.9
(-3)
A 		58.6
(-2.9)
A 		3862.9
(3)
P 		493.2
(-2.2)
M 		3857
avr 8.1
(-3) 		11.2
(-3) 		18.2
(-3) 		39.6
(-2.9) 		3489.1
(3) 		623.1
(-1.9) 		3481
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 4
1 2 3 4 range
A 2.9
(1.3)
A 		3.8
(3)
A 		3.7
(2.8)
A 		0.7
(-3)
A 		3
B 1.8
(-2)
A 		3.8
(3)
A 		3.6
(2.5)
A 		1.4
(-3)
A 		2
C 2
(-0.7)
A 		4.3
(3)
A 		4.1
(2.7)
A 		0.6
(-3)
A 		4
avr 2.2
(-0.5) 		4
(3) 		3.8
(2.6) 		0.9
(-3) 		3

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 1480
1 2 3 4 5 6 range
A 1
(-3)
A 		4.3
(-3)
A 		4.5
(-3)
A 		8.9
(-2.9)
A 		892.6
(3)
P 		141.8
(-2.1)
A 		892
B 4.7
(-3)
A 		2.8
(-3)
A 		3.8
(-3)
A 		6.7
(-3)
A 		1481.4
(3)
P 		296.1
(-1.8)
P 		1479
C 2.1
(-3)
A 		4.1
(-3)
A 		4.8
(-3)
A 		11.8
(-3)
A 		1250
(3)
P 		165.1
(-2.2)
M 		1248
avr 2.6
(-3) 		3.7
(-3) 		4.4
(-3) 		9.1
(-3) 		1208
(3) 		201
(-2) 		1205
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 192163_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.18473
Sequence Type Exemplar sequence
Representative Public ID ZK1193.1 NCBI
Target Description ZK1193.1 /REP_DB=WormBase Gene ID /WP=CE05126 /GEN=col-19 /TR=Q23411 /GB=AAA83293.1 /SUBMIT=ST.LOUIS /CHR=X /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_001029811(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_001029811 NCBI Caenorhabditis elegans COLlagen family member (col-19) (col-19) mRNA, complete cds. 11/11 None
SNAP00000031652 ENSEMBL cdna:SNAP chromosome:CEL140:X:421724:422646:1 11/11 None
GENEFINDER00000031658 ENSEMBL cdna:GeneFinder chromosome:CEL140:X:421724:422646:1 11/11 None
ZK1193.1a ENSEMBL cdna:known chromosome:CEL140:X:421710:422776:1 gene:ZK1193.1 11/11 None
Annotation Notes
There are no noteworthy cross hybridizing mRNAs found for this probe set.
Splice Variants
Entrez Total Refseq Isoforms Total Detected By This Probeset Refseq Probesets
180397 2 1 NM_001029811 192163_at (11)
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrX:421723-422646(+) 100.0 100.0
Public Domain and Genome References
Gene Title cuticular collagen
Gene Symbol col-19
Ensembl ZK1193.1
Entrez Gene 180397 Entrez gene
SwissProt P18835 EMBL-EBI
WormBase CE05126 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 AAA83293 Collagen protein 19 [Caenorhabditis elegans] ref|NP_001024982.1| COLlagen family member (col-19) [Caenorhabditis elegans] sp|P18835|COL19_CAEEL Cuticle collagen 19 precursor 1.0E-51
blast CAE63664 Hypothetical protein CBG08166 [Caenorhabditis briggsae] 2.0E-46
blast AAA27987 collagen 1.0E-34
Protein Domains
Database ID Description E-Value
Pfam IPR002486 EMBL-EBI Nematode cuticle collagen, N-terminal 5.6E-22
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 1.2E-14
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 8.7E-17
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_001024982.1 1 5-27
ZK1193.1a 1 5-27
SNAP00000031652 1 5-27
GENEFINDER00000031658 1 5-27
Sequence
Target Sequence 
>C. ELEGANS:192163_AT
tcgtcaagctggattcgagcaatgtaactgcggaccaaaatccgagggttgcccagctgg
accaccaggaccaccaggagagggtggacagaagggaaatccaggacacgatggagacga
tggaaagccaggagctcctggagttattgttgccatcacccacgatattccaggaggatg
catcaagtgcccaccaggacgtccaggaccaaaaggaccatcaggacttccaggatctgc
tggaccagccggaggaaacggaagacgcggaccaccaggaccagttggaggaccaggaga
gcaaggaccacagggagatgcaggaagaccaggagccgccggacgtccaggaccagcagg
accacgtggagaaccaggaaccgagtacaagccaggacagccaggacgtccaggaccaca
aggaccacgcggagaaaccggaccagccggaaatccaggagcaccaggaaacgatggaga
ggctggaaagaacggaaacgccggaagaccaggaccaccagggcatccaggaaagaatgg
agttccaggacaaaagggagaggatgccgcaccagg

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
TCGTCAAGCTGGATTCGAGCAATGT 124 605 255 Antisense
TGGATTCGAGCAATGTAACTGCGGA 227 551 264 Antisense
GTAACTGCGGACCAAAATCCGAGGG 241 461 278 Antisense
AAAATCCGAGGGTTGCCCAGCTGGA 416 131 291 Antisense
GACAGAAGGGAAATCCAGGACACGA 500 363 341 Antisense
AGGACACGATGGAGACGATGGAAAG 31 55 357 Antisense
GGAGCTCCTGGAGTTATTGTTGCCA 146 521 385 Antisense
TGGAGTTATTGTTGCCATCACCCAC 565 549 393 Antisense
GACCAGCCGGAGGAAACGGAAGACG 629 383 497 Antisense
GACCACAGGGAGATGCAGGAAGACC 9 385 560 Antisense
AAAAGGGAGAGGATGCCGCACCAGG 233 131 806 Antisense
Sequence Source Affymetrix Proprietary Database