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[190142_s_at] collagen

Description C15A11.1 /REP_DB=WormBase Gene ID /WP=CE08169 /GEN=col-35 /TR=Q93208 /GB=CAB01959.1 /SUBMIT=HINXTON /CHR=1 /FEA=Sanger Annotation /DEF=collagen
Cluster 6grp_total > 93      4grp_total > 48      6grp_cgc > 87      6grp_cgc_sub > 05      6grp_total_sub > Hat      6grp_rule_based > S5      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 51
1 2 3 4 range
A 5.9
(-2.3)
A 		5.3
(-2.5)
A 		28.1
(3)
A 		3.2
(-3)
A 		25
B 5.5
(-3)
A 		36.3
(0.8)
A 		54.4
(3)
A 		22.5
(-0.9)
A 		49
C 8.6
(-0.4)
A 		5.5
(-2.4)
A 		13.8
(3)
A 		4.5
(-3)
A 		9
avr 6.7
(-3) 		15.7
(-0.9) 		32.1
(3) 		10.1
(-2.2) 		25

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 5455
1 2 3 4 5 6 range
A 4
(-3)
A 		10.4
(-3)
A 		7.7
(-3)
A 		3719.4
(2.6)
P 		3973.3
(3)
P 		727.6
(-1.9)
P 		3969
B 4.4
(-3)
A 		12.3
(-3)
A 		3.4
(-3)
A 		2544.7
(0.5)
P 		4320.4
(3)
P 		653
(-2.1)
P 		4317
C 24.4
(-3)
A 		9.2
(-3)
A 		65.1
(-2.9)
A 		2553.9
(-0.2)
P 		5458
(3)
P 		585.8
(-2.4)
P 		5449
avr 10.9
(-3) 		10.6
(-3) 		25.4
(-3) 		2939.3
(0.8) 		4583.9
(3) 		655.5
(-2.2) 		4573
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 12
1 2 3 4 range
A 2.1
(-1.6)
A 		1.2
(-2.4)
A 		7.4
(3)
A 		0.5
(-3)
A 		7
B 1.7
(-3)
A 		9
(1)
A 		12.6
(3)
A 		4.8
(-1.3)
A 		11
C 2.9
(0.1)
A 		1.6
(-1.8)
A 		4.8
(3)
A 		0.8
(-3)
A 		4
avr 2.2
(-2.8) 		3.9
(-1.2) 		8.3
(3) 		2
(-3) 		6

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 1765
1 2 3 4 5 6 range
A 0.7
(-3)
A 		3.7
(-3)
A 		1.7
(-3)
A 		943.3
(1.7)
P 		1199
(3)
P 		177.1
(-2.1)
P 		1198
B 1.5
(-3)
A 		4.1
(-3)
A 		0.8
(-3)
A 		674
(-0.7)
P 		1755.3
(3)
P 		243.5
(-2.2)
P 		1755
C 9
(-3)
A 		2.8
(-3)
A 		16.6
(-3)
A 		513.6
(-1.3)
P 		1766.1
(3)
P 		196.1
(-2.3)
P 		1763
avr 3.7
(-3) 		3.5
(-3) 		6.4
(-3) 		710.3
(-0.3) 		1573.5
(3) 		205.6
(-2.2) 		1570
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 190142_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.791
Sequence Type Exemplar sequence
Representative Public ID C15A11.1 NCBI
Target Description C15A11.1 /REP_DB=WormBase Gene ID /WP=CE08169 /GEN=col-35 /TR=Q93208 /GB=CAB01959.1 /SUBMIT=HINXTON /CHR=1 /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_059685(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_059685 NCBI Caenorhabditis elegans C15A11.1 (collagen) mRNA, complete cds. 11/11 None
SNAP00000007964 ENSEMBL cdna:SNAP chromosome:CEL140:I:7394036:7395064:-1 11/11 None
GENEFINDER00000007975 ENSEMBL cdna:GeneFinder chromosome:CEL140:I:7394036:7395160:-1 11/11 None
C15A11.1 ENSEMBL cdna:known chromosome:CEL140:I:7394036:7394947:-1 gene:C15A11.1 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
chrI:7393966-7394878(-) 100.0 100.0
Public Domain and Genome References
Gene Title collagen
Gene Symbol col-35
Ensembl C15A11.1
Entrez Gene 172492 Entrez gene
SwissProt Q93208 EMBL-EBI
WormBase CE08169 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 CAE66597 Hypothetical protein CBG11921 [Caenorhabditis briggsae] 2.0E-43
blast CAB01959 Hypothetical protein C15A11.1 [Caenorhabditis elegans] ref|NP_492086.1| C15A11.1 [Caenorhabditis elegans] 4.0E-43
blast CAB01959 Hypothetical protein C15A11.1 [Caenorhabditis elegans] ref|NP_492086.1| C15A11.1 [Caenorhabditis elegans] 5.0E-43
blast CAE66597 Hypothetical protein CBG11921 [Caenorhabditis briggsae] 3.0E-22
blast CAE66648 Hypothetical protein CBG11985 [Caenorhabditis briggsae] 2.0E-13
blast CAE66648 Hypothetical protein CBG11985 [Caenorhabditis briggsae] 3.0E-13
Protein Domains
Database ID Description E-Value
Pfam IPR002486 EMBL-EBI Nematode cuticle collagen, N-terminal 2.1E-11
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 3.6E-5
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 1.7E-9
Pfam IPR002486 EMBL-EBI Nematode cuticle collagen, N-terminal 2.1E-11
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 3.6E-5
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 1.7E-9
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 3.6E-5
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 1.7E-9
Trans Membrane
ID Number Of Domains Domain Boundaries
SNAP00000007964 1 7-29
GENEFINDER00000007975 1 41-63
Sequence
Target Sequence 
>C. ELEGANS:190142_S_AT
gttgctgatagtttccttggagtcgaaggtaactgtatcaaatgtcctgctggaccacca
gggccaccgggaccagatggaaatgctggaccagaaggaccatcaggagctcctggagct
gatggagatgctgctggaccaggagaagctggaccagcaggaccagccggaccaccgggg
ccagatgggcagccaggagcaccaggaccaaatggacaaccaggagccgcaggaactaca
agtaccaacgaaccgggatctcctggaccggctggacctccaggaccagctggaccagct
ggagaagacgctgctgctccagaatccccaccaggaccaccggggccaccgggcccacca
ggaaaagacggagaagcaggagctccaggagcgccaggagggccaggaacagatggagca
ccaggagtcgacgccgcctattgtccatgcccaccaagaacagcaggattggcccaagaa
gctccagcaggtgctgctacaggtgcggatgcaagctctggagctgccggtggtgcaccg
gatgcaggagctggagct

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GTTGCTGATAGTTTCCTTGGAGTCG 399 439 304 Antisense
TAACTGTATCAAATGTCCTGCTGGA 386 639 333 Antisense
GGAGCCGCAGGAACTACAAGTACCA 709 521 526 Antisense
TACCAACGAACCGGGATCTCCTGGA 153 651 546 Antisense
AGCTGGAGAAGACGCTGCTGCTCCA 206 81 600 Antisense
GAGGGCCAGGAACAGATGGAGCACC 265 401 701 Antisense
CAGGATTGGCCCAAGAAGCTCCAGC 330 209 767 Antisense
AGCAGGTGCTGCTACAGGTGCGGAT 294 77 789 Antisense
AGGTGCGGATGCAAGCTCTGGAGCT 59 59 804 Antisense
GGAGCTGCCGGTGGTGCACCGGATG 118 521 823 Antisense
TGCACCGGATGCAGGAGCTGGAGCT 538 577 837 Antisense
Sequence Source Affymetrix Proprietary Database