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[189814_s_at] cuticular collagen

Description F41C6.5 /REP_DB=WormBase Gene ID /WP=CE04542 /TR=Q20270 /GB=AAA80446.1 /SUBMIT=ST.LOUIS /CHR=X /FEA=Sanger Annotation /DEF=cuticular collagen
Cluster 6grp_high1_10_10 > 91      6grp_total > 82      4grp_total > 57      6grp_cgc > 98      6grp_high1_sub > 05      4grp_rule_based > L3      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 1448
1 2 3 4 range
A 152.7
(-2.7)
A 		951.7
(1.2)
P 		1308.5
(3)
P 		101.6
(-3)
A 		1207
B 199
(-2.4)
A 		1116
(1.5)
P 		1479.2
(3)
P 		49.7
(-3)
A 		1430
C 40.6
(-3)
A 		1096.5
(1.8)
P 		1376.1
(3)
P 		31.6
(-3)
A 		1345
avr 130.8
(-2.7) 		1054.7
(1.5) 		1387.9
(3) 		61
(-3) 		1327

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 1200
1 2 3 4 5 6 range
A 307.6
(-2.9)
A 		802.9
(0.2)
P 		450.1
(-2)
P 		1169.3
(2.5)
P 		1251.2
(3)
P 		292.7
(-3)
P 		959
B 218.4
(-3)
A 		679.1
(-0.5)
P 		509.9
(-1.4)
P 		952.4
(1)
P 		1321.7
(3)
P 		220.2
(-3)
P 		1103
C 259.8
(-2.5)
P 		620
(-0.7)
P 		684
(-0.3)
P 		867
(0.6)
P 		1350.9
(3)
P 		150.9
(-3)
P 		1200
avr 261.9
(-2.8) 		700.7
(-0.4) 		548
(-1.2) 		996.2
(1.3) 		1307.9
(3) 		221.3
(-3) 		1087
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 474
1 2 3 4 range
A 55.6
(-2.3)
A 		206.6
(0.5)
P 		342.1
(3)
P 		14.9
(-3)
A 		327
B 63.5
(-2)
A 		275.6
(1.8)
P 		342.8
(3)
P 		10.6
(-3)
A 		332
C 13.5
(-2.9)
A 		315.2
(0.9)
P 		479.6
(3)
P 		5.3
(-3)
A 		474
avr 44.2
(-2.5) 		265.8
(1.1) 		388.2
(3) 		10.3
(-3) 		378

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 487
1 2 3 4 5 6 range
A 56.7
(-3)
A 		285.6
(1.3)
P 		98
(-2.2)
P 		296.6
(1.5)
P 		377.6
(3)
P 		71.3
(-2.7)
P 		321
B 76
(-3)
A 		226
(-1)
P 		123.8
(-2.4)
P 		252.3
(-0.7)
P 		537
(3)
P 		82.1
(-2.9)
P 		461
C 96.3
(-2.3)
P 		189.2
(-0.8)
P 		174.1
(-1.1)
P 		174.3
(-1.1)
P 		437.1
(3)
P 		50.5
(-3)
P 		387
avr 76.3
(-2.9) 		233.6
(-0.4) 		132
(-2) 		241.1
(-0.3) 		450.6
(3) 		68
(-3) 		383
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 189814_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.16276
Sequence Type Exemplar sequence
Representative Public ID F41C6.5 NCBI
Target Description F41C6.5 /REP_DB=WormBase Gene ID /WP=CE04542 /TR=Q20270 /GB=AAA80446.1 /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_076761(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_076761 NCBI Caenorhabditis elegans COLlagen family member (col-173) (col-173) mRNA, complete cds. 11/11 None
SNAP00000012723 ENSEMBL cdna:SNAP chromosome:CEL140:X:6875260:6876189:-1 11/11 None
GENEFINDER00000012729 ENSEMBL cdna:GeneFinder chromosome:CEL140:X:6875260:6877486:-1 11/11 None
F41C6.5 ENSEMBL cdna:known chromosome:CEL140:X:6875179:6877486:-1 gene:F41C6.5 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
chrX:6875259-6877486(-) 100.0 100.0
Public Domain and Genome References
Gene Title cuticular collagen
Gene Symbol col-173
Ensembl F41C6.5
Entrez Gene 180960 Entrez gene
SwissProt Q20270 EMBL-EBI
WormBase CE04542 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 AAA80446 Collagen protein 173 [Caenorhabditis elegans] ref|NP_509162.1| COLlagen family member (col-173) [Caenorhabditis elegans] 3.0E-71
blast CAE65811 Hypothetical protein CBG10919 [Caenorhabditis briggsae] 1.0E-63
blast AAA80446 Collagen protein 173 [Caenorhabditis elegans] ref|NP_509162.1| COLlagen family member (col-173) [Caenorhabditis elegans] 1.0E-44
blast CAE65811 Hypothetical protein CBG10919 [Caenorhabditis briggsae] 1.0E-38
blast AAO44907 Collagen protein 170 [Caenorhabditis elegans] ref|NP_872267.1| T10E10.6 [Caenorhabditis elegans] 9.0E-14
Protein Domains
Database ID Description E-Value
Pfam IPR002486 EMBL-EBI Nematode cuticle collagen, N-terminal 4.3E-6
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 6.0E-5
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 4.1E-6
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 1.4E-9
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 6.0E-5
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 4.1E-6
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 1.4E-9
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_509162.1 1 21-43
F41C6.5 1 21-43
GENEFINDER00000012729 1 21-43
Sequence
Target Sequence 
>C. ELEGANS:189814_S_AT
tggatgcggatttgggtcacctggagagccgggatccccaggtcaagacggtcatgacgg
agtggacggtagacctggttcagatggaaacccaggtgcagacatgcatcttgatgacac
ttacaacatggctgatcaattttgctttgaatgccttccagcccctacaggacctcctgg
accaccaggtctcaagggaatgcctggtatacctggaaatcaaggagaggatgctggtcc
aggaagacaaggaatgccaggtccaacagggccacctggcccaaggggaccacctggaga
aactggagatgaaggagaaggcggtccagatggaattccaatggagaaaaaatcacctcc
aggcccacgtggaccaccaggaccggctggaccagatggaccacaaggaccagaaggaag
atctggaaagcagggaccaccgggaccaacaggtcagga

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
TGGATGCGGATTTGGGTCACCTGGA 396 549 402 Antisense
CACCTGGAGAGCCGGGATCCCCAGG 489 199 419 Antisense
GATCCCCAGGTCAAGACGGTCATGA 205 417 434 Antisense
GAGTGGACGGTAGACCTGGTTCAGA 668 399 461 Antisense
AACCCAGGTGCAGACATGCATCTTG 79 145 490 Antisense
GACACTTACAACATGGCTGATCAAT 603 365 517 Antisense
ATTTTGCTTTGAATGCCTTCCAGCC 211 15 540 Antisense
GGACCACCAGGTCTCAAGGGAATGC 558 521 580 Antisense
GGGAATGCCTGGTATACCTGGAAAT 283 493 597 Antisense
CCAACAGGGCCACCTGGCCCAAGGG 75 269 664 Antisense
GACCACCGGGACCAACAGGTCAGGA 576 381 836 Antisense
Sequence Source Affymetrix Proprietary Database