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[189301_at] cuticle collagen

Description E03G2.4 /REP_DB=WormBase Gene ID /WP=CE03121 /TR=Q19050 /GB=CAA92150.1 /SUBMIT=HINXTON /CHR=X /FEA=Sanger Annotation /DEF=cuticle collagen
Cluster 6grp_total > 20      4grp_total > 50      6grp_cgc > 63      6grp_cgc_sub > 02      6grp_total_sub > Hat      4grp_rule_based > L2      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 205
1 2 3 4 range
A 9.9
(-2.9)
A 		208.3
(3)
P 		130.3
(0.7)
A 		6.5
(-3)
A 		202
B 22.6
(-2.2)
A 		154.7
(3)
A 		147.2
(2.7)
P 		3.3
(-3)
A 		151
C 82.6
(1)
A 		122.1
(3)
A 		113.6
(2.6)
M 		4.6
(-3)
A 		118
avr 38.4
(-1.7) 		161.7
(3) 		130.4
(1.8) 		4.8
(-3) 		157

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 123
1 2 3 4 5 6 range
A 47.2
(-0.1)
A 		92.8
(3)
M 		37.7
(-0.7)
A 		43.6
(-0.3)
A 		51.6
(0.2)
A 		3.8
(-3)
A 		89
B 69.2
(1.1)
A 		87.2
(3)
A 		77
(1.9)
A 		31.3
(-3)
A 		83.5
(2.6)
A 		60.5
(0.1)
A 		56
C 13.4
(-2.8)
A 		115.3
(2.4)
A 		93.6
(1.3)
A 		127.1
(3)
A 		78.4
(0.5)
A 		9.9
(-3)
A 		117
avr 43.3
(-1.5) 		98.4
(3) 		69.4
(0.6) 		67.3
(0.5) 		71.2
(0.8) 		24.7
(-3) 		74
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 45
1 2 3 4 range
A 3.6
(-2.6)
A 		45.2
(3)
P 		34.1
(1.5)
A 		0.9
(-3)
A 		44
B 7.2
(-2)
A 		38.2
(3)
A 		34.1
(2.3)
P 		0.7
(-3)
A 		38
C 27.3
(1.1)
A 		35.1
(2.3)
A 		39.6
(3)
M 		0.8
(-3)
A 		39
avr 12.7
(-1.2) 		39.5
(3) 		35.9
(2.4) 		0.8
(-3) 		39

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 34
1 2 3 4 5 6 range
A 8.7
(-1.5)
A 		33
(3)
M 		8.2
(-1.6)
A 		11.1
(-1.1)
A 		15.6
(-0.3)
A 		0.9
(-3)
A 		32
B 24.1
(0.7)
A 		29
(1.9)
A 		18.7
(-0.6)
A 		8.3
(-3)
A 		33.9
(3)
A 		22.6
(0.4)
A 		26
C 5
(-2.7)
A 		35.2
(3)
A 		23.8
(0.9)
A 		25.6
(1.2)
A 		25.4
(1.2)
A 		3.3
(-3)
A 		32
avr 12.6
(-2.1) 		32.4
(3) 		16.9
(-1) 		15
(-1.4) 		25
(1.1) 		8.9
(-3) 		24
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 189301_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.17464
Sequence Type Exemplar sequence
Representative Public ID E03G2.4 NCBI
Target Description E03G2.4 /REP_DB=WormBase Gene ID /WP=CE03121 /TR=Q19050 /GB=CAA92150.1 /SUBMIT=HINXTON /CHR=X /FEA=Sanger Annotation /DEF=cuticle 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_078216(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_078216 NCBI Caenorhabditis elegans COLlagen family member (col-186) (col-186) mRNA, complete cds. 11/11 None
SNAP00000041429 ENSEMBL cdna:SNAP chromosome:CEL140:X:15951420:15954051:1 11/11 None
GENEFINDER00000041431 ENSEMBL cdna:GeneFinder chromosome:CEL140:X:15951420:15954394:1 11/11 None
E03G2.4 ENSEMBL cdna:known chromosome:CEL140:X:15952314:15954363:1 gene:E03G2.4 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
chrX:15952313-15954363(+) 100.0 100.0
Public Domain and Genome References
Gene Title cuticle collagen
Gene Symbol col-186
Ensembl E03G2.4
Entrez Gene 184015 Entrez gene
SwissProt Q19050 EMBL-EBI
WormBase CE03121 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 CAA92150 Hypothetical protein E03G2.4 [Caenorhabditis elegans] ref|NP_510617.1| COLlagen family member (col-186) [Caenorhabditis elegans] 1.0E-108
blast CAA92150 Hypothetical protein E03G2.4 [Caenorhabditis elegans] ref|NP_510617.1| COLlagen family member (col-186) [Caenorhabditis elegans] 4.0E-92
blast CAA92150 Hypothetical protein E03G2.4 [Caenorhabditis elegans] ref|NP_510617.1| COLlagen family member (col-186) [Caenorhabditis elegans] 3.0E-82
blast CAE69720 Hypothetical protein CBG15991 [Caenorhabditis briggsae] 2.0E-78
blast CAE69720 Hypothetical protein CBG15991 [Caenorhabditis briggsae] 5.0E-69
blast CAE69720 Hypothetical protein CBG15991 [Caenorhabditis briggsae] 6.0E-62
blast CAA65506 cuticular collagen [Teladorsagia circumcincta] 2.0E-18
blast CAA65506 cuticular collagen [Teladorsagia circumcincta] 2.0E-11
Protein Domains
Database ID Description E-Value
Pfam IPR002486 EMBL-EBI Nematode cuticle collagen, N-terminal 4.7E-19
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 4.3E-4
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 9.2E-9
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 4.1E-13
Pfam IPR002486 EMBL-EBI Nematode cuticle collagen, N-terminal 2.8E-8
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 4.3E-4
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 9.2E-9
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 5.5E-11
Pfam IPR002486 EMBL-EBI Nematode cuticle collagen, N-terminal 4.7E-19
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 4.3E-4
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 9.2E-9
Trans Membrane
ID Number Of Domains Domain Boundaries
SNAP00000041429 1 23-45
GENEFINDER00000041431 1 23-45
Sequence
Target Sequence 
>C. ELEGANS:189301_AT
tggatgtgggcaatctccacctggaccaccgggacgacctggaagcgatggttccccggg
ttcggatggtgaagctggaatccctggtagagacggaccagacgcaccgcgtgccacccc
cgcgcctaactttgactggtgctttgattgcccgccaggtgagccaggacggcaaggaaa
gcagggaagaaagggcccaccgggaagaccaggaggcagcggacttccaggagacaaagg
actgccaggattgccaggatcgatggggccagttggaccagagggaagacccggaattcc
aggattgcctggaggaaagggtattcctggaaaacttattgaagttgccggacttgaagg
accaccaggacagtctggactgcccggaatgccaggactacaaggaaaacccgggaacga
cggctacccaggacgagatggttctccaggtgatcaaggtgacgatggaattcctggtgg
tcctggtaaacctgggcagaagggttacccaggtcccgacggaagtgctggc

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
TGGATGTGGGCAATCTCCACCTGGA 226 551 429 Antisense
GACGACCTGGAAGCGATGGTTCCCC 364 371 461 Antisense
CCGCCAGGTGAGCCAGGACGGCAAG 331 261 580 Antisense
CCCACCGGGAAGACCAGGAGGCAGC 413 253 624 Antisense
GGATCGATGGGGCCAGTTGGACCAG 449 511 685 Antisense
TCTGGACTGCCCGGAATGCCAGGAC 590 607 802 Antisense
GACGGCTACCCAGGACGAGATGGTT 689 373 847 Antisense
GGTTCTCCAGGTGATCAAGGTGACG 114 507 868 Antisense
GACGATGGAATTCCTGGTGGTCCTG 43 379 889 Antisense
TGGTGGTCCTGGTAAACCTGGGCAG 307 549 903 Antisense
CCCAGGTCCCGACGGAAGTGCTGGC 413 257 936 Antisense
Sequence Source Affymetrix Proprietary Database