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[188747_at] collagen

Description Y54E10BL.2 /REP_DB=WormBase Gene ID /WP=CE25434 /TR=Q9N3D7 /GB=AAF60775.1 /SUBMIT=ST.LOUIS /CHR=1 /FEA=Sanger Annotation /DEF=collagen
Cluster 6grp_highest_10_10 > 19      6grp_high1_10_10 > 91      4grp_high_8_8 > 55      6grp_highest_nonorm > 49      6grp_total > 93      4grp_total > 56      6grp_highest_sub > 05      6grp_cgc > 87      6grp_high1_sub > 05      6grp_cgc_sub > 05      6grp_total_sub > Hat      6grp_rule_based > S5      4grp_rule_based > L3      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 5631
1 2 3 4 range
A 63.4
(-3)
P 		4510.8
(1.7)
P 		5694.4
(3)
P 		75.3
(-3)
P 		5631
B 80.8
(-3)
A 		3979.8
(1.3)
P 		5566.7
(3)
P 		115.4
(-3)
P 		5486
C 90.9
(-3)
P 		3889.1
(1.6)
P 		5069.2
(3)
P 		84.6
(-3)
M 		4985
avr 78.4
(-3) 		4126.6
(1.5) 		5443.4
(3) 		91.8
(-3) 		5365

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 10375
1 2 3 4 5 6 range
A 936.1
(-3)
P 		2227.4
(-2)
P 		1346.1
(-2.7)
P 		6157.4
(1.2)
P 		8461.5
(3)
P 		1914.4
(-2.2)
P 		7525
B 822.6
(-3)
P 		1949.2
(-2.2)
P 		1736.7
(-2.4)
P 		5322
(0.1)
P 		9659.9
(3)
P 		1812.2
(-2.3)
P 		8837
C 937
(-3)
P 		1875.4
(-2.5)
P 		1825.8
(-2.5)
P 		4914.1
(-0.7)
P 		11197.2
(3)
P 		1331.3
(-2.8)
P 		10260
avr 898.6
(-3) 		2017.3
(-2.2) 		1636.2
(-2.5) 		5464.5
(0.1) 		9772.9
(3) 		1686
(-2.5) 		8874
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 1756
1 2 3 4 range
A 23.1
(-3)
P 		979.2
(0.9)
P 		1488.6
(3)
P 		11
(-3)
P 		1478
B 25.8
(-3)
A 		982.9
(1.5)
P 		1289.9
(3)
P 		24.6
(-3)
P 		1265
C 30.1
(-2.9)
P 		1118.1
(0.8)
P 		1766.8
(3)
P 		14.3
(-3)
M 		1753
avr 26.3
(-3) 		1026.7
(1) 		1515.1
(3) 		16.6
(-3) 		1499

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 3752
1 2 3 4 5 6 range
A 172.6
(-3)
P 		792.2
(-1.4)
P 		293.1
(-2.7)
P 		1561.7
(0.5)
P 		2553.3
(3)
P 		466.1
(-2.3)
P 		2381
B 286.2
(-3)
P 		648.8
(-2.4)
P 		421.7
(-2.8)
P 		1409.6
(-1.1)
P 		3924.7
(3)
P 		675.8
(-2.4)
P 		3639
C 347.3
(-3)
P 		572.2
(-2.6)
P 		464.7
(-2.8)
P 		988.2
(-1.8)
P 		3623.2
(3)
P 		445.6
(-2.8)
P 		3276
avr 268.7
(-3) 		671.1
(-2.2) 		393.2
(-2.8) 		1319.8
(-1) 		3367.1
(3) 		529.2
(-2.5) 		3098
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 188747_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.44
Sequence Type Exemplar sequence
Representative Public ID Y54E10BL.2 NCBI
Target Description Y54E10BL.2 /REP_DB=WormBase Gene ID /WP=CE25434 /TR=Q9N3D7 /GB=AAF60775.1 /SUBMIT=ST.LOUIS /CHR=1 /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_058687(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_058687 NCBI Caenorhabditis elegans Y54E10BL.2 (collagen) mRNA, complete cds. 11/11 None
GENEFINDER00000040901 ENSEMBL cdna:GeneFinder chromosome:CEL140:I:3010052:3011608:1 11/11 None
SNAP00000040894 ENSEMBL cdna:SNAP chromosome:CEL140:I:3010691:3011608:1 11/11 None
Y54E10BL.2 ENSEMBL cdna:known chromosome:CEL140:I:3010691:3011649:1 gene:Y54E10BL.2 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
chrI:3010690-3011608(+) 100.0 100.0
Public Domain and Genome References
Gene Title collagen
Gene Symbol col-48
Ensembl Y54E10BL.2
Entrez Gene 171873 Entrez gene
SwissProt Q9N3D7 EMBL-EBI
WormBase CE25434 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 AAF60775 Collagen protein 48 [Caenorhabditis elegans] ref|NP_491088.1| Y54E10BL.2 [Caenorhabditis elegans] 6.0E-45
blast AAF60775 Collagen protein 48 [Caenorhabditis elegans] ref|NP_491088.1| Y54E10BL.2 [Caenorhabditis elegans] 8.0E-45
blast CAE60562 Hypothetical protein CBG04191 [Caenorhabditis briggsae] 9.0E-44
blast CAE60562 Hypothetical protein CBG04191 [Caenorhabditis briggsae] 1.0E-43
blast CAB85466 putative cuticular collagen [Ascaris suum] 2.0E-32
Protein Domains
Database ID Description E-Value
Pfam IPR002486 EMBL-EBI Nematode cuticle collagen, N-terminal 1.1E-16
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 9.1E-11
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 1.1E-13
Pfam IPR002486 EMBL-EBI Nematode cuticle collagen, N-terminal 1.1E-16
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 9.1E-11
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 1.1E-13
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_491088.1 1 12-34
Y54E10BL.2 1 12-34
GENEFINDER00000040901 1 53-75
SNAP00000040894 1 12-34
Sequence
Target Sequence 
>C. ELEGANS:188747_AT
ttctgctcagagctacacgtcaagctgatgctcaatgctgcacatgccaacagggaccac
caggaccagatggagagccaggaactcctggaaaagacggagaaccaggtcaaggaccag
gagagccaggaccaccaggacctgatgccgagcttcatgatcgaattctcccggttccac
cacaatgcccatgcactgctgctccaggacttggaggaccaccaggaccaccaggacaag
atggaattccaggtaacccgg

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
TTCTGCTCAGAGCTACACGTCAAGC 48 695 242 Antisense
GCTACACGTCAAGCTGATGCTCAAT 278 303 253 Antisense
GTCAAGCTGATGCTCAATGCTGCAC 77 465 260 Antisense
GCTGATGCTCAATGCTGCACATGCC 218 291 265 Antisense
GATGCTCAATGCTGCACATGCCAAC 606 413 268 Antisense
ATGCTGCACATGCCAACAGGGACCA 379 41 276 Antisense
GAACCAGGTCAAGGACCAGGAGAGC 423 345 343 Antisense
GACCTGATGCCGAGCTTCATGATCG 666 381 380 Antisense
GATGCCGAGCTTCATGATCGAATTC 96 415 385 Antisense
GAGCTTCATGATCGAATTCTCCCGG 288 389 391 Antisense
CAAGATGGAATTCCAGGTAACCCGG 22 159 478 Antisense
Sequence Source Affymetrix Proprietary Database