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[189873_at] cuticular collagen

Description T13B5.4 /REP_DB=WormBase Gene ID /WP=CE13609 /TR=O17374 /GB=AAB71295.1 /SUBMIT=ST.LOUIS /CHR=2 /FEA=Sanger Annotation /DEF=cuticular collagen
Cluster 6grp_total > 91      4grp_total > 05      6grp_cgc > 96      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 143
1 2 3 4 range
A 28.8
(-3)
A 		29.2
(-3)
A 		54.7
(-1.7)
A 		148.3
(3)
P 		120
B 83.2
(3)
P 		5.4
(-3)
A 		6.9
(-2.9)
A 		57.4
(1)
P 		78
C 36.9
(-1.6)
A 		12.4
(-3)
A 		28.2
(-2.1)
A 		117.3
(3)
P 		105
avr 49.6
(-0.8) 		15.7
(-3) 		29.9
(-2.1) 		107.7
(3) 		92

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 55
1 2 3 4 5 6 range
A 37
(0.2)
A 		21.8
(-3)
A 		30.7
(-1.1)
P 		50.6
(3)
P 		36.8
(0.1)
P 		37.7
(0.3)
A 		29
B 24.6
(-2.6)
A 		34.3
(-0.8)
A 		28.6
(-1.9)
A 		22.4
(-3)
A 		54.8
(3)
M 		26.6
(-2.2)
P 		32
C 32.1
(-1.7)
A 		75.2
(3)
A 		20.7
(-3)
A 		61.6
(1.5)
P 		27.2
(-2.3)
A 		34.3
(-1.5)
P 		55
avr 31.2
(-1.5) 		43.8
(2.6) 		26.7
(-3) 		44.9
(3) 		39.6
(1.3) 		32.9
(-1) 		18
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 25
1 2 3 4 range
A 10.5
(-1.4)
A 		6.3
(-3)
A 		14.3
(0.1)
A 		21.7
(3)
P 		15
B 26.5
(3)
P 		1.3
(-3)
A 		1.6
(-2.9)
A 		12.2
(-0.4)
P 		25
C 12.2
(0.2)
A 		3.6
(-3)
A 		9.8
(-0.7)
A 		19.8
(3)
P 		16
avr 16.4
(2.4) 		3.7
(-3) 		8.6
(-0.9) 		17.9
(3) 		14

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 18
1 2 3 4 5 6 range
A 6.8
(-2.9)
A 		7.8
(-1.9)
A 		6.7
(-3)
P 		12.8
(3)
P 		11.1
(1.3)
P 		9.2
(-0.5)
A 		6
B 8.6
(-2)
A 		11.4
(-1)
A 		7
(-2.6)
A 		5.9
(-3)
A 		22.3
(3)
M 		9.9
(-1.5)
P 		16
C 11.9
(-0.8)
A 		23
(3)
A 		5.3
(-3)
A 		12.4
(-0.6)
P 		8.8
(-1.8)
A 		11.5
(-0.9)
P 		18
avr 9.1
(-0.8) 		14.1
(3) 		6.3
(-3) 		10.4
(0.2) 		14.1
(3) 		10.2
(-0) 		8
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 189873_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.4152
Sequence Type Exemplar sequence
Representative Public ID T13B5.4 NCBI
Target Description T13B5.4 /REP_DB=WormBase Gene ID /WP=CE13609 /TR=O17374 /GB=AAB71295.1 /SUBMIT=ST.LOUIS /CHR=2 /FEA=Sanger Annotation /DEF=cuticular 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_061512(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_061512 NCBI Caenorhabditis elegans COLlagen family member (col-40) (col-40) mRNA, complete cds. 11/11 None
T13B5.4 ENSEMBL cdna:known chromosome:CEL140:II:1104616:1106929:-1 gene:T13B5.4 11/11 None
Annotation Notes
Cross Hybridizing mRNA Matched Probes Nature of Assignment Related Probesets by Grade
SNAP00000003625 1/11 Cross Hyb Matching Probes None
GENEFINDER00000003631 1/11 Cross Hyb Matching Probes None
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrII:1104614-1106928(-) 75.46 100.0
Public Domain and Genome References
Gene Title cuticular collagen
Gene Symbol col-40
Ensembl T13B5.4
Entrez Gene 173495 Entrez gene
SwissProt P34804 EMBL-EBI
WormBase CE13609 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 AAB71295 Collagen protein 40 [Caenorhabditis elegans] ref|NP_493913.1| COLlagen family member (col-40) [Caenorhabditis elegans] pir||T32458 hypothetical protein T13B5.4 - Caenorhabditis elegans 7.0E-53
blast P34804 Cuticle collagen 4.0E-43
blast CAE62989 Hypothetical protein CBG07217 [Caenorhabditis briggsae] 1.0E-39
Protein Domains
Database ID Description E-Value
Pfam IPR002486 EMBL-EBI Nematode cuticle collagen, N-terminal 6.1E-10
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 5.3E-4
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 7.7E-11
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 1.0E-4
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_493913.1 2 17-39,344-366
T13B5.4 2 17-39,344-366
Sequence
Target Sequence 
>C. ELEGANS:189873_AT
gacaagtcaccgagactccaggaaccccaggaccagccggagccgccggaccaccaggac
caccaggaccagctggaaacccaggatccgctggagcttccgagccaggaccagctggac
cagctggagatgctggaccagacggagcaccaggaaacgctggagccccaggagcaccag
gagaggccggagcaccaggatccggaggaggatgcgaccactgcccaccaccacgtacca
actttcagacaatccctagcctaggtttagtcttaagcttaggcttaggctcagacttgg
ggttaggcttaagcgtaggcctagacttagcctttggctttggcataggctcaggcttag
gcctaggtttaggcttatgcttatgtctaggcttaggtttatgctcagtcttatgcttac
gctcaggcttaggcttggactttgacttaagtctaggtttaggctcagactcagtcctag
acatatattcaggcttgggcctaggctcaaactt

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GACAAGTCACCGAGACTCCAGGAAC 623 363 716 Antisense
GTACCAACTTTCAGACAATCCCTAG 569 457 950 Antisense
GGCTTAGGCTCAGACTTGGGGTTAG 405 533 997 Antisense
GTAGGCCTAGACTTAGCCTTTGGCT 421 455 1030 Antisense
TTGGCTTTGGCATAGGCTCAGGCTT 270 705 1049 Antisense
GTCTAGGCTTAGGTTTATGCTCAGT 624 467 1100 Antisense
TATGCTCAGTCTTATGCTTACGCTC 212 657 1115 Antisense
TTATGCTTACGCTCAGGCTTAGGCT 232 653 1126 Antisense
GGCTTAGGCTTGGACTTTGACTTAA 404 533 1141 Antisense
CTAGGTTTAGGCTCAGACTCAGTCC 256 1 1168 Antisense
CAGGCTTGGGCCTAGGCTCAAACTT 397 207 1205 Antisense
Sequence Source Affymetrix Proprietary Database