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[189545_s_at] cuticle collagen

Description F41F3.4 /REP_DB=WormBase Gene ID /WP=CE07218 /TR=Q20282 /GB=AAA97982.1 /SUBMIT=ST.LOUIS /CHR=5 /FEA=Sanger Annotation /DEF=cuticle collagen
Cluster 6grp_total > 94      4grp_total > 59      6grp_cgc > 89      6grp_total_sub > Hat      6grp_rule_based > S5      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 331
1 2 3 4 range
A 99.8
(-2.7)
A 		338.7
(3)
A 		287.2
(1.8)
A 		85.5
(-3)
A 		253
B 123.6
(0.3)
A 		51.2
(-1.7)
A 		215.6
(3)
A 		7.3
(-3)
A 		208
C 139.6
(2.1)
A 		129.7
(1.8)
A 		160.9
(3)
A 		10.7
(-3)
A 		150
avr 121
(-0.2) 		173.2
(1.5) 		221.2
(3) 		34.5
(-3) 		187

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 7219
1 2 3 4 5 6 range
A 109.8
(-3)
A 		93.5
(-3)
A 		74.8
(-3)
A 		405.8
(-2.6)
A 		5133.9
(3)
P 		2719.9
(0.1)
P 		5059
B 115.2
(-3)
A 		122.1
(-3)
A 		95
(-3)
A 		322.6
(-2.7)
A 		5206.8
(3)
P 		2721.5
(0.1)
P 		5112
C 169.3
(-3)
A 		151.6
(-3)
A 		159
(-3)
A 		263.1
(-2.9)
A 		7293.9
(3)
P 		1996.3
(-1.5)
P 		7142
avr 131.4
(-3) 		122.4
(-3) 		109.6
(-3) 		330.5
(-2.8) 		5878.2
(3) 		2479.2
(-0.5) 		5769
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 74
1 2 3 4 range
A 36.3
(-0.7)
A 		73.5
(2.8)
A 		75.1
(3)
A 		12.5
(-3)
A 		63
B 39.4
(1.7)
A 		12.7
(-1.6)
A 		50
(3)
A 		1.6
(-3)
A 		48
C 46.2
(1.9)
A 		37.3
(0.9)
A 		56.1
(3)
A 		1.8
(-3)
A 		54
avr 40.6
(0.8) 		41.2
(0.9) 		60.4
(3) 		5.3
(-3) 		55

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 2344
1 2 3 4 5 6 range
A 20.2
(-3)
A 		33.2
(-2.9)
A 		16.3
(-3)
A 		102.9
(-2.7)
A 		1549.2
(3)
P 		662.2
(-0.5)
P 		1533
B 40.1
(-3)
A 		40.6
(-2.9)
A 		23.1
(-3)
A 		85.5
(-2.8)
A 		2115.5
(3)
P 		1014.8
(-0.2)
P 		2092
C 62.7
(-2.9)
A 		46.3
(-3)
A 		40.5
(-3)
A 		52.9
(-3)
A 		2360.2
(3)
P 		668.3
(-1.4)
P 		2320
avr 41
(-3) 		40
(-3) 		26.6
(-3) 		80.4
(-2.8) 		2008.3
(3) 		781.8
(-0.7) 		1982
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 189545_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.15795
Sequence Type Exemplar sequence
Representative Public ID F41F3.4 NCBI
Target Description F41F3.4 /REP_DB=WormBase Gene ID /WP=CE07218 /TR=Q20282 /GB=AAA97982.1 /SUBMIT=ST.LOUIS /CHR=5 /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_071851(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_071851 NCBI Caenorhabditis elegans COLlagen family member (col-139) (col-139) mRNA, complete cds. 11/11 None
SNAP00000023063 ENSEMBL cdna:SNAP chromosome:CEL140:V:4652724:4653826:-1 11/11 None
GENEFINDER00000023069 ENSEMBL cdna:GeneFinder chromosome:CEL140:V:4652420:4653826:-1 11/11 None
F41F3.4 ENSEMBL cdna:known chromosome:CEL140:V:4652694:4653800:-1 gene:F41F3.4 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
chrV:4652723-4653772(-) 100.0 100.0
Public Domain and Genome References
Gene Title cuticle collagen
Gene Symbol col-139
Ensembl F41F3.4
Entrez Gene 178857 Entrez gene
SwissProt Q20282 EMBL-EBI
WormBase CE07218 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 AAA97982 Collagen protein 139 [Caenorhabditis elegans] ref|NP_504252.1| COLlagen family member (col-139) [Caenorhabditis elegans] 3.0E-42
blast AAA97982 Collagen protein 139 [Caenorhabditis elegans] ref|NP_504252.1| COLlagen family member (col-139) [Caenorhabditis elegans] 4.0E-42
blast CAE64161 Hypothetical protein CBG08781 [Caenorhabditis briggsae] 3.0E-40
blast CAE64161 Hypothetical protein CBG08781 [Caenorhabditis briggsae] 5.0E-39
blast CAB63321 Hypothetical protein W05B2.5 [Caenorhabditis elegans] ref|NP_499409.1| COLlagen family member (col-93) [Caenorhabditis elegans] 1.0E-19
Protein Domains
Database ID Description E-Value
Pfam IPR002486 EMBL-EBI Nematode cuticle collagen, N-terminal 6.0E-7
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 3.2E-8
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 2.2E-10
Pfam IPR002486 EMBL-EBI Nematode cuticle collagen, N-terminal 6.0E-7
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 3.2E-8
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 2.2E-10
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_504252.1 1 12-34
F41F3.4 1 12-34
SNAP00000023063 1 30-52
GENEFINDER00000023069 1 30-52
Sequence
Target Sequence 
>C. ELEGANS:189545_S_AT
aggatcttgccaaggatgctgccttccaggaccaccaggaacccctggaccagctggacg
accaggaaagccaggaagaccaggagcatgcggaaaccacggaaacccaggaaagccaac
cggactaccatgcgatccagtcaccgttccaccatgcaaaccatgcccaccaggaccagc
cggagagccaggacacgatggagctccaggagcaccaggaaagccaggagccccaggagt
cggaggaggatccggagcaccaggagcaccaggaccaaagggagccccaggaggcccagg
acagccaggaagagatggacaaccaggacaagccggtcagccaggatccagctcttctga
gccaggacagccaggaccaaacggacaaccaggaccacgtggaccaccaggacaagctgg
aagcccaggaggcaacggacagccaggaggcccaggacaaccaggacaacgcggaagcga
tggacagccaggaaacgatggacagccaggtgccccagggcagccagggcaaagcggtgg
atccggagaaa

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
AGGATCTTGCCAAGGATGCTGCCTT 405 57 321 Antisense
GGAAGACCAGGAGCATGCGGAAACC 424 531 394 Antisense
GCATGCGGAAACCACGGAAACCCAG 201 311 406 Antisense
CAGGAAAGCCAACCGGACTACCATG 364 153 428 Antisense
ATCCAGCTCTTCTGAGCCAGGACAG 628 37 666 Antisense
GAAGCCCAGGAGGCAACGGACAGCC 205 345 740 Antisense
CCAGGAGGCAACGGACAGCCAGGAG 2 273 745 Antisense
AACGCGGAAGCGATGGACAGCCAGG 461 145 788 Antisense
GCCCCAGGGCAGCCAGGGCAAAGCG 628 285 832 Antisense
GCAGCCAGGGCAAAGCGGTGGATCC 105 313 840 Antisense
GGGCAAAGCGGTGGATCCGGAGAAA 230 493 847 Antisense
Sequence Source Affymetrix Proprietary Database