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[188281_s_at] collagen

Description F38A3.1 /REP_DB=WormBase Gene ID /WP=CE02213 /TR=Q20135 /GB=CAA90187.1 /SUBMIT=HINXTON /CHR=2 /FEA=Sanger Annotation /DEF=collagen
Cluster 6grp_total > 94      4grp_total > 58      6grp_cgc > 89      6grp_total_sub > Hat      6grp_rule_based > S5      4grp_rule_based > L2      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 187
1 2 3 4 range
A 61.3
(-1.2)
A 		165.6
(3)
A 		145.6
(2.2)
P 		16.4
(-3)
A 		149
B 62.7
(-1.1)
A 		190
(3)
P 		141
(1.4)
A 		2.9
(-3)
A 		187
C 86.4
(0.5)
A 		134.4
(2.5)
A 		145.6
(3)
P 		6.1
(-3)
A 		140
avr 70.1
(-0.6) 		163.3
(3) 		144.1
(2.3) 		8.5
(-3) 		155

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 5606
1 2 3 4 5 6 range
A 62
(-3)
A 		86.6
(-3)
A 		83.4
(-3)
M 		361.5
(-2.5)
P 		3648.6
(3)
P 		1907.5
(0.1)
P 		3587
B 89.2
(-3)
A 		91.3
(-3)
A 		99.3
(-3)
P 		299.4
(-2.6)
P 		3610.3
(3)
P 		1655.3
(-0.3)
P 		3521
C 91
(-3)
A 		102.5
(-3)
A 		140.5
(-2.9)
P 		277.8
(-2.8)
P 		5667.5
(3)
P 		1304.5
(-1.7)
P 		5577
avr 80.7
(-3) 		93.5
(-3) 		107.7
(-3) 		312.9
(-2.7) 		4308.8
(3) 		1622.4
(-0.8) 		4228
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 50
1 2 3 4 range
A 22.3
(0.3)
A 		35.9
(2.6)
A 		38.1
(3)
P 		2.4
(-3)
A 		36
B 20
(-0.5)
A 		46.9
(3)
P 		32.7
(1.2)
A 		0.6
(-3)
A 		46
C 28.6
(0.3)
A 		38.6
(1.5)
A 		50.7
(3)
P 		1
(-3)
A 		50
avr 23.6
(0.4) 		40.5
(3) 		40.5
(3) 		1.3
(-3) 		39

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 1823
1 2 3 4 5 6 range
A 11.4
(-3)
A 		30.8
(-2.9)
A 		18.2
(-3)
M 		91.7
(-2.6)
P 		1101
(3)
P 		464.4
(-0.5)
P 		1090
B 31
(-3)
A 		30.4
(-3)
A 		24.1
(-3)
P 		79.3
(-2.8)
P 		1466.8
(3)
P 		617.3
(-0.5)
P 		1443
C 33.7
(-3)
A 		31.3
(-3)
A 		35.8
(-3)
P 		55.9
(-2.9)
P 		1833.9
(3)
P 		436.7
(-1.7)
P 		1803
avr 25.4
(-3) 		30.8
(-3) 		26
(-3) 		75.6
(-2.8) 		1467.2
(3) 		506.1
(-1) 		1442
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 188281_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.3997
Sequence Type Exemplar sequence
Representative Public ID F38A3.1 NCBI
Target Description F38A3.1 /REP_DB=WormBase Gene ID /WP=CE02213 /TR=Q20135 /GB=CAA90187.1 /SUBMIT=HINXTON /CHR=2 /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_063960(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_063960 NCBI Caenorhabditis elegans F38A3.1 (collagen) mRNA, complete cds. 11/11 None
SNAP00000020588 ENSEMBL cdna:SNAP chromosome:CEL140:II:11012406:11013672:-1 11/11 None
GENEFINDER00000020591 ENSEMBL cdna:GeneFinder chromosome:CEL140:II:11012406:11013672:-1 11/11 None
F38A3.1 ENSEMBL cdna:known chromosome:CEL140:II:11012307:11013691:-1 gene:F38A3.1 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
chrII:11012402-11013669(-) 90.55 100.0
Public Domain and Genome References
Gene Title collagen
Gene Symbol col-81
Ensembl F38A3.1
Entrez Gene 174686 Entrez gene
SwissProt Q20135 EMBL-EBI
WormBase CE02213 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 CAA90187 Hypothetical protein F38A3.1 [Caenorhabditis elegans] ref|NP_496361.1| F38A3.1 [Caenorhabditis elegans] 1.0E-58
blast CAE59587 Hypothetical protein CBG02988 [Caenorhabditis briggsae] 1.0E-55
blast CAE59586 Hypothetical protein CBG02987 [Caenorhabditis briggsae] 4.0E-17
Protein Domains
Database ID Description E-Value
Pfam IPR002486 EMBL-EBI Nematode cuticle collagen, N-terminal 6.1E-5
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 1.7E-4
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 5.5E-10
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 1.5E-11
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_496361.1 1 20-42
F38A3.1 1 20-42
SNAP00000020588 1 20-42
GENEFINDER00000020591 1 20-42
Sequence
Target Sequence 
>C. ELEGANS:188281_S_AT
gaagacgtcaagccgagtgctgctcatgcggagttggagccgctggaccacaaggaccac
caggacgtccaggaaatgacggaaacgatggacaatctggaaacccaggatccccaggac
aagatggatccgacagctacgagcaccaacaaaacagagaattctgcttcgaatgcgccg
acgctccagctggaccaccaggagctccaggacaggccggagccccaggaaacgatggac
gaccaggacaaagcggaggagctgctattccaggaccaccaggaccaccaggaccatcag
gacaaccaggacaagatggacatccaggacaagacggacagccaggacagccaggagaga
gccgcgaagttccaggagccccaggaccagctggacaaccaggatcccaaggagagccag
gaccatccggaccagacggaagaccaggacaaccaggacaagccggacagccaggaggtc
caggagacgccggaaatgacggacaaccaggacaaccaggaggtccaggagaggacggag
aagatggagattctggatcatccggatcttgcgatcac

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GAAGACGTCAAGCCGAGTGCTGCTC 427 339 323 Antisense
TCAAGCCGAGTGCTGCTCATGCGGA 560 631 330 Antisense
GCTCATGCGGAGTTGGAGCCGCTGG 540 299 344 Antisense
AGATGGATCCGACAGCTACGAGCAC 423 65 444 Antisense
ACAGCTACGAGCACCAACAAAACAG 548 107 455 Antisense
AGAGAATTCTGCTTCGAATGCGCCG 643 67 478 Antisense
TGGACGACCAGGACAAAGCGGAGGA 537 547 558 Antisense
AAAGCGGAGGAGCTGCTATTCCAGG 416 123 572 Antisense
GACAGCCAGGAGAGAGCCGCGAAGT 173 369 668 Antisense
AGGAGGTCCAGGAGACGCCGGAAAT 57 1 795 Antisense
TGGATCATCCGGATCTTGCGATCAC 688 549 876 Antisense
Sequence Source Affymetrix Proprietary Database