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[180552_at]

Description T08B2.2 /REP_DB=WormBase Gene ID /WP=CE17221 /TR=Q9GYS2 /GB=AAG00021.1 /SUBMIT=ST.LOUIS /CHR=1 /FEA=Sanger Annotation
Cluster 6grp_total > 92      4grp_total > 18      6grp_cgc > 98      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 28
1 2 3 4 range
A 14.9
(0.1)
A 		11
(-3)
A 		14.2
(-0.5)
A 		18.6
(3)
A 		8
B 9.9
(-3)
A 		23.3
(0.9)
A 		13.3
(-2)
A 		30.3
(3)
A 		20
C 12.8
(-2.4)
A 		14.2
(-2.1)
A 		9.9
(-3)
A 		37.6
(3)
A 		28
avr 12.5
(-3) 		16.2
(-1.6) 		12.5
(-3) 		28.8
(3) 		16

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 22
1 2 3 4 5 6 range
A 13.9
(0.1)
A 		18.5
(3)
A 		12
(-1.1)
A 		15.2
(0.9)
A 		16.5
(1.7)
A 		9.1
(-3)
A 		9
B 9.2
(-2.5)
A 		15.9
(-0.4)
A 		9.1
(-2.5)
A 		9.1
(-2.5)
A 		26.6
(3)
A 		7.5
(-3)
A 		19
C 5
(-3)
A 		14.2
(1.1)
A 		8.1
(-1.6)
A 		15.6
(1.7)
A 		18.6
(3)
A 		7.4
(-1.9)
A 		14
avr 9.4
(-2.3) 		16.2
(0.9) 		9.7
(-2.2) 		13.3
(-0.5) 		20.6
(3) 		8
(-3) 		13
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 4
1 2 3 4 range
A 5.4
(3)
A 		2.4
(-3)
A 		3.7
(-0.4)
A 		2.7
(-2.4)
A 		3
B 3.2
(-2.8)
A 		5.8
(1.8)
A 		3.1
(-3)
A 		6.5
(3)
A 		3
C 4.2
(-1.5)
A 		4.1
(-1.7)
A 		3.5
(-3)
A 		6.3
(3)
A 		3
avr 4.3
(-0) 		4.1
(-0.7) 		3.4
(-3) 		5.2
(3) 		2

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 9
1 2 3 4 5 6 range
A 2.6
(-2.5)
A 		6.6
(3)
A 		2.6
(-2.5)
A 		3.8
(-0.8)
A 		5
(0.8)
A 		2.2
(-3)
A 		4
B 3.2
(-2.3)
A 		5.3
(-0.8)
A 		2.2
(-3)
A 		2.4
(-2.9)
A 		10.8
(3)
A 		2.8
(-2.6)
A 		9
C 1.8
(-3)
A 		4.3
(0.6)
A 		2.1
(-2.6)
A 		3.1
(-1.1)
A 		6
(3)
A 		2.5
(-2)
A 		4
avr 2.5
(-2.8) 		5.4
(0.7) 		2.3
(-3) 		3.1
(-2) 		7.3
(3) 		2.5
(-2.8) 		5
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 180552_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.565
Sequence Type Exemplar sequence
Representative Public ID T08B2.2 NCBI
Target Description T08B2.2 /REP_DB=WormBase Gene ID /WP=CE17221 /TR=Q9GYS2 /GB=AAG00021.1 /SUBMIT=ST.LOUIS /CHR=1 /FEA=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_059399(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_059399 NCBI Caenorhabditis elegans COLlagen family member (col-56) (col-56) mRNA, complete cds. 11/11 None
GENEFINDER00000035014 ENSEMBL cdna:GeneFinder chromosome:CEL140:I:6240912:6242415:1 11/11 None
SNAP00000035009 ENSEMBL cdna:SNAP chromosome:CEL140:I:6241113:6242415:1 11/11 None
T08B2.2 ENSEMBL cdna:known chromosome:CEL140:I:6240912:6242415:1 gene:T08B2.2 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
chrI:6240840-6242344(+) 100.0 100.0
Public Domain and Genome References
Gene Title
Gene Symbol col-56
Ensembl T08B2.2
Entrez Gene 188271 Entrez gene
SwissProt Q9GYS2 EMBL-EBI
WormBase CE17221 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 NP_491800 COLlagen family member (col-56) [Caenorhabditis elegans] gb|AAG00021.1| Collagen protein 56 [Caenorhabditis elegans] 5.0E-74
blast NP_491800 COLlagen family member (col-56) [Caenorhabditis elegans] gb|AAG00021.1| Collagen protein 56 [Caenorhabditis elegans] 5.0E-68
blast CAE67144 Hypothetical protein CBG12567 [Caenorhabditis briggsae] 4.0E-46
blast CAE67144 Hypothetical protein CBG12567 [Caenorhabditis briggsae] 5.0E-46
blast CAE73738 Hypothetical protein CBG21264 [Caenorhabditis briggsae] 9.0E-9
Protein Domains
Database ID Description E-Value
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 2.4E-10
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 3.4E-4
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 2.4E-10
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 3.4E-4
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_491800.1 1 7-29
T08B2.2 1 7-29
GENEFINDER00000035014 1 7-29
Sequence
Target Sequence 
>C. ELEGANS:180552_AT
tggtgaaccgggattcgacgggcttccgggaagagactataattatatggaattaatgac
ggagcactgtattttgtgtcctgctggaccaccaggagatccaggtatggaaggatctga
tggtattccaggaccgccgggcctcattggccccccaggcccgaatggagaatctggagt
aattggatcagttggggctgcaggaagagaaggaactcctgggaaacgaggaataggtgg
tgaagaaggagaacctggtcttattgtaatgaaaatgatgaatacaagaggcccaaaagg
ttctgtaggaccgcgaggtcttactgggcaacctggaatgcctggaagaacagtcaatgc
accacctggatcgccaggtatcagaggacgtcctggtatgcctggtgcaagtggaaggtc
aggaatcattggaaagagaggaatccacggagagcctggactcgacgcatcatattgtcc
ctgcccacgccgatcgtatcaaatgcag

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
TGGTGAACCGGGATTCGACGGGCTT 58 545 351 Antisense
CGGAGCACTGTATTTTGTGTCCTGC 470 243 410 Antisense
ATCTGATGGTATTCCAGGACCGCCG 310 29 465 Antisense
CCCCCAGGCCCGAATGGAGAATCTG 291 261 502 Antisense
AGGACCGCGAGGTCTTACTGGGCAA 530 55 657 Antisense
GAACAGTCAATGCACCACCTGGATC 315 349 698 Antisense
GATCGCCAGGTATCAGAGGACGTCC 203 415 719 Antisense
GTCCTGGTATGCCTGGTGCAAGTGG 67 477 740 Antisense
AGGAATCCACGGAGAGCCTGGACTC 228 55 789 Antisense
GGACTCGACGCATCATATTGTCCCT 250 525 808 Antisense
CCCACGCCGATCGTATCAAATGCAG 13 259 834 Antisense
Sequence Source Affymetrix Proprietary Database