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[189600_at] cuticular collagen

Description F17C8.2 /REP_DB=WormBase Gene ID /WP=CE00956 /TR=Q19528 /GB=CAA84800.1 /SUBMIT=HINXTON /CHR=3 /FEA=Sanger Annotation /DEF=cuticular collagen
Cluster 6grp_high1_10_10 > 91      6grp_total > 93      4grp_total > 49      6grp_cgc > 88      6grp_high1_sub > 05      6grp_total_sub > Hat      6grp_rule_based > S5      4grp_rule_based > L2      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 273
1 2 3 4 range
A 83.5
(-3)
P 		339.3
(3)
P 		211.4
(0)
P 		86.2
(-2.9)
A 		256
B 95.4
(-3)
A 		336.1
(3)
P 		281.8
(1.6)
P 		103.7
(-2.8)
A 		241
C 66
(-3)
A 		261.5
(2.9)
M 		266.5
(3)
P 		117.1
(-1.5)
M 		201
avr 81.6
(-3) 		312.3
(3) 		253.2
(1.5) 		102.3
(-2.5) 		231

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 1990
1 2 3 4 5 6 range
A 39.3
(-3)
A 		103.6
(-2.5)
P 		126.8
(-2.4)
M 		874.2
(3)
P 		844
(2.8)
P 		294.2
(-1.2)
P 		835
B 81.2
(-3)
P 		140.2
(-2.6)
P 		137.4
(-2.6)
P 		447.8
(-0.6)
P 		990.5
(3)
P 		184.6
(-2.3)
P 		909
C 144.5
(-2.8)
P 		80.5
(-3)
A 		107.9
(-2.9)
P 		568.5
(-1.5)
P 		2029.4
(3)
P 		195.2
(-2.6)
P 		1949
avr 88.3
(-3) 		108.1
(-2.9) 		124
(-2.8) 		630.2
(-0.3) 		1288
(3) 		224.7
(-2.3) 		1200
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 80
1 2 3 4 range
A 30.4
(-1.2)
P 		73.6
(3)
P 		55.3
(1.2)
P 		12.6
(-3)
A 		61
B 30.4
(-2.2)
A 		83
(3)
P 		65.3
(1.3)
P 		22.1
(-3)
A 		61
C 21.8
(-2.8)
A 		75.2
(1.5)
M 		92.9
(3)
P 		19.7
(-3)
M 		73
avr 27.5
(-2) 		77.3
(3) 		71.2
(2.4) 		18.1
(-3) 		59

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 649
1 2 3 4 5 6 range
A 7.3
(-3)
A 		36.9
(-2.3)
P 		27.6
(-2.5)
M 		221.7
(2.2)
P 		254.7
(3)
P 		71.6
(-1.4)
P 		247
B 28.2
(-3)
P 		46.7
(-2.7)
P 		33.4
(-2.9)
P 		118.6
(-1.6)
P 		402.4
(3)
P 		68.8
(-2.3)
P 		374
C 53.5
(-2.7)
P 		24.6
(-3)
A 		27.5
(-3)
P 		114.3
(-2.1)
P 		656.7
(3)
P 		65.3
(-2.6)
P 		632
avr 29.7
(-3) 		36.1
(-2.9) 		29.5
(-3) 		151.5
(-1.2) 		437.9
(3) 		68.6
(-2.4) 		408
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 189600_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.7009
Sequence Type Exemplar sequence
Representative Public ID F17C8.2 NCBI
Target Description F17C8.2 /REP_DB=WormBase Gene ID /WP=CE00956 /TR=Q19528 /GB=CAA84800.1 /SUBMIT=HINXTON /CHR=3 /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_065574(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_065574 NCBI Caenorhabditis elegans COLlagen family member (col-89) (col-89) mRNA, complete cds. 11/11 None
SNAP00000012150 ENSEMBL cdna:SNAP chromosome:CEL140:III:4748153:4749094:1 11/11 None
GENEFINDER00000012155 ENSEMBL cdna:GeneFinder chromosome:CEL140:III:4748153:4749094:1 11/11 None
F17C8.2 ENSEMBL cdna:known chromosome:CEL140:III:4748142:4749118:1 gene:F17C8.2 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
chrIII:4748152-4749094(+) 97.19 100.0
Public Domain and Genome References
Gene Title cuticular collagen
Gene Symbol col-89
Ensembl F17C8.2
Entrez Gene 175627 Entrez gene
SwissProt Q19528 EMBL-EBI
WormBase CE00956 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 CAA84800 Hypothetical protein F17C8.2 [Caenorhabditis elegans] ref|NP_497975.1| COLlagen family member (col-89) [Caenorhabditis elegans] 7.0E-64
blast CAE71140 Hypothetical protein CBG17995 [Caenorhabditis briggsae] 4.0E-62
blast CAA84800 Hypothetical protein F17C8.2 [Caenorhabditis elegans] ref|NP_497975.1| COLlagen family member (col-89) [Caenorhabditis elegans] 1.0E-60
blast CAE71140 Hypothetical protein CBG17995 [Caenorhabditis briggsae] 7.0E-59
blast AAA92325 Collagen protein 10 [Caenorhabditis elegans] ref|NP_505376.1| COLlagen family member (col-10) [Caenorhabditis elegans] 4.0E-48
Protein Domains
Database ID Description E-Value
Pfam IPR002486 EMBL-EBI Nematode cuticle collagen, N-terminal 9.9E-26
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 1.8E-11
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 3.0E-9
Pfam IPR002486 EMBL-EBI Nematode cuticle collagen, N-terminal 1.8E-14
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 1.8E-11
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 3.0E-9
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_497975.1 1 5-24
F17C8.2 1 5-24
SNAP00000012150 1 5-24
GENEFINDER00000012155 1 5-27
Sequence
Target Sequence 
>C. ELEGANS:189600_AT
gtgtcaatgtgaacctgcaaaaccagtatgtccaccaggaccaccgggaccaccaggaga
gccaggacaacctggaagtgctggaccaccgggaccaccaggagaagacaatactgctac
atttgctcctatcacgtgcccaccaaaagatccttcatgtgtcaaatgtccagaagggcc
tgccgggcctccaggaccagaagggccagctggaccagcaggatccgatggtcaaccagg
cgcgccaggagatgctggaaaagatggaccacctggaccacctggaccagacggagattc
tggaccaaatggagaagcgggaccgaatggagaacctggagcacctggaaaagacggaga
aaagggcaagggagagccagggccagctggaccaccaggacctccaggaccaggaggtcc
acctggagatgctggaggcgccggaagcgatggtgctccaggaccacagggaccaccagg
acaagatggaactccaggaaatgcaggaccagacggacagccaggatccccaggagggcc
aggattaccaggaaacgatgcagcttactgtccatgtcc

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GTGTCAATGTGAACCTGCAAAACCA 70 485 285 Antisense
TGCAAAACCAGTATGTCCACCAGGA 194 575 300 Antisense
ACAATACTGCTACATTTGCTCCTAT 47 115 392 Antisense
TGCCCACCAAAAGATCCTTCATGTG 617 583 421 Antisense
TCAAATGTCCAGAAGGGCCTGCCGG 645 619 446 Antisense
ACCAGCAGGATCCGATGGTCAACCA 405 85 498 Antisense
CAACCAGGCGCGCCAGGAGATGCTG 168 187 517 Antisense
GAAGCGGGACCGAATGGAGAACCTG 335 341 598 Antisense
GATGCTGGAGGCGCCGGAAGCGATG 145 413 712 Antisense
CCCCAGGAGGGCCAGGATTACCAGG 304 259 812 Antisense
ACGATGCAGCTTACTGTCCATGTCC 255 93 839 Antisense
Sequence Source Affymetrix Proprietary Database