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[192480_s_at] cuticular collagen

Description C27H5.5 /REP_DB=WormBase Gene ID /WP=CE06893 /GEN=col-36 /TR=SW:P34803 /GB=AAC46659.1 /SUBMIT=ST.LOUIS /CHR=2 /FEA=Sanger Annotation /DEF=cuticular collagen
Cluster 6grp_high1_10_10 > 92      6grp_total > 83      4grp_total > 49      6grp_cgc > 87      6grp_high1_sub > 04_05      6grp_cgc_sub > 05      6grp_total_sub > Hat      6grp_rule_based > S4      4grp_rule_based > L2      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 569
1 2 3 4 range
A 121.3
(-2.3)
M 		543.3
(2.6)
P 		576
(3)
P 		62
(-3)
A 		514
B 80.9
(-3)
A 		480.5
(2.3)
P 		532.2
(3)
P 		82
(-3)
A 		451
C 99.5
(-2.7)
A 		631.3
(3)
P 		458.4
(1.1)
P 		74.1
(-3)
A 		557
avr 100.6
(-2.7) 		551.7
(3) 		522.2
(2.6) 		72.7
(-3) 		479

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 16549
1 2 3 4 5 6 range
A 249.6
(-3)
M 		334.5
(-3)
P 		1578.6
(-2.5)
P 		16096.7
(3)
P 		15075.2
(2.6)
P 		4657.8
(-1.3)
P 		15847
B 200.7
(-3)
P 		307.6
(-3)
P 		1999.9
(-2.3)
P 		15997.5
(3)
P 		10857
(1)
P 		3866
(-1.6)
P 		15797
C 253.9
(-3)
P 		281.1
(-3)
P 		1815.2
(-2.4)
P 		14302.3
(2.1)
P 		16749.7
(3)
P 		3103.8
(-2)
P 		16496
avr 234.7
(-3) 		307.7
(-3) 		1797.9
(-2.4) 		15465.5
(3) 		14227.3
(2.5) 		3875.9
(-1.6) 		15231
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 172
1 2 3 4 range
A 44.1
(-1.5)
M 		117.9
(1.6)
P 		150.6
(3)
P 		9.1
(-3)
A 		142
B 25.8
(-2.5)
A 		118.7
(2.7)
P 		123.3
(3)
P 		17.5
(-3)
A 		106
C 32.9
(-2.3)
A 		181.5
(3)
P 		159.8
(2.2)
P 		12.5
(-3)
A 		169
avr 34.3
(-2) 		139.4
(2.8) 		144.6
(3) 		13
(-3) 		132

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 5374
1 2 3 4 5 6 range
A 46
(-3)
M 		119
(-2.9)
P 		343.8
(-2.6)
P 		4082.5
(2.4)
P 		4549
(3)
P 		1134
(-1.6)
P 		4503
B 69.8
(-3)
P 		102.4
(-3)
P 		485.6
(-2.4)
P 		4237.2
(2.8)
P 		4411.1
(3)
P 		1441.6
(-1.1)
P 		4341
C 94.1
(-3)
P 		85.8
(-3)
P 		462
(-2.6)
P 		2876.2
(0.1)
P 		5420
(3)
P 		1039
(-1.9)
P 		5334
avr 70
(-3) 		102.4
(-3) 		430.5
(-2.5) 		3732
(1.7) 		4793.4
(3) 		1204.9
(-1.6) 		4723
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 192480_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.4310
Sequence Type Exemplar sequence
Representative Public ID C27H5.5 NCBI
Target Description C27H5.5 /REP_DB=WormBase Gene ID /WP=CE06893 /GEN=col-36 /TR=SW:P34803 /GB=AAC46659.1 /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_063086(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_063086 NCBI Caenorhabditis elegans COLlagen family member (col-36) (col-36) mRNA, complete cds. 11/11 None
SNAP00000006114 ENSEMBL cdna:SNAP chromosome:CEL140:II:7167607:7168578:-1 11/11 None
GENEFINDER00000006126 ENSEMBL cdna:GeneFinder chromosome:CEL140:II:7167607:7172119:-1 11/11 None
C27H5.5 ENSEMBL cdna:known chromosome:CEL140:II:7167452:7168593:-1 gene:C27H5.5 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
chrII:7167602-7168574(-) 95.67 100.0
Public Domain and Genome References
Gene Title cuticular collagen
Gene Symbol col-36
Ensembl C27H5.5
Entrez Gene 174178 Entrez gene
SwissProt P34803 EMBL-EBI
WormBase CE06893 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 T15670 hypothetical protein C27H5.5 - Caenorhabditis elegans 0.0
blast AAK84493 Hypothetical protein C27H5.7a [Caenorhabditis elegans] ref|NP_741021.1| abnormal DYe Filling family member (dyf-13) [Caenorhabditis elegans] 0.0
blast AAM81107 Hypothetical protein C27H5.7b [Caenorhabditis elegans] ref|NP_741022.1| abnormal DYe Filling family member (dyf-13) [Caenorhabditis elegans] 0.0
blast AAK84492 Collagen protein 36 [Caenorhabditis elegans] ref|NP_495487.1| COLlagen family member (col-36) [Caenorhabditis elegans] sp|P34803|COL36_CAEEL Cuticle collagen 36 gb|AAA17445.1| col-36 collagen 8.0E-55
blast T15670 hypothetical protein C27H5.5 - Caenorhabditis elegans 8.0E-55
blast CAE67553 Hypothetical protein CBG13078 [Caenorhabditis briggsae] 2.0E-45
Protein Domains
Database ID Description E-Value
Pfam IPR002486 EMBL-EBI Nematode cuticle collagen, N-terminal 9.3E-22
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 4.1E-5
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 0.0012
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 1.1E-4
Pfam IPR002486 EMBL-EBI Nematode cuticle collagen, N-terminal 9.3E-22
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 4.1E-5
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 0.0012
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 1.1E-4
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_495487.1 1 17-39
C27H5.5 1 17-39
SNAP00000006114 1 17-39
Sequence
Target Sequence 
>C. ELEGANS:192480_S_AT
gctggagccgatattggaccaacttgctgcccatgtcaacagggaccagctggaccaccg
ggaccagcaggagatactggaccaaacggaaatgatggacatcacggagctccaggagtt
ccaggaaaggaaggatccattctcagctctgcacttccaccatcagagccatgcatcatc
tgcccaccaggcccacaaggagccgttggacaacaaggaccaaagggaccaccaggacca
aagggtaaatctcaagagagagctgccgacggaaagaacggagaacctggaatgattgga
cccccaggaccaccaggaggtgttggagagccaggaccaccaggaccagctggacaacca
ggaagagttattcaagtaaacggagctgctggaccagcaggaccacgtggagtcaagggg
cca

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GCTGGAGCCGATATTGGACCAACTT 654 293 322 Antisense
CAACTTGCTGCCCATGTCAACAGGG 274 187 341 Antisense
GCCCATGTCAACAGGGACCAGCTGG 157 287 350 Antisense
ACCACCGGGACCAGCAGGAGATACT 279 85 375 Antisense
AATGATGGACATCACGGAGCTCCAG 128 165 412 Antisense
AAAGGAAGGATCCATTCTCAGCTCT 140 121 447 Antisense
GCTCTGCACTTCCACCATCAGAGCC 128 301 467 Antisense
CATCAGAGCCATGCATCATCTGCCC 160 213 482 Antisense
CTCAAGAGAGAGCTGCCGACGGAAA 602 225 572 Antisense
CCTGGAATGATTGGACCCCCAGGAC 14 267 607 Antisense
AGGACCACGTGGAGTCAAGGGGCCA 633 49 720 Antisense
Sequence Source Affymetrix Proprietary Database