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[190091_at] cuticular collagen /// ---

Description C01B12.1 /REP_DB=WormBase Gene ID /WP=CE07789 /TR=O17209 /GB=AAB70974.1 /SUBMIT=ST.LOUIS /CHR=2 /FEA=Sanger Annotation /DEF=cuticular collagen
Cluster 6grp_highest_10_10 > 34      6grp_high1_10_10 > 43      6grp_highest_nonorm > 33      6grp_total > 10      4grp_total > 49      6grp_highest_sub > 02_03      6grp_cgc > 63      6grp_high1_sub > 02      6grp_cgc_sub > 02      6grp_total_sub > Hat      6grp_rule_based > S2      4grp_rule_based > L3      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 7215
1 2 3 4 range
A 28.9
(-3)
A 		6631.7
(3)
P 		6297.2
(2.7)
P 		95
(-2.9)
A 		6603
B 9.3
(-3)
A 		6128.9
(2.1)
P 		7224.4
(3)
P 		18.3
(-3)
A 		7215
C 38.4
(-3)
A 		5365.6
(1.7)
P 		6856.7
(3)
P 		98
(-2.9)
P 		6818
avr 25.5
(-3) 		6042.1
(2.3) 		6792.8
(3) 		70.4
(-3) 		6767

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 2909
1 2 3 4 5 6 range
A 477.1
(-2.6)
P 		3204.6
(3)
P 		2467.7
(1.5)
P 		1633.2
(-0.2)
P 		1405.5
(-0.7)
P 		295.5
(-3)
P 		2909
B 475.8
(-3)
P 		2666.7
(3)
P 		2460.8
(2.4)
P 		1235
(-0.9)
P 		1224.4
(-0.9)
P 		500.1
(-2.9)
P 		2191
C 643.9
(-2.3)
P 		2606.1
(3)
P 		1821.1
(0.9)
P 		1247.4
(-0.7)
P 		1666
(0.5)
P 		374.8
(-3)
P 		2231
avr 532.3
(-2.6) 		2825.8
(3) 		2249.9
(1.6) 		1371.9
(-0.6) 		1432
(-0.4) 		390.1
(-3) 		2436
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 2387
1 2 3 4 range
A 10.5
(-3)
A 		1439.6
(2.2)
P 		1646.2
(3)
P 		13.9
(-3)
A 		1636
B 3
(-3)
A 		1513.7
(2.4)
P 		1674.1
(3)
P 		3.9
(-3)
A 		1671
C 12.7
(-3)
A 		1542.7
(0.9)
P 		2389.8
(3)
P 		16.5
(-3)
P 		2377
avr 8.7
(-3) 		1498.7
(1.7) 		1903.4
(3) 		11.4
(-3) 		1895

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 1068
1 2 3 4 5 6 range
A 88
(-2.9)
P 		1139.7
(3)
P 		537.4
(-0.4)
P 		414.2
(-1.1)
P 		424.1
(-1)
P 		71.9
(-3)
P 		1068
B 165.5
(-3)
P 		887.6
(3)
P 		597.6
(0.6)
P 		327.1
(-1.7)
P 		497.5
(-0.2)
P 		186.5
(-2.8)
P 		722
C 238.7
(-2)
P 		795.2
(3)
P 		463.5
(0)
P 		250.9
(-1.9)
P 		539.1
(0.7)
P 		125.5
(-3)
P 		670
avr 164.1
(-2.7) 		940.8
(3) 		532.8
(-0) 		330.7
(-1.5) 		486.9
(-0.4) 		128
(-3) 		813
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 190091_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.4744
Sequence Type Exemplar sequence
Representative Public ID C01B12.1 NCBI
Target Description C01B12.1 /REP_DB=WormBase Gene ID /WP=CE07789 /TR=O17209 /GB=AAB70974.1 /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_061235(9), NM_061234(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_061235 NCBI Caenorhabditis elegans C01B12.8 (C01B12.8) mRNA, complete cds. 9/11 None
NM_061234 NCBI Caenorhabditis elegans SQuaT family member (sqt-2) (sqt-2) mRNA, complete cds. 11/11 None
SNAP00000043178 ENSEMBL cdna:SNAP chromosome:CEL140:II:23347:24347:1 11/11 None
GENEFINDER00000043184 ENSEMBL cdna:GeneFinder chromosome:CEL140:II:23347:24347:1 11/11 None
C01B12.1 ENSEMBL cdna:known chromosome:CEL140:II:23347:24428:1 gene:C01B12.1 11/11 None
C01B12.8 ENSEMBL cdna:known chromosome:CEL140:II:23881:25381:1 gene:C01B12.8 9/11 A 
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
chrII:23346-24347(+) 100.0 100.0
Public Domain and Genome References
Gene Title cuticular collagen

Gene Symbol sqt-2
Ensembl C01B12.1
C01B12.8
Entrez Gene 173382 Entrez gene
3565099 Entrez gene
SwissProt O17209 EMBL-EBI
O17210 EMBL-EBI
WormBase CE07789 Wormbase
CE07796 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 AAB70974 Squat protein 2 [Caenorhabditis elegans] ref|NP_493635.1| SQuaT family member (sqt-2) [Caenorhabditis elegans] 6.0E-84
blast CAE62835 Hypothetical protein CBG07014 [Caenorhabditis briggsae] 7.0E-82
blast AAB70980 Hypothetical protein C01B12.8 [Caenorhabditis elegans] ref|NP_493636.1| C01B12.8 [Caenorhabditis elegans] 2.0E-52
Protein Domains
Database ID Description E-Value
Pfam IPR002486 EMBL-EBI Nematode cuticle collagen, N-terminal 2.2E-16
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 2.7E-7
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 2.5E-4
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_493635.1 1 13-35
C01B12.1 1 13-35
SNAP00000043178 1 13-35
GENEFINDER00000043184 1 13-35
Sequence
Target Sequence 
>C. ELEGANS:190091_AT
gagctccagttacgaactccgagccagctccaacttgctgctcttgccaacaaggaccag
ccggaccaccaggaccacctggagatgacggaaatggcgggcaagatggtgttcgtggaa
acgatggaactgacggaaaggaaggaagccttttggaaagtgctattgtaaatgaaccat
gcattatctgccctccaggaccaccaggaccacaaggaatggcaggagctaaggggccac
aaggaccaaagggaggaaatggagataatggaccagatggaaaggctggagccaacggaa
tgcaaggaccaccaggaatgatgggcccaccaggaagacaaggagtaagtggaccaaagg
gagctccaggacgtatcaatcaaatcaatggaccagctggaccagctggacataagggag
tccgcggaccaccaggaccacgcggagaagctggacttgatggtggaaactctgaaggac
cacaaggaccacaaggagatgctggaagaccaggaccagttggagagcaaggaccacaag
gaccagagggaccacaaggaccaccaggagaaccaggaggctgtgagcattgc

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GAGCTCCAGTTACGAACTCCGAGCC 635 385 287 Antisense
TGGCGGGCAAGATGGTGTTCGTGGA 488 543 381 Antisense
GGAGCTAAGGGGCCACAAGGACCAA 477 521 511 Antisense
GAGCCAACGGAATGCAAGGACCACC 3 385 575 Antisense
GAATGATGGGCCCACCAGGAAGACA 481 331 602 Antisense
GGAGCTCCAGGACGTATCAATCAAA 535 521 646 Antisense
CATAAGGGAGTCCGCGGACCACCAG 372 209 697 Antisense
ACCACGCGGAGAAGCTGGACTTGAT 575 81 723 Antisense
GCTGGACTTGATGGTGGAAACTCTG 379 295 736 Antisense
CACAAGGACCAGAGGGACCACAAGG 294 1 821 Antisense
AGAACCAGGAGGCTGTGAGCATTGC 349 73 855 Antisense
Sequence Source Affymetrix Proprietary Database