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[188456_at] collagen

Description T15B7.3 /REP_DB=WormBase Gene ID /WP=CE13652 /TR=O17038 /GB=AAB69959.1 /SUBMIT=ST.LOUIS /CHR=5 /FEA=Sanger Annotation /DEF=collagen
Cluster 6grp_total > 93      4grp_total > 49      6grp_cgc > 99      6grp_total_sub > Hat      6grp_rule_based > S5      4grp_rule_based > L2      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 19
1 2 3 4 range
A 5.1
(-3)
A 		21.6
(3)
A 		15.4
(0.7)
A 		6.4
(-2.5)
A 		17
B 3.9
(-2.8)
A 		13.7
(0.9)
A 		19.1
(3)
A 		3.4
(-3)
A 		16
C 2.9
(-3)
A 		18.4
(3)
A 		14
(1.3)
A 		5.8
(-1.9)
A 		16
avr 4
(-3) 		17.9
(3) 		16.2
(2.3) 		5.2
(-2.5) 		14

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 2499
1 2 3 4 5 6 range
A 4.8
(-3)
A 		16
(-2.9)
A 		14.2
(-3)
A 		4.7
(-3)
A 		1294.1
(3)
P 		165.8
(-2.3)
A 		1289
B 6.1
(-3)
A 		12.4
(-3)
A 		17
(-3)
A 		21.9
(-2.9)
A 		1629.3
(3)
P 		166.8
(-2.4)
A 		1623
C 11.8
(-3)
A 		8.5
(-3)
A 		4.6
(-3)
A 		10.5
(-3)
A 		2503.5
(3)
P 		71.2
(-2.8)
A 		2499
avr 7.6
(-3) 		12.3
(-3) 		11.9
(-3) 		12.4
(-3) 		1809
(3) 		134.6
(-2.6) 		1801
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 5
1 2 3 4 range
A 1.8
(-1.6)
A 		4.7
(3)
A 		4
(1.9)
A 		0.9
(-3)
A 		4
B 1.2
(-2.2)
A 		3.4
(1.4)
A 		4.4
(3)
A 		0.7
(-3)
A 		4
C 1
(-3)
A 		5.3
(3)
A 		4.9
(2.4)
A 		1
(-3)
A 		4
avr 1.3
(-2.3) 		4.5
(3) 		4.4
(2.8) 		0.9
(-3) 		4

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 809
1 2 3 4 5 6 range
A 0.9
(-3)
A 		5.7
(-2.9)
A 		3.1
(-3)
A 		1.2
(-3)
A 		390.5
(3)
P 		40.4
(-2.4)
A 		390
B 2.1
(-3)
A 		4.1
(-3)
A 		4.1
(-3)
A 		5.8
(-3)
A 		661.9
(3)
P 		62.2
(-2.5)
A 		660
C 4.4
(-3)
A 		2.6
(-3)
A 		1.2
(-3)
A 		2.1
(-3)
A 		810.1
(3)
P 		23.8
(-2.8)
A 		809
avr 2.5
(-3) 		4.1
(-3) 		2.8
(-3) 		3
(-3) 		620.8
(3) 		42.1
(-2.6) 		618
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 188456_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.11566
Sequence Type Exemplar sequence
Representative Public ID T15B7.3 NCBI
Target Description T15B7.3 /REP_DB=WormBase Gene ID /WP=CE13652 /TR=O17038 /GB=AAB69959.1 /SUBMIT=ST.LOUIS /CHR=5 /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_072337(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_072337 NCBI Caenorhabditis elegans T15B7.3 (collagen) mRNA, complete cds. 11/11 None
SNAP00000035390 ENSEMBL cdna:SNAP chromosome:CEL140:V:6838248:6839257:1 11/11 None
GENEFINDER00000035407 ENSEMBL cdna:GeneFinder chromosome:CEL140:V:6838248:6839257:1 11/11 None
T15B7.3 ENSEMBL cdna:known chromosome:CEL140:V:6838248:6839293:1 gene:T15B7.3 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
chrV:6838248-6839258(+) 96.88 100.0
Public Domain and Genome References
Gene Title collagen
Gene Symbol col-143
Ensembl T15B7.3
Entrez Gene 179073 Entrez gene
SwissProt O17038 EMBL-EBI
WormBase CE13652 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 AAB69959 Collagen protein 143 [Caenorhabditis elegans] ref|NP_504738.1| T15B7.3 [Caenorhabditis elegans] 2.0E-47
blast CAE71959 Hypothetical protein CBG19029 [Caenorhabditis briggsae] 2.0E-45
blast AAB69961 Collagen protein 142 [Caenorhabditis elegans] ref|NP_504736.1| T15B7.4 [Caenorhabditis elegans] 4.0E-45
Protein Domains
Database ID Description E-Value
Pfam IPR002486 EMBL-EBI Nematode cuticle collagen, N-terminal 8.0E-28
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 6.4E-4
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 8.8E-9
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 2.6E-10
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_504738.1 1 7-29
T15B7.3 1 7-29
SNAP00000035390 1 7-29
GENEFINDER00000035407 1 7-29
Sequence
Target Sequence 
>C. ELEGANS:188456_AT
ggagcaagaattaacccagctacgggaagaccaggattctgtatcacttgcccagcagga
gcaccaggaccagctggaccaccaggagccccaggaccaaagggaaacaacggacaacca
ggagccccagctcaatcaggtggacgtggaccaccaggaccacgcggaccagccggagat
gccggatcaccaggacagccaggacatccaggatctccaggaaatccaggtcgtggagga
caacgcagccgtggaactccaggagcatccggaagaccaggaccacagggaccagctgga
gccccaggacagccaggacgttctggaggagctggaactccaggacctcaaggaccacca
ggaccatccggacaaccaggacattctggaaacgacggagttccaggaaccccaggaaac
ccaggagccccaggaggagatgctgcctactgcccatgcccagcccgttcttctgtcatg
gccgtcaaccgccgcgtcgctgtcaatcgaaatgttgcccgcaaccgtgttgttg

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GGAGCAAGAATTAACCCAGCTACGG 63 519 364 Antisense
TTAACCCAGCTACGGGAAGACCAGG 569 555 374 Antisense
CAGCTCAATCAGGTGGACGTGGACC 302 203 491 Antisense
CAGGAAATCCAGGTCGTGGAGGACA 348 207 581 Antisense
TCCAGGTCGTGGAGGACAACGCAGC 454 587 588 Antisense
GGAACTCCAGGAGCATCCGGAAGAC 706 529 616 Antisense
CTCCAGGAGCATCCGGAAGACCAGG 613 233 620 Antisense
ACAGCCAGGACGTTCTGGAGGAGCT 521 109 672 Antisense
CCGCGTCGCTGTCAATCGAAATGTT 45 263 855 Antisense
GTCAATCGAAATGTTGCCCGCAACC 694 459 865 Antisense
AATGTTGCCCGCAACCGTGTTGTTG 275 163 874 Antisense
Sequence Source Affymetrix Proprietary Database