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[188430_at] cuticular collagen

Description F14H12.1 /REP_DB=WormBase Gene ID /WP=CE07061 /GB=AAK68323.1 /SUBMIT=ST.LOUIS /CHR=X /FEA=Sanger Annotation /DEF=cuticular collagen
Cluster 6grp_total > 48      4grp_total > 33      6grp_cgc > 07      6grp_total_sub > Cup      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 276
1 2 3 4 range
A 96.3
(-3)
A 		257.3
(3)
A 		258
(3)
A 		245.8
(2.5)
A 		162
B 124.6
(-3)
A 		372.7
(3)
A 		240.1
(-0.2)
A 		252.3
(0.1)
P 		248
C 141.4
(-3)
A 		225.5
(0.8)
A 		222.1
(0.6)
A 		275.7
(3)
P 		134
avr 120.8
(-3) 		285.2
(3) 		240.1
(1.4) 		257.9
(2) 		164

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 718
1 2 3 4 5 6 range
A 803.2
(3)
P 		176.7
(-2.2)
A 		150.6
(-2.5)
A 		213.1
(-1.9)
A 		85.5
(-3)
A 		665.1
(1.8)
P 		718
B 797.6
(3)
P 		134.4
(-2.7)
A 		225.8
(-1.9)
A 		132.1
(-2.8)
A 		104.3
(-3)
A 		571.4
(1)
P 		693
C 784.8
(3)
P 		217.7
(-1.9)
A 		120.5
(-2.8)
A 		95.9
(-3)
A 		119.9
(-2.8)
A 		486
(0.4)
P 		689
avr 795.2
(3) 		176.3
(-2.4) 		165.6
(-2.5) 		147
(-2.6) 		103.2
(-3) 		574.2
(1.1) 		692
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 57
1 2 3 4 range
A 35.1
(-3)
A 		55.9
(0.9)
A 		67.5
(3)
A 		36
(-2.8)
A 		32
B 39.7
(-3)
A 		92.1
(3)
A 		55.6
(-1.2)
A 		53.8
(-1.4)
P 		52
C 46.8
(-2.9)
A 		64.8
(0.6)
A 		77.4
(3)
A 		46.5
(-3)
P 		31
avr 40.5
(-3) 		70.9
(3) 		66.8
(2.2) 		45.4
(-2) 		30

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 272
1 2 3 4 5 6 range
A 148.1
(2.4)
P 		62.8
(-1.4)
A 		32.8
(-2.7)
A 		54.1
(-1.8)
A 		25.8
(-3)
A 		161.9
(3)
P 		136
B 277.5
(3)
P 		44.7
(-2.8)
A 		54.8
(-2.5)
A 		35
(-3)
A 		42.4
(-2.8)
A 		213.1
(1.4)
P 		243
C 290.9
(3)
P 		66.4
(-2)
A 		30.7
(-2.7)
A 		19.3
(-3)
A 		38.8
(-2.6)
A 		162.7
(0.2)
P 		272
avr 238.8
(3) 		58
(-2.3) 		39.4
(-2.9) 		36.1
(-3) 		35.7
(-3) 		179.2
(1.2) 		203
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 188430_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.16865
Sequence Type Exemplar sequence
Representative Public ID F14H12.1 NCBI
Target Description F14H12.1 /REP_DB=WormBase Gene ID /WP=CE07061 /GB=AAK68323.1 /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_076346(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_076346 NCBI Caenorhabditis elegans COLlagen family member (col-165) (col-165) mRNA, complete cds. 11/11 None
SNAP00000002234 ENSEMBL cdna:SNAP chromosome:CEL140:X:4353610:4354760:1 11/11 None
GENEFINDER00000002246 ENSEMBL cdna:GeneFinder chromosome:CEL140:X:4353610:4354760:1 11/11 None
F14H12.1 ENSEMBL cdna:known chromosome:CEL140:X:4353606:4354784:1 gene:F14H12.1 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
chrX:4353610-4354761(+) 100.0 100.0
Public Domain and Genome References
Gene Title cuticular collagen
Gene Symbol col-165
Ensembl F14H12.1
Entrez Gene 180710 Entrez gene
SwissProt Q966K5 EMBL-EBI
WormBase CE07061 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 AAK68323 Collagen protein 165 [Caenorhabditis elegans] ref|NP_508747.1| COLlagen family member (col-165) [Caenorhabditis elegans] 1.0E-154
blast CAE68564 Hypothetical protein CBG14399 [Caenorhabditis briggsae] 1.0E-136
blast AAF39908 Dumpy : shorter than wild-type protein 14 [Caenorhabditis elegans] ref|NP_491958.1| DumPY : shorter than wild-type family member (dpy-14) [Caenorhabditis elegans] gb|AAP97871.1| COLlagen structural gene, probably a critical component of the embryonically derived outer layer of the L1 cuticle (31.8 kD) (col-59) [Caenorhabditis elegans] 7.0E-89
Protein Domains
Database ID Description E-Value
Pfam IPR002486 EMBL-EBI Nematode cuticle collagen, N-terminal 1.4E-7
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 4.7E-12
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 7.7E-4
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_508747.1 1 12-34
F14H12.1 1 12-34
SNAP00000002234 1 12-34
GENEFINDER00000002246 1 12-34
Sequence
Target Sequence 
>C. ELEGANS:188430_AT
acggaccagttgtcaatgccgagccagctccacaatgctgcacttgccagcaaggaaatg
ccggaccaccaggaccaccaggagatgatggacacgatggaaaggacggaaacgccggat
ctgatgctcacaatggaaaggacggtggagtcgctccatctgacggacttcaaagcgagc
catgcatgatctgcccaccaggaccacaaggacttatgggacaagctggaaagaagggac
caaccggaccacgtggatccccaggacttgctggaattgacggaagacgtggagagccag
gtatggttggaccaactggactagacggagagcagggaccacaaggacctccaggaaaga
gaggagaagatggacgtgtcatcgatatcaacggaccacaaggagccccaggagcaccag
gagctcaaggacgcaagggagaatccggaccaaagggacgtcgtggaaacactattccag
gaccacaaggaccaaacggagatgccggaagaaagggacgtgcaggacacaagggagagg
caggaggaccaggaggtctcggatcca

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
ACGGACCAGTTGTCAATGCCGAGCC 91 97 395 Antisense
CTCCACAATGCTGCACTTGCCAGCA 337 235 422 Antisense
CGCCGGATCTGATGCTCACAATGGA 674 255 507 Antisense
GGAAAGGACGGTGGAGTCGCTCCAT 604 527 529 Antisense
TCGCTCCATCTGACGGACTTCAAAG 433 599 545 Antisense
TCAAAGCGAGCCATGCATGATCTGC 16 629 564 Antisense
GAGAGCCAGGTATGGTTGGACCAAC 594 393 686 Antisense
GGACCAACTGGACTAGACGGAGAGC 5 523 703 Antisense
GTGTCATCGATATCAACGGACCACA 553 483 770 Antisense
GGACGCAAGGGAGAATCCGGACCAA 561 523 823 Antisense
GGAGGACCAGGAGGTCTCGGATCCA 604 515 937 Antisense
Sequence Source Affymetrix Proprietary Database