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[177032_at] Cuticle collagen

Description F09G8.6 /REP_DB=WormBase Gene ID /WP=CE00141 /SUBMIT=ST.LOUIS /CHR=3 /FEA=Sanger Annotation /DEF=Cuticle collagen
Cluster 6grp_highest_10_10 > 44      6grp_high1_10_10 > 43      6grp_highest_nonorm > 34      6grp_total > 10      4grp_total > 50      6grp_highest_sub > 02      6grp_cgc > 63      6grp_high1_sub > 02      6grp_cgc_sub > 02      6grp_total_sub > Hat      6grp_rule_based > S2      4grp_rule_based > L2      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 4402
1 2 3 4 range
A 258.7
(-2.7)
P 		4411.1
(3)
P 		3754.2
(2.1)
P 		9
(-3)
A 		4402
B 302.1
(-2.6)
P 		4072.1
(3)
P 		3868.8
(2.7)
P 		8.8
(-3)
A 		4063
C 255.8
(-2.7)
P 		4027.5
(3)
P 		3211.1
(1.8)
P 		30.4
(-3)
A 		3997
avr 272.2
(-2.6) 		4170.2
(3) 		3611.4
(2.2) 		16.1
(-3) 		4154

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 4263
1 2 3 4 5 6 range
A 230.9
(-3)
P 		4460.4
(3)
P 		2785.4
(0.6)
P 		2133.5
(-0.3)
P 		1628.6
(-1)
P 		1822
(-0.7)
P 		4230
B 197.2
(-3)
P 		4100.2
(3)
P 		3064.3
(1.4)
P 		1836.2
(-0.5)
P 		1445.9
(-1.1)
P 		1762.8
(-0.6)
P 		3903
C 237.3
(-3)
P 		3691.2
(3)
P 		2952.4
(1.7)
P 		1768
(-0.3)
P 		2172.5
(0.4)
P 		1528.4
(-0.8)
P 		3454
avr 221.8
(-3) 		4083.9
(3) 		2934
(1.2) 		1912.6
(-0.4) 		1749
(-0.6) 		1704.4
(-0.7) 		3862
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 1157
1 2 3 4 range
A 94.2
(-2.4)
P 		957.5
(2.9)
P 		981.4
(3)
P 		1.3
(-3)
A 		980
B 96.3
(-2.4)
P 		1005.7
(3)
P 		896.5
(2.3)
P 		1.9
(-3)
A 		1004
C 84.7
(-2.6)
P 		1157.9
(3)
P 		1119.2
(2.8)
P 		5.1
(-3)
A 		1153
avr 91.7
(-2.5) 		1040.4
(3) 		999
(2.8) 		2.8
(-3) 		1038

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 1544
1 2 3 4 5 6 range
A 42.6
(-3)
P 		1586.3
(3)
P 		606.6
(-0.8)
P 		541.1
(-1.1)
P 		491.4
(-1.3)
P 		443.6
(-1.4)
P 		1544
B 68.6
(-3)
P 		1364.8
(3)
P 		744.1
(0.1)
P 		486.4
(-1.1)
P 		587.5
(-0.6)
P 		657.3
(-0.3)
P 		1296
C 87.9
(-3)
P 		1126.3
(3)
P 		751.4
(0.8)
P 		355.5
(-1.5)
P 		703
(0.6)
P 		511.6
(-0.6)
P 		1038
avr 66.4
(-3) 		1359.1
(3) 		700.7
(-0.1) 		461
(-1.2) 		594
(-0.6) 		537.5
(-0.8) 		1293
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 177032_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.6102
Sequence Type Exemplar sequence
Representative Public ID F09G8.6 NCBI
Target Description F09G8.6 /REP_DB=WormBase Gene ID /WP=CE00141 /SUBMIT=ST.LOUIS /CHR=3 /FEA=Sanger Annotation /DEF=Cuticle 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_066413(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_066413 NCBI Caenorhabditis elegans COLlagen family member (col-91) (col-91) mRNA, complete cds. 11/11 None
SNAP00000034500 ENSEMBL cdna:SNAP chromosome:CEL140:III:8262382:8263545:-1 11/11 None
GENEFINDER00000034516 ENSEMBL cdna:GeneFinder chromosome:CEL140:III:8262382:8263545:-1 11/11 None
F09G8.6 ENSEMBL cdna:known chromosome:CEL140:III:8262293:8263580:-1 gene:F09G8.6 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:8262377-8263541(-) 96.77 100.0
Public Domain and Genome References
Gene Title Cuticle collagen
Gene Symbol col-91
Ensembl F09G8.6
Entrez Gene 184269 Entrez gene
SwissProt P34391 EMBL-EBI
WormBase CE00141 Wormbase
Functional Annotations
Gene Ontology
GO Biological Process (view graph)
ID Description Evidence Links
6817 phosphate transport inferred from mutant phenotype 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 NP_498814 COLlagen family member (col-91) [Caenorhabditis elegans] gb|AAA28008.1| Collagen protein 91 [Caenorhabditis elegans] sp|P34391|YLS6_CAEEL Putative cuticle collagen F09G8.6 3.0E-38
blast CAE70181 Hypothetical protein CBG16654 [Caenorhabditis briggsae] 5.0E-33
blast CAB02849 Hypothetical protein C50B6.4 [Caenorhabditis elegans] ref|NP_506300.1| C50B6.4 [Caenorhabditis elegans] 4.0E-15
Protein Domains
Database ID Description E-Value
Pfam IPR002486 EMBL-EBI Nematode cuticle collagen, N-terminal 4.2E-21
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 4.0E-4
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 5.1E-11
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 7.0E-13
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_498814.1 1 7-29
F09G8.6 1 7-29
SNAP00000034500 1 7-29
GENEFINDER00000034516 1 7-29
Sequence
Target Sequence 
>C. ELEGANS:177032_AT
cttccagactgtcaagctcttgctaaaaactgcccaccaggaccaccaggaccaccagga
gctccaggagctgctggtgagccaggagtagacggagacgctggagccgctggaatcgac
ggagttgccattcaattcgcttcggccgccggtggagcatgcatccaatgcccagcagga
gaagccggtccagcaggagccccaggagcacctgggccagccggaccagacggacagcca
ggagctgatggacaaggaggagccccaggaccagcaggaccagaaggaccagctggagat
gccggagcaccaggagcccccggggcaccaggaaacgatggacaaccaggacaaaacgga
caaagatctactggaacaccaggcgccgctggagctccaggaccacaaggaccagtcgga
tctgatggacaaccaggatcagctggagcaccaggagcaccagggccagctggagctcca
ggagtcgatggacagccaggagccaacggacaaccaggaccagatggagaacaaggacat
gatggccaaccaggaccggatgctgcttattgcc

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
CTTCCAGACTGTCAAGCTCTTGCTA 400 219 244 Antisense
TCTTGCTAAAAACTGCCCACCAGGA 268 617 261 Antisense
AGGAGTAGACGGAGACGCTGGAGCC 228 57 327 Antisense
GGAATCGACGGAGTTGCCATTCAAT 596 531 355 Antisense
GAGTTGCCATTCAATTCGCTTCGGC 579 397 365 Antisense
GCCGGTGGAGCATGCATCCAATGCC 588 283 391 Antisense
CAATGCCCAGCAGGAGAAGCCGGTC 225 181 409 Antisense
AGATCTACTGGAACACCAGGCGCCG 420 65 607 Antisense
GGACCAGTCGGATCTGATGGACAAC 480 523 652 Antisense
GAGAACAAGGACATGATGGCCAACC 656 391 770 Antisense
CCAGGACCGGATGCTGCTTATTGCC 124 273 793 Antisense
Sequence Source Affymetrix Proprietary Database