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[189797_s_at] cuticular collagen

Description F58F6.1 /REP_DB=WormBase Gene ID /WP=CE17136 /TR=O44174 /GB=AAB88358.1 /SUBMIT=ST.LOUIS /CHR=4 /FEA=Sanger Annotation /DEF=cuticular collagen
Cluster 6grp_highest_10_10 > 19      6grp_high1_10_10 > 91      6grp_highest_nonorm > 59      6grp_total > 83      4grp_total > 57      6grp_highest_sub > 05      6grp_cgc > 87      6grp_high1_sub > 05      6grp_cgc_sub > 05      6grp_total_sub > Hat      4grp_rule_based > L3      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 5155
1 2 3 4 range
A 88.1
(-3)
A 		3373
(1.8)
P 		4188.5
(3)
P 		128.3
(-2.9)
A 		4100
B 67.4
(-3)
A 		3424.6
(0.9)
P 		5168.3
(3)
P 		152.8
(-2.9)
A 		5101
C 13.6
(-3)
A 		2789.7
(1.6)
P 		3619.5
(3)
P 		133.6
(-2.8)
A 		3606
avr 56.4
(-3) 		3195.8
(1.4) 		4325.4
(3) 		138.2
(-2.9) 		4269

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 8703
1 2 3 4 5 6 range
A 378.6
(-3)
P 		2763.1
(-0.6)
P 		1524.9
(-1.8)
P 		5559.3
(2.3)
P 		6247
(3)
P 		1691.9
(-1.7)
P 		5868
B 513.6
(-3)
P 		2338.2
(-1.2)
P 		1792
(-1.7)
P 		5034.9
(1.5)
P 		6546.6
(3)
P 		1648.9
(-1.9)
P 		6033
C 622.3
(-3)
P 		2048.3
(-2)
P 		2100.2
(-2)
P 		4888.9
(0)
P 		9081.6
(3)
P 		1168.7
(-2.6)
P 		8459
avr 504.8
(-3) 		2383.2
(-1.3) 		1805.7
(-1.8) 		5161
(1.1) 		7291.7
(3) 		1503.2
(-2.1) 		6787
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 1257
1 2 3 4 range
A 32.1
(-2.9)
A 		732.2
(1)
P 		1095
(3)
P 		18.8
(-3)
A 		1076
B 21.5
(-3)
A 		845.8
(1.2)
P 		1197.6
(3)
P 		32.6
(-2.9)
A 		1176
C 4.5
(-3)
A 		802
(0.8)
P 		1261.5
(3)
P 		22.5
(-2.9)
A 		1257
avr 19.4
(-3) 		793.3
(1) 		1184.7
(3) 		24.6
(-3) 		1165

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 2869
1 2 3 4 5 6 range
A 69.8
(-3)
P 		982.7
(0)
P 		332.1
(-2.1)
P 		1410
(1.4)
P 		1885.1
(3)
P 		411.9
(-1.9)
P 		1815
B 178.7
(-3)
P 		778.3
(-1.5)
P 		435.2
(-2.4)
P 		1333.6
(-0.2)
P 		2659.8
(3)
P 		614.9
(-1.9)
P 		2481
C 230.7
(-3)
P 		625
(-2.1)
P 		534.5
(-2.3)
P 		983.2
(-1.3)
P 		2938.7
(3)
P 		391.2
(-2.6)
P 		2708
avr 159.7
(-3) 		795.3
(-1.4) 		433.9
(-2.3) 		1242.3
(-0.2) 		2494.5
(3) 		472.7
(-2.2) 		2335
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 189797_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.10493
Sequence Type Exemplar sequence
Representative Public ID F58F6.1 NCBI
Target Description F58F6.1 /REP_DB=WormBase Gene ID /WP=CE17136 /TR=O44174 /GB=AAB88358.1 /SUBMIT=ST.LOUIS /CHR=4 /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_067669(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_067669 NCBI Caenorhabditis elegans COLlagen family member (col-104) (col-104) mRNA, complete cds. 11/11 None
SNAP00000017981 ENSEMBL cdna:SNAP chromosome:CEL140:IV:1344579:1356652:-1 11/11 None
GENEFINDER00000017990 ENSEMBL cdna:GeneFinder chromosome:CEL140:IV:1353700:1355294:-1 11/11 None
F58F6.1 ENSEMBL cdna:known chromosome:CEL140:IV:1353700:1355304:-1 gene:F58F6.1 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
chrIV:1353705-1355300(-) 100.0 100.0
Public Domain and Genome References
Gene Title cuticular collagen
Gene Symbol col-104
Ensembl F58F6.1
Entrez Gene 176947 Entrez gene
SwissProt O44174 EMBL-EBI
WormBase CE17136 Wormbase
Functional Annotations
Gene Ontology
GO Biological Process (view graph)
ID Description Evidence Links
6817 phosphate transport inferred from electronic annotation QuickGO AmiGO
8152 metabolism 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
3824 catalytic activity inferred from electronic annotation QuickGO AmiGO
42302 structural constituent of cuticle inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast AAB88358 Collagen protein 104 [Caenorhabditis elegans] ref|NP_500070.1| COLlagen family member (col-104) [Caenorhabditis elegans] 5.0E-57
blast AAB88358 Collagen protein 104 [Caenorhabditis elegans] ref|NP_500070.1| COLlagen family member (col-104) [Caenorhabditis elegans] 6.0E-57
blast CAE69231 Hypothetical protein CBG15273 [Caenorhabditis briggsae] 3.0E-54
blast CAE69231 Hypothetical protein CBG15273 [Caenorhabditis briggsae] 4.0E-54
Protein Domains
Database ID Description E-Value
Pfam IPR002486 EMBL-EBI Nematode cuticle collagen, N-terminal 4.0E-15
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 1.0E-5
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 1.2E-5
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 5.3E-6
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 2.0E-11
Pfam IPR002486 EMBL-EBI Nematode cuticle collagen, N-terminal 4.0E-15
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 1.0E-5
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 1.2E-5
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 5.3E-6
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 2.0E-11
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_500070.1 1 7-29
F58F6.1 1 7-29
SNAP00000017981 1 26-48
GENEFINDER00000017990 1 7-29
Sequence
Target Sequence 
>C. ELEGANS:189797_S_AT
gacaactcgcccgggagaatgcgtttgcaactcgaacagcgcttgcccaccaggagaagc
cggtccacaaggaatcccaggacacgacggtaccccaggactcgccggagacgccggagc
tccaggacttccaggaaactacccatcaatcaatatggatgctcatcaacaatgccgtat
gtgcccaccaggagctccaggattcccaggaccagccgggccgccaggagctccaggaga
caaaggaaacgacggtgctccagggctccgcggtccagacggacacccaggtcatccagg
aaatccaggatatggtggagagccaggagctccaggaaacaacggagagccgggagacaa
gggacgtgatggatctcacggaaccaagggagcaccaggaccacaaggaccttctggacc
cgttggacagccaggattcccaggacaacctggaaatgatggaaatagcggagttccagg
gatccaaggatcctctggaggccctggagaggatggagctccaggagcaccaggattcga
tggacaacagggaccgagtggaacacctggaga

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GACAACTCGCCCGGGAGAATGCGTT 510 365 237 Antisense
ATGCGTTTGCAACTCGAACAGCGCT 189 41 255 Antisense
GCCGGTCCACAAGGAATCCCAGGAC 572 283 295 Antisense
GACTTCCAGGAAACTACCCATCAAT 293 371 362 Antisense
CATCAACAATGCCGTATGTGCCCAC 280 213 400 Antisense
CGGAGAGCCGGGAGACAAGGGACGT 273 243 579 Antisense
GATCTCACGGAACCAAGGGAGCACC 424 419 608 Antisense
CTTCTGGACCCGTTGGACAGCCAGG 29 219 647 Antisense
ATAGCGGAGTTCCAGGGATCCAAGG 322 21 701 Antisense
TCCAAGGATCCTCTGGAGGCCCTGG 379 585 719 Antisense
AGGGACCGAGTGGAACACCTGGAGA 437 57 785 Antisense
Sequence Source Affymetrix Proprietary Database