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[189968_s_at] collagen

Description F54C9.4 /REP_DB=WormBase Gene ID /WP=CE20864 /GEN=col-38 /TR=Q20754 /GB=CAA90250.1 /SUBMIT=HINXTON /CHR=2 /FEA=Sanger Annotation /DEF=collagen
Cluster 6grp_total > 94      4grp_total > 49      6grp_cgc > 88      6grp_total_sub > Hat      6grp_rule_based > S5      4grp_rule_based > L3      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 154
1 2 3 4 range
A 12.7
(-3)
A 		166.6
(3)
A 		166.8
(3)
A 		52.7
(-1.4)
A 		154
B 59.4
(-3)
A 		146.9
(2.2)
A 		159.7
(3)
A 		59.7
(-3)
A 		100
C 56.1
(-1.5)
A 		133.3
(1.7)
A 		163.2
(3)
A 		20.1
(-3)
A 		143
avr 42.7
(-3) 		148.9
(2.3) 		163.2
(3) 		44.2
(-2.9) 		121

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 5974
1 2 3 4 5 6 range
A 25.9
(-3)
A 		58.1
(-3)
A 		100.6
(-2.9)
A 		1948.3
(-0.6)
P 		4914.8
(3)
P 		2774.4
(0.4)
P 		4889
B 43.7
(-3)
A 		141.3
(-2.9)
A 		95
(-2.9)
A 		1662.5
(-1.2)
P 		5415.2
(3)
P 		2938.3
(0.2)
P 		5372
C 3.9
(-3)
A 		134.8
(-2.9)
A 		121.1
(-2.9)
A 		1556.3
(-1.4)
P 		5977.6
(3)
P 		2732.6
(-0.3)
P 		5974
avr 24.5
(-3) 		111.4
(-2.9) 		105.6
(-2.9) 		1722.4
(-1.1) 		5435.9
(3) 		2815.1
(0.1) 		5411
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 54
1 2 3 4 range
A 4.6
(-3)
A 		36.2
(1.9)
A 		43.6
(3)
A 		7.7
(-2.5)
A 		39
B 19
(-1.4)
A 		36.3
(2.8)
A 		37
(3)
A 		12.7
(-3)
A 		24
C 18.6
(-1.3)
A 		38.3
(0.9)
A 		56.9
(3)
A 		3.4
(-3)
A 		54
avr 14.1
(-2) 		36.9
(1.6) 		45.8
(3) 		7.9
(-3) 		38

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 2199
1 2 3 4 5 6 range
A 4.8
(-3)
A 		20.7
(-2.9)
A 		21.9
(-2.9)
A 		494.1
(-1)
P 		1483.1
(3)
P 		675.5
(-0.3)
P 		1478
B 15.2
(-3)
A 		47
(-2.9)
A 		23.1
(-3)
A 		440.3
(-1.8)
P 		2200.1
(3)
P 		1095.7
(-0)
P 		2185
C 1.5
(-3)
A 		41.1
(-2.9)
A 		30.8
(-2.9)
A 		313
(-2)
P 		1934.3
(3)
P 		914.7
(-0.2)
P 		1933
avr 7.2
(-3) 		36.3
(-2.9) 		25.3
(-2.9) 		415.8
(-1.7) 		1872.5
(3) 		895.3
(-0.1) 		1865
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 189968_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.3464
Sequence Type Exemplar sequence
Representative Public ID F54C9.4 NCBI
Target Description F54C9.4 /REP_DB=WormBase Gene ID /WP=CE20864 /GEN=col-38 /TR=Q20754 /GB=CAA90250.1 /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_063409(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_063409 NCBI Caenorhabditis elegans F54C9.4 (collagen) mRNA, complete cds. 11/11 None
SNAP00000013421 ENSEMBL cdna:SNAP chromosome:CEL140:II:8568000:8568991:-1 11/11 None
GENEFINDER00000013453 ENSEMBL cdna:GeneFinder chromosome:CEL140:II:8567686:8568991:-1 11/11 None
F54C9.4 ENSEMBL cdna:known chromosome:CEL140:II:8567973:8568991:-1 gene:F54C9.4 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
chrII:8567996-8568988(-) 96.41 100.0
Public Domain and Genome References
Gene Title collagen
Gene Symbol col-38
Ensembl F54C9.4
Entrez Gene 174370 Entrez gene
SwissProt Q20754 EMBL-EBI
WormBase CE20864 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 CAA90250 Hypothetical protein F54C9.4 [Caenorhabditis elegans] ref|NP_495810.1| F54C9.4 [Caenorhabditis elegans] 8.0E-91
blast CAA90250 Hypothetical protein F54C9.4 [Caenorhabditis elegans] ref|NP_495810.1| F54C9.4 [Caenorhabditis elegans] 1.0E-88
blast CAE57583 Hypothetical protein CBG00562 [Caenorhabditis briggsae] 2.0E-81
blast CAE57583 Hypothetical protein CBG00562 [Caenorhabditis briggsae] 3.0E-79
blast CAE66911 Hypothetical protein CBG12296 [Caenorhabditis briggsae] 3.0E-32
Protein Domains
Database ID Description E-Value
Pfam IPR002486 EMBL-EBI Nematode cuticle collagen, N-terminal 1.1E-20
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 1.0E-11
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 3.2E-11
Pfam IPR002486 EMBL-EBI Nematode cuticle collagen, N-terminal 1.6E-15
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 1.0E-11
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 3.2E-11
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_495810.1 1 7-29
F54C9.4 1 7-29
SNAP00000013421 1 7-29
GENEFINDER00000013453 1 7-29
Sequence
Target Sequence 
>C. ELEGANS:189968_S_AT
aacaagcgttctgcttatccatctcaatgtaattgtgatgccaactctcaaggatgccca
ccaggaccaccaggaccaccaggacttccaggaggacgtggagatcaaggaccatctgga
gataagggacgtgatggagcttctggagtatctctggctgttacccatcatcttccagga
ggatgcattcaatgcccacaaggaccaccaggagaaactggaccagacggagatattgga
gagccaggattcccaggagcatctggatctgcaggacaatgtggagaagatggagctcca
ggagaggccggaatcactggagaacaaggaccacaaggagagccaggaactgaaggatct
gaaggaccaactggacaagatggaactattggaggaccaggacttccaggacaaccagga
actccaggatggccaggatctcaaggagaaccaggaaagaacggagattctggagttgat
ggagagcaaggaccacaaggaccacagggaccagatggacaaccaggacgtgatgctgat
aatggacaaccaggattgccaggaaaggatggatctattggaccagatgctaactattg

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
AACAAGCGTTCTGCTTATCCATCTC 438 133 247 Antisense
AAGGGACGTGATGGAGCTTCTGGAG 456 159 370 Antisense
TGGAGTATCTCTGGCTGTTACCCAT 327 549 390 Antisense
GATATTGGAGAGCCAGGATTCCCAG 164 427 478 Antisense
GAGCATCTGGATCTGCAGGACAATG 638 387 503 Antisense
AGGAGAGGCCGGAATCACTGGAGAA 64 57 546 Antisense
CCAGGAACTCCAGGATGGCCAGGAT 292 271 661 Antisense
GGATGGCCAGGATCTCAAGGAGAAC 615 513 673 Antisense
ACCACAGGGACCAGATGGACAACCA 284 85 747 Antisense
GACAACCAGGACGTGATGCTGATAA 445 365 764 Antisense
CTATTGGACCAGATGCTAACTATTG 672 223 821 Antisense
Sequence Source Affymetrix Proprietary Database