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[188356_at] collagen

Description F14F7.1 /REP_DB=WormBase Gene ID /WP=CE15821 /TR=O17805 /GB=CAB04111.1 /SUBMIT=HINXTON /CHR=3 /FEA=Sanger Annotation /DEF=collagen
Cluster 6grp_highest_10_10 > 04      6grp_high1_10_10 > 21      6grp_highest_nonorm > 06      6grp_total > 42      4grp_total > 61      6grp_cgc > 70      6grp_high1_sub > 03      6grp_total_sub > Hat      4grp_rule_based > L1      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 4258
1 2 3 4 range
A 4170.5
(3)
P 		3685.1
(2.3)
P 		3439.5
(1.9)
P 		66.1
(-3)
A 		4104
B 4133.5
(3)
P 		3232.5
(1.7)
P 		3541
(2.1)
P 		28.9
(-3)
A 		4105
C 4286.8
(3)
P 		3173.6
(1.4)
P 		3253.6
(1.5)
P 		29.3
(-3)
A 		4258
avr 4196.9
(3) 		3363.7
(1.8) 		3411.4
(1.9) 		41.4
(-3) 		4156

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 13240
1 2 3 4 5 6 range
A 10815.9
(1.7)
P 		9377.8
(1)
P 		13490.9
(3)
P 		9297.5
(0.9)
P 		6194.1
(-0.6)
P 		1445.3
(-3)
P 		12046
B 9821.8
(1)
P 		8157.5
(0.2)
P 		13889.4
(3)
P 		9547
(0.9)
P 		6157.7
(-0.7)
P 		1418.6
(-3)
P 		12471
C 11469.7
(1.8)
P 		7876.2
(0.1)
P 		14216.8
(3)
P 		8327.7
(0.3)
P 		7860.1
(0.1)
P 		976.9
(-3)
P 		13240
avr 10702.5
(1.5) 		8470.5
(0.4) 		13865.7
(3) 		9057.4
(0.7) 		6737.3
(-0.4) 		1280.3
(-3) 		12585
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 1514
1 2 3 4 range
A 1518.5
(3)
P 		799.9
(0.1)
P 		899.1
(0.5)
P 		9.7
(-3)
A 		1509
B 1318.1
(3)
P 		798.4
(0.6)
P 		820.5
(0.7)
P 		6.2
(-3)
A 		1312
C 1419
(3)
P 		912.4
(0.9)
P 		1134
(1.8)
P 		4.9
(-3)
A 		1414
avr 1418.5
(3) 		836.9
(0.5) 		951.2
(1) 		6.9
(-3) 		1412

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 3924
1 2 3 4 5 6 range
A 1993.8
(0.3)
P 		3335.2
(3)
P 		2938
(2.2)
P 		2358.1
(1)
P 		1869.1
(0.1)
P 		351.9
(-3)
P 		2983
B 3417.5
(3)
P 		2715.3
(1.5)
P 		3372.8
(2.9)
P 		2528.7
(1.2)
P 		2501.8
(1.1)
P 		529
(-3)
P 		2889
C 4251.3
(3)
P 		2403.3
(0.2)
P 		3618.4
(2)
P 		1674.7
(-0.9)
P 		2543.4
(0.4)
P 		327
(-3)
P 		3924
avr 3220.9
(2.8) 		2817.9
(2) 		3309.7
(3) 		2187.2
(0.7) 		2304.8
(0.9) 		402.6
(-3) 		2907
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 188356_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.7450
Sequence Type Exemplar sequence
Representative Public ID F14F7.1 NCBI
Target Description F14F7.1 /REP_DB=WormBase Gene ID /WP=CE15821 /TR=O17805 /GB=CAB04111.1 /SUBMIT=HINXTON /CHR=3 /FEA=Sanger Annotation /DEF=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_067302(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_067302 NCBI Caenorhabditis elegans F14F7.1 (collagen) mRNA, complete cds. 11/11 None
SNAP00000000290 ENSEMBL cdna:SNAP chromosome:CEL140:III:13016547:13023465:1 11/11 None
GENEFINDER00000000294 ENSEMBL cdna:GeneFinder chromosome:CEL140:III:13018503:13023465:1 11/11 None
F14F7.1.2 ENSEMBL cdna:known chromosome:CEL140:III:13018042:13019742:1 gene:F14F7.1 11/11 None
F14F7.1.1 ENSEMBL cdna:known chromosome:CEL140:III:13018451:13019742:1 gene:F14F7.1 11/11 None
F14F7.1.3 ENSEMBL cdna:known chromosome:CEL140:III:13018451:13020147:1 gene:F14F7.1 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
chrIII:13018531-13019629(+) 97.28 100.0
Public Domain and Genome References
Gene Title collagen
Gene Symbol col-98
Ensembl F14F7.1
Entrez Gene 176724 Entrez gene
SwissProt O17805 EMBL-EBI
WormBase CE15821 Wormbase
Functional Annotations
Gene Ontology
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 CAB04112 Hypothetical protein F14F7.2 [Caenorhabditis elegans] ref|NP_499704.1| CYtochrome P450 family member (cyp-13A11) [Caenorhabditis elegans] 0.0
blast CAB04113 Hypothetical protein F14F7.3 [Caenorhabditis elegans] ref|NP_499705.1| CYtochrome P450 family member (cyp-13A12) [Caenorhabditis elegans] 0.0
blast CAE57968 Hypothetical protein CBG01029 [Caenorhabditis briggsae] 0.0
blast CAB04111 Hypothetical protein F14F7.1 [Caenorhabditis elegans] ref|NP_499703.1| F14F7.1 [Caenorhabditis elegans] 3.0E-40
Protein Families
Method ID Description E-Value
p450 CP13_ONCMY Animalia; CYP1A3; tro; CP13_ONCMY; Trout; Q92109 1.0E-139
p450 CP13_ONCMY Animalia; CYP1A3; tro; CP13_ONCMY; Trout; Q92109 1.0E-142
Protein Domains
Database ID Description E-Value
Pfam IPR002486 EMBL-EBI Nematode cuticle collagen, N-terminal 9.6E-9
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 8.9E-4
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 6.7E-5
Pfam IPR001128 EMBL-EBI Cytochrome P450 1.2E-95
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 8.9E-4
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 6.7E-5
Pfam IPR002486 EMBL-EBI Nematode cuticle collagen, N-terminal 9.6E-9
Pfam IPR001128 EMBL-EBI Cytochrome P450 2.1E-95
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 8.9E-4
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 6.7E-5
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_499703.1 1 13-35
F14F7.1.2 1 13-35
F14F7.1.1 1 13-35
F14F7.1.3 1 13-35
GENEFINDER00000000294 1 24-46
Sequence
Target Sequence 
>C. ELEGANS:188356_AT
ggagccccaggagcatggggaatgccaggaaacccaggaaagggaggaagcggaccatgc
cacccggttgtcccaactccatgcaaaccatgcccaggaggacgtccaggaccaccagga
ccaccaggacgcccaggatcggatggacagccaggaagaccagctactggaggaggtgcc
gcaccaagaccaggaccaccaggaccaaagggaccacgtggagccccaggaaactctgga
agagccggagcaccaggacagccaggaaacgatgctcacggatacggaggaggagtcgga
gccccaggaccagccggaccacgcggagccccaggaccagctggacacccaggatcgtcg
ggaggtggccgtccgggaccagccggaccaaagggagccccaggacagccaggaagaccg
ggacccgatggacacccaggacaaccaggacgtccaggacaatccggtggatccggaaat
cgtggagtgt

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GGAGCCCCAGGAGCATGGGGAATGC 484 521 376 Antisense
AAAGGGAGGAAGCGGACCATGCCAC 570 119 414 Antisense
GACGCCCAGGATCGGATGGACAGCC 448 381 503 Antisense
ACAGCCAGGAAGACCAGCTACTGGA 202 109 522 Antisense
GACCAGCTACTGGAGGAGGTGCCGC 370 379 533 Antisense
AGGAGGTGCCGCACCAAGACCAGGA 332 55 546 Antisense
AGGAAACGATGCTCACGGATACGGA 505 55 639 Antisense
ATACGGAGGAGGAGTCGGAGCCCCA 6 7 657 Antisense
TGGACACCCAGGATCGTCGGGAGGT 694 545 717 Antisense
CCAGGATCGTCGGGAGGTGGCCGTC 460 263 724 Antisense
GGTGGATCCGGAAATCGTGGAGTGT 643 499 841 Antisense
Sequence Source Affymetrix Proprietary Database