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[188615_s_at] collagen

Description W09G10.1 /REP_DB=WormBase Gene ID /WP=CE28512 /TR=O16640 /GB=AAB66109.1 /SUBMIT=ST.LOUIS /CHR=2 /FEA=Sanger Annotation /DEF=collagen
Cluster 6grp_total > 93      4grp_total > 40      6grp_cgc > 87      6grp_cgc_sub > 05      6grp_total_sub > Hat      6grp_rule_based > S5      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 74
1 2 3 4 range
A 65.1
(-3)
A 		101
(0.6)
A 		125
(3)
A 		124
(2.9)
A 		60
B 69.6
(-0.6)
A 		88.5
(3)
A 		61.6
(-2.1)
A 		56.9
(-3)
A 		32
C 73.8
(-0)
A 		51
(-3)
A 		96.7
(3)
A 		67.8
(-0.8)
A 		46
avr 69.5
(-3) 		80.2
(-0.4) 		94.4
(3) 		82.9
(0.2) 		25

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 5267
1 2 3 4 5 6 range
A 26.7
(-3)
A 		81.6
(-2.9)
A 		58
(-3)
A 		2860.4
(1.5)
P 		3798.8
(3)
P 		407.9
(-2.4)
P 		3772
B 26.4
(-3)
A 		52.6
(-3)
A 		72.7
(-2.9)
P 		2658.7
(0.7)
P 		4272.8
(3)
P 		555.5
(-2.3)
P 		4246
C 94.3
(-3)
M 		101.3
(-3)
A 		75.9
(-3)
A 		2636.1
(-0.1)
P 		5293.1
(3)
P 		347.8
(-2.7)
P 		5217
avr 49.1
(-3) 		78.5
(-3) 		68.9
(-3) 		2718.4
(0.6) 		4454.9
(3) 		437.1
(-2.5) 		4406
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 22
1 2 3 4 range
A 23.7
(-0.7)
A 		21.9
(-1.4)
A 		32.7
(3)
A 		18.1
(-3)
A 		15
B 22.2
(3)
A 		21.9
(2.8)
A 		14.3
(-1.7)
A 		12.1
(-3)
A 		10
C 24.4
(0.5)
A 		14.7
(-2.1)
A 		33.7
(3)
A 		11.4
(-3)
A 		22
avr 23.4
(1.4) 		19.5
(-0.4) 		26.9
(3) 		13.9
(-3) 		13

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 1731
1 2 3 4 5 6 range
A 4.9
(-3)
A 		29
(-2.9)
A 		12.6
(-3)
A 		725.5
(0.8)
P 		1146.3
(3)
P 		99.3
(-2.5)
P 		1141
B 9.2
(-3)
A 		17.5
(-3)
A 		17.6
(-3)
P 		704.2
(-0.6)
P 		1736
(3)
P 		207.1
(-2.3)
P 		1727
C 35
(-2.9)
M 		30.9
(-3)
A 		19.3
(-3)
A 		530.1
(-1.2)
P 		1712.8
(3)
P 		116.4
(-2.7)
P 		1694
avr 16.4
(-3) 		25.8
(-3) 		16.5
(-3) 		653.3
(-0.5) 		1531.7
(3) 		140.9
(-2.5) 		1515
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 188615_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.5160
Sequence Type Exemplar sequence
Representative Public ID W09G10.1 NCBI
Target Description W09G10.1 /REP_DB=WormBase Gene ID /WP=CE28512 /TR=O16640 /GB=AAB66109.1 /SUBMIT=ST.LOUIS /CHR=2 /FEA=Sanger Annotation /DEF=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_062167(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_062167 NCBI Caenorhabditis elegans W09G10.1 (collagen) mRNA, complete cds. 11/11 None
SNAP00000024965 ENSEMBL cdna:SNAP chromosome:CEL140:II:3520735:3521403:-1 11/11 None
GENEFINDER00000024974 ENSEMBL cdna:GeneFinder chromosome:CEL140:II:3520735:3521403:-1 11/11 None
W09G10.1 ENSEMBL cdna:known chromosome:CEL140:II:3520735:3521403:-1 gene:W09G10.1 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
chrII:3520733-3521402(-) 100.0 100.0
Public Domain and Genome References
Gene Title collagen
Gene Symbol col-72
Ensembl W09G10.1
Entrez Gene 173698 Entrez gene
SwissProt O16640 EMBL-EBI
WormBase CE28512 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
Protein Similarities
Method ID Description E-Value
blast AAB66109 Collagen protein 72 [Caenorhabditis elegans] ref|NP_494568.1| W09G10.1 [Caenorhabditis elegans] 2.0E-53
blast A88102 protein W09G10.1 [imported] - Caenorhabditis elegans 3.0E-50
blast CAE73812 Hypothetical protein CBG21362 [Caenorhabditis briggsae] 3.0E-20
Protein Domains
Database ID Description E-Value
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 6.4E-4
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 1.2E-12
Sequence
Target Sequence 
>C. ELEGANS:188615_S_AT
taaagccggtggaccaggaagccctggaagagacggaatccgcggatcgaagggatccac
tggagataaggggccaaatggaccacccggacagaatgggccacctggatgggctggacg
tgatggaaacatcggaccacaaggaacacctggaggacgtggagaaccaggaggcccagg
aactgatggattccctggattcgctggaaatcctggaccagatgtgagttacaatatatt
gaggaagatcggggtgcaatttaatatttttcagggagctcctggagttgactctggcta
ctgcaagtgccc

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
TAAAGCCGGTGGACCAGGAAGCCCT 116 639 324 Antisense
GACGGAATCCGCGGATCGAAGGGAT 690 373 355 Antisense
GATAAGGGGCCAAATGGACCACCCG 289 423 388 Antisense
TGGACCACCCGGACAGAATGGGCCA 317 547 402 Antisense
GACAGAATGGGCCACCTGGATGGGC 701 367 413 Antisense
CCTGGATGGGCTGGACGTGATGGAA 40 265 427 Antisense
GAACACCTGGAGGACGTGGAGAACC 413 351 467 Antisense
AGGAGGCCCAGGAACTGATGGATTC 386 57 492 Antisense
TGATGGATTCCCTGGATTCGCTGGA 287 567 507 Antisense
AGCTCCTGGAGTTGACTCTGGCTAC 313 81 600 Antisense
TTGACTCTGGCTACTGCAAGTGCCC 708 703 611 Antisense
Sequence Source Affymetrix Proprietary Database