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[188485_at] collagen

Description W07A12.5 /REP_DB=WormBase Gene ID /WP=CE03796 /TR=Q9U336 /GB=CAB63328.1 /SUBMIT=HINXTON /CHR=2 /FEA=Sanger Annotation /DEF=collagen
Cluster 6grp_total > 10      4grp_total > 02      6grp_cgc > 64      6grp_total_sub > Hat      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 117
1 2 3 4 range
A 11.8
(-2.8)
A 		8.1
(-3)
A 		13
(-2.7)
A 		124.6
(3)
A 		117
B 14.2
(-1.8)
A 		13.5
(-2.4)
A 		20.1
(3)
A 		12.7
(-3)
A 		7
C 13.9
(3)
A 		11.4
(-1.5)
A 		10.6
(-3)
A 		12.4
(0.3)
A 		3
avr 13.3
(-2.6) 		11
(-3) 		14.6
(-2.4) 		49.9
(3) 		39

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 59
1 2 3 4 5 6 range
A 21.7
(-1.4)
A 		48.1
(1.3)
A 		5.8
(-3)
A 		7
(-2.9)
A 		64.4
(3)
A 		7.2
(-2.9)
A 		59
B 12.7
(-2.2)
A 		29.2
(-0.3)
A 		56.5
(3)
A 		17.3
(-1.7)
A 		13.3
(-2.2)
A 		6.4
(-3)
A 		50
C 13.3
(-3)
A 		32.8
(1.9)
A 		25.9
(0.2)
A 		37.3
(3)
A 		15.8
(-2.4)
A 		20.6
(-1.2)
A 		24
avr 15.9
(-1.9) 		36.7
(3) 		29.4
(1.3) 		20.5
(-0.8) 		31.2
(1.7) 		11.4
(-3) 		25
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 17
1 2 3 4 range
A 4.3
(-2.1)
A 		1.7
(-3)
A 		3.4
(-2.4)
A 		18.2
(3)
A 		17
B 4.5
(2.4)
A 		3.3
(-1.2)
A 		4.7
(3)
A 		2.7
(-3)
A 		2
C 4.6
(3)
A 		3.3
(-0.1)
A 		3.7
(0.8)
A 		2.1
(-3)
A 		3
avr 4.5
(-0.9) 		2.8
(-3) 		3.9
(-1.7) 		7.7
(3) 		5

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 18
1 2 3 4 5 6 range
A 4
(-2.1)
A 		17.1
(2.2)
A 		1.3
(-3)
A 		1.8
(-2.8)
A 		19.4
(3)
A 		1.8
(-2.8)
A 		18
B 4.4
(-1.9)
A 		9.7
(0.9)
A 		13.7
(3)
A 		4.6
(-1.8)
A 		5.4
(-1.4)
A 		2.4
(-3)
A 		11
C 4.9
(-3)
A 		10
(3)
A 		6.6
(-1)
A 		7.5
(0.1)
A 		5.1
(-2.8)
A 		6.9
(-0.6)
A 		5
avr 4.4
(-2.5) 		12.3
(3) 		7.2
(-0.6) 		4.6
(-2.4) 		10
(1.4) 		3.7
(-3) 		9
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 188485_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.3465
Sequence Type Exemplar sequence
Representative Public ID W07A12.5 NCBI
Target Description W07A12.5 /REP_DB=WormBase Gene ID /WP=CE03796 /TR=Q9U336 /GB=CAB63328.1 /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_063551(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_063551 NCBI Caenorhabditis elegans W07A12.5 (collagen) mRNA, complete cds. 11/11 None
SNAP00000000167 ENSEMBL cdna:SNAP chromosome:CEL140:II:9152721:9154220:1 11/11 None
GENEFINDER00000000171 ENSEMBL cdna:GeneFinder chromosome:CEL140:II:9152441:9154220:1 11/11 None
W07A12.5 ENSEMBL cdna:known chromosome:CEL140:II:9152441:9154220:1 gene:W07A12.5 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:9152437-9154217(+) 100.0 100.0
Public Domain and Genome References
Gene Title collagen
Gene Symbol col-78
Ensembl W07A12.5
Entrez Gene 189274 Entrez gene
SwissProt Q9U336 EMBL-EBI
WormBase CE37854 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
Protein Similarities
Method ID Description E-Value
blast CAB63328 Hypothetical protein W07A12.5 [Caenorhabditis elegans] ref|NP_495952.2| W07A12.5 [Caenorhabditis elegans] 2.0E-94
blast CAB63328 Hypothetical protein W07A12.5 [Caenorhabditis elegans] ref|NP_495952.2| W07A12.5 [Caenorhabditis elegans] 3.0E-87
blast CAB63328 Hypothetical protein W07A12.5 [Caenorhabditis elegans] ref|NP_495952.2| W07A12.5 [Caenorhabditis elegans] 1.0E-77
blast CAE57699 Hypothetical protein CBG00703 [Caenorhabditis briggsae] 6.0E-24
blast CAE57699 Hypothetical protein CBG00703 [Caenorhabditis briggsae] 2.0E-23
blast CAE57699 Hypothetical protein CBG00703 [Caenorhabditis briggsae] 5.0E-23
blast CAA91290 Hypothetical protein M195.1 [Caenorhabditis elegans] ref|NP_495759.1| COLlagen family member (col-77) [Caenorhabditis elegans] 3.0E-22
blast CAA91290 Hypothetical protein M195.1 [Caenorhabditis elegans] ref|NP_495759.1| COLlagen family member (col-77) [Caenorhabditis elegans] 8.0E-22
Protein Domains
Database ID Description E-Value
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 3.1E-4
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 0.0013
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 2.7E-9
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 3.1E-4
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 0.0013
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 2.7E-9
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 3.1E-4
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 0.0013
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 2.7E-9
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_495952.2 1 25-47
W07A12.5 1 25-47
GENEFINDER00000000171 1 25-47
Sequence
Target Sequence 
>C. ELEGANS:188485_AT
aaccgctgctccggatgtttcaaaatgttgtacatgttcacaaggaccatctggagagaa
gggtgataagggaagtgatggaagagacgggaacgatggttatccgggatcacctggaaa
atctggtcaagatgcacttgaacgcatgataacggatggatatatagatttttgctttga
atgtccaccgggcgcacctggaagtcctggagaagtaggtcacaaagggccggaaggtgt
attgggaccatcaggaaagaaaggaaaaacagggcaaagtcttccaggaccagtggggcc
accaggacctcctggcaaagatggttcaatcggtgctccaggtcctgatggtgcatctgg
aaaaattctaacgatggaagggcctcctggtttacccggtgtacccggctctgttggttt
acctggtattccaggaaaacctggcccttctggaccagatgggaaaattggagcaactgg
tcccggtggagatcctggaaaacctggaggaaatggaatccccggagaacccggacctat
tggaaatca

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
AACCGCTGCTCCGGATGTTTCAAAA 363 147 384 Antisense
GGAACGATGGTTATCCGGGATCACC 626 529 473 Antisense
GATTTTTGCTTTGAATGTCCACCGG 461 427 550 Antisense
GGCAAAGTCTTCCAGGACCAGTGGG 32 535 656 Antisense
AGATGGTTCAATCGGTGCTCCAGGT 40 67 702 Antisense
GTGCTCCAGGTCCTGATGGTGCATC 99 479 716 Antisense
TAACGATGGAAGGGCCTCCTGGTTT 248 637 752 Antisense
GGCTCTGTTGGTTTACCTGGTATTC 194 539 790 Antisense
CCTGGCCCTTCTGGACCAGATGGGA 513 265 823 Antisense
TGGTCCCGGTGGAGATCCTGGAAAA 576 187 861 Antisense
GAGAACCCGGACCTATTGGAAATCA 178 391 908 Antisense
Sequence Source Affymetrix Proprietary Database