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[190013_at] cuticular collagen

Description T21D12.2 /REP_DB=WormBase Gene ID /WP=CE18266 /TR=O16787 /GB=AAC48094.1 /SUBMIT=ST.LOUIS /CHR=4 /FEA=Sanger Annotation /DEF=cuticular collagen
Cluster 6grp_total > 03      4grp_total > 49      6grp_cgc > 50      4grp_rule_based > L2      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 2708
1 2 3 4 range
A 13
(-3)
A 		2713
(3)
P 		2316.7
(2.1)
P 		26
(-3)
A 		2700
B 14.8
(-3)
A 		2399
(3)
P 		1770.6
(1.4)
P 		4.8
(-3)
A 		2394
C 10.9
(-3)
A 		1867.2
(3)
P 		1475.9
(1.7)
P 		11.2
(-3)
A 		1856
avr 12.9
(-3) 		2326.4
(3) 		1854.4
(1.8) 		14
(-3) 		2314

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 1346
1 2 3 4 5 6 range
A 835.4
(0.3)
P 		1061.2
(1.3)
P 		810.3
(0.2)
P 		1433.2
(3)
P 		474.5
(-1.3)
P 		86.8
(-3)
A 		1346
B 812.4
(1.8)
P 		983.3
(3)
P 		819.3
(1.9)
P 		886.4
(2.3)
P 		681.8
(0.9)
P 		110.9
(-3)
A 		872
C 1244.4
(3)
P 		885.7
(1.1)
P 		992
(1.6)
P 		1038.8
(1.9)
P 		849
(0.9)
P 		123.6
(-3)
A 		1121
avr 964.1
(2.1) 		976.7
(2.2) 		873.9
(1.5) 		1119.5
(3) 		668.4
(0.3) 		107.1
(-3) 		1012
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 605
1 2 3 4 range
A 4.7
(-3)
A 		588.9
(2.8)
P 		605.6
(3)
P 		3.8
(-3)
A 		602
B 4.7
(-3)
A 		592.5
(3)
P 		410.3
(1.2)
P 		1
(-3)
A 		592
C 3.6
(-3)
A 		536.8
(3)
P 		514.4
(2.7)
P 		1.9
(-3)
A 		535
avr 4.3
(-3) 		572.7
(3) 		510.1
(2.3) 		2.2
(-3) 		571

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 440
1 2 3 4 5 6 range
A 154
(-0.8)
P 		377.4
(3)
P 		176.5
(-0.4)
P 		363.5
(2.8)
P 		143.2
(-0.9)
P 		21.1
(-3)
A 		356
B 282.7
(2.1)
P 		327.3
(3)
P 		198.9
(0.3)
P 		234.8
(1.1)
P 		277
(1.9)
P 		41.4
(-3)
A 		286
C 461.3
(3)
P 		270.3
(0.3)
P 		252.5
(0)
P 		208.9
(-0.6)
P 		274.7
(0.3)
P 		41.4
(-3)
A 		420
avr 299.3
(2.5) 		325
(3) 		209.3
(0.6) 		269.1
(1.8) 		231.6
(1.1) 		34.6
(-3) 		290
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 190013_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.11013
Sequence Type Exemplar sequence
Representative Public ID T21D12.2 NCBI
Target Description T21D12.2 /REP_DB=WormBase Gene ID /WP=CE18266 /TR=O16787 /GB=AAC48094.1 /SUBMIT=ST.LOUIS /CHR=4 /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_067488(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_067488 NCBI Caenorhabditis elegans DumPY : shorter than wild-type family member (dpy-9) (dpy-9) mRNA, complete cds. 11/11 None
SNAP00000019184 ENSEMBL cdna:SNAP chromosome:CEL140:IV:257503:259203:-1 11/11 None
GENEFINDER00000019197 ENSEMBL cdna:GeneFinder chromosome:CEL140:IV:257503:259203:-1 11/11 None
T21D12.2 ENSEMBL cdna:known chromosome:CEL140:IV:257403:259204:-1 gene:T21D12.2 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
chrIV:257502-259203(-) 100.0 100.0
Public Domain and Genome References
Gene Title cuticular collagen
Gene Symbol dpy-9
Ensembl T21D12.2
Entrez Gene 176846 Entrez gene
SwissProt O16787 EMBL-EBI
WormBase CE35021 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 AAC48094 Dumpy : shorter than wild-type protein 9 [Caenorhabditis elegans] ref|NP_499889.2| DumPY : shorter than wild-type family member (dpy-9) [Caenorhabditis elegans] 1.0E-117
blast AAC48094 Dumpy : shorter than wild-type protein 9 [Caenorhabditis elegans] ref|NP_499889.2| DumPY : shorter than wild-type family member (dpy-9) [Caenorhabditis elegans] 1.0E-115
blast CAE74729 Hypothetical protein CBG22547 [Caenorhabditis briggsae] 1.0E-102
blast CAE74729 Hypothetical protein CBG22547 [Caenorhabditis briggsae] 1.0E-100
blast AAB00598 Dumpy : shorter than wild-type protein 3 [Caenorhabditis elegans] ref|NP_508395.1| DumPY : shorter than wild-type family member (dpy-3) [Caenorhabditis elegans] 2.0E-27
Protein Domains
Database ID Description E-Value
Pfam IPR002486 EMBL-EBI Nematode cuticle collagen, N-terminal 1.4E-7
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 1.6E-5
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 2.7E-8
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 1.1E-10
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 1.6E-5
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 2.7E-8
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 1.1E-10
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_499889.2 1 12-34
T21D12.2 1 12-34
SNAP00000019184 1 12-34
GENEFINDER00000019197 1 12-34
Sequence
Target Sequence 
>C. ELEGANS:190013_AT
gtgacggtttcccgggcagagaaggtgacaatggtatagctggaaagtatctaccagctc
caccaccaggaaccaacgcatgtcagaaatgtccaactggagctccaggaccaccaggac
ttccaggaccaaaaggaccacgtggaccagcaggaattgagggtaaaccagggagactcg
gtgaagacaatcgtccaggacccccaggaccgccaggagtacgtggagaacctggatcac
cgggagagaagggaccaaccggcgatcgtggaaaagtattgaatggagcaccaccaggtc
ctactggcccacctggaaaggtcggtccacgtggattgtctggcggaaaaggacacgatg
gtaaaccaggacttggtgggcaaccaggtgtccgaggagccgttggagcacgtggagatg
ctggaaacccaggacttccaggaccacaaggaccaaagggagaaccaggaaatccaggaa
cgtgtcatcactgccaaaacagagcaccagcaccttccgaggcaccaggaaaagctccac
ct

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GTGACGGTTTCCCGGGCAGAGAAGG 394 483 323 Antisense
TGGAAAGTATCTACCAGCTCCACCA 10 549 363 Antisense
CACCAGGAACCAACGCATGTCAGAA 170 203 386 Antisense
TGAAGACAATCGTCCAGGACCCCCA 245 575 504 Antisense
GAGAACCTGGATCACCGGGAGAGAA 709 389 548 Antisense
GGACCAACCGGCGATCGTGGAAAAG 402 521 574 Antisense
TGGCCCACCTGGAAAGGTCGGTCCA 370 545 627 Antisense
GGACTTGGTGGGCAACCAGGTGTCC 392 521 691 Antisense
TGTCCGAGGAGCCGTTGGAGCACGT 228 555 711 Antisense
ATCCAGGAACGTGTCATCACTGCCA 80 41 794 Antisense
CGAGGCACCAGGAAAAGCTCCACCT 37 251 840 Antisense
Sequence Source Affymetrix Proprietary Database