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[188045_at] collagen

Description AC3.6 /REP_DB=WormBase Gene ID /WP=CE05136 /TR=Q17402 /GB=CAA94869.1 /SUBMIT=HINXTON /CHR=5 /FEA=Sanger Annotation /DEF=collagen
Cluster 6grp_total > 95      4grp_total > 19      6grp_cgc > 78      6grp_cgc_sub > In      6grp_total_sub > Increase      6grp_rule_based > S5      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 107
1 2 3 4 range
A 33.1
(-1.1)
A 		28.1
(-1.5)
A 		7.5
(-3)
A 		89.8
(3)
A 		82
B 31.9
(-1.6)
A 		9.1
(-2.9)
A 		7.3
(-3)
A 		114.2
(3)
A 		107
C 9.1
(-3)
A 		67.3
(2.1)
A 		9.8
(-2.9)
A 		78.1
(3)
A 		69
avr 24.7
(-1.8) 		34.8
(-1.1) 		8.2
(-3) 		94
(3) 		86

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 98
1 2 3 4 5 6 range
A 11
(-2.7)
A 		31.2
(-1.4)
A 		5.5
(-3)
A 		22
(-2)
A 		103.2
(3)
P 		75.8
(1.3)
P 		98
B 13.4
(-2.6)
A 		6.8
(-3)
A 		24.2
(-1.9)
A 		26.2
(-1.7)
A 		99.1
(3)
P 		82
(1.9)
A 		92
C 32.5
(-0.9)
A 		6.7
(-3)
A 		18.4
(-2.1)
A 		62.8
(1.5)
A 		81.8
(3)
P 		58.1
(1.1)
M 		75
avr 19
(-2.7) 		14.9
(-3) 		16
(-2.9) 		37
(-1.3) 		94.7
(3) 		72
(1.3) 		80
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 23
1 2 3 4 range
A 12
(2.4)
A 		6.1
(-0.8)
A 		2
(-3)
A 		13.1
(3)
A 		11
B 10.2
(-0.7)
A 		2.2
(-2.9)
A 		1.7
(-3)
A 		24.3
(3)
A 		23
C 3
(-3)
A 		19.4
(3)
A 		3.4
(-2.9)
A 		13.2
(0.7)
A 		16
avr 8.4
(-0.5) 		9.2
(-0.2) 		2.4
(-3) 		16.9
(3) 		15

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 39
1 2 3 4 5 6 range
A 2
(-2.8)
A 		11.1
(-1)
A 		1.2
(-3)
A 		5.6
(-2.1)
A 		31.1
(3)
P 		18.5
(0.5)
P 		30
B 4.7
(-2.6)
A 		2.3
(-3)
A 		5.9
(-2.4)
A 		6.9
(-2.3)
A 		40.3
(3)
P 		30.6
(1.5)
A 		38
C 12
(-0.6)
A 		2.1
(-3)
A 		4.7
(-2.4)
A 		12.6
(-0.4)
A 		26.5
(3)
P 		19.4
(1.3)
M 		24
avr 6.2
(-2.5) 		5.2
(-2.7) 		3.9
(-3) 		8.4
(-2.1) 		32.6
(3) 		22.8
(1) 		29
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 188045_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.11712
Sequence Type Exemplar sequence
Representative Public ID AC3.6 NCBI
Target Description AC3.6 /REP_DB=WormBase Gene ID /WP=CE05136 /TR=Q17402 /GB=CAA94869.1 /SUBMIT=HINXTON /CHR=5 /FEA=Sanger Annotation /DEF=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_073269(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_073269 NCBI Caenorhabditis elegans AC3.6 (collagen) mRNA, complete cds. 11/11 None
SNAP00000028838 ENSEMBL cdna:SNAP chromosome:CEL140:V:10396113:10396983:-1 11/11 None
GENEFINDER00000028850 ENSEMBL cdna:GeneFinder chromosome:CEL140:V:10396113:10397805:-1 11/11 None
AC3.6 ENSEMBL cdna:known chromosome:CEL140:V:10396113:10397805:-1 gene:AC3.6 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
chrV:10396112-10397805(-) 100.0 100.0
Public Domain and Genome References
Gene Title collagen
Gene Symbol col-151
Ensembl AC3.6
Entrez Gene 179448 Entrez gene
SwissProt Q17402 EMBL-EBI
WormBase CE05136 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 CAA94869 Hypothetical protein AC3.6 [Caenorhabditis elegans] ref|NP_505670.1| AC3.6 [Caenorhabditis elegans] 1.0E-94
blast CAE75204 Hypothetical protein CBG23151 [Caenorhabditis briggsae] 4.0E-61
blast CAA94869 Hypothetical protein AC3.6 [Caenorhabditis elegans] ref|NP_505670.1| AC3.6 [Caenorhabditis elegans] 5.0E-35
blast CAE75204 Hypothetical protein CBG23151 [Caenorhabditis briggsae] 3.0E-22
Protein Domains
Database ID Description E-Value
Pfam IPR002486 EMBL-EBI Nematode cuticle collagen, N-terminal 4.2E-15
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 3.5E-8
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 0.0013
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 3.5E-8
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 0.0013
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_505670.1 1 7-29
AC3.6 1 7-29
GENEFINDER00000028850 1 7-29
Sequence
Target Sequence 
>C. ELEGANS:188045_AT
tgaagacggctcagctggacaacctggaagccccggaggagtcggcgtattgctatcaat
gaagctaccatataatgggtgtattcaatgtccaatgggaccacaaggacaacctggaag
gccaggattaatgggacatcctggagatgtgggtgttactggaatggatggaattcctgg
agggagaggtcttccaggatatccaggaatgccaggagacaatggatcgggcggagctaa
tgggcatgatggagcaactgggcaaccaggcagatcaggaaccagatcatatggatcacc
aggacctgccggatcccctggaagagtcgggagagggggaccgcctggtccagatggcgg
ttatcccatgtctggggagcctgggtcttctgggccgcaaggaaaagcaggtcaaccggg
tggacctggagtcgatgggcatcctggaaggcctggtggcagtggtcgtcctgggccgga
ttctggatactgcaaatgcccacaaagaggaaaaactgacgagttttctaattacaatac
gaaggcatccacgccaacaga

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
TGAAGACGGCTCAGCTGGACAACCT 144 575 372 Antisense
GGAGGAGTCGGCGTATTGCTATCAA 692 515 406 Antisense
GGGAGAGGTCTTCCAGGATATCCAG 619 495 553 Antisense
GGATCGGGCGGAGCTAATGGGCATG 317 511 595 Antisense
GCCGGATCCCCTGGAAGAGTCGGGA 280 281 679 Antisense
GCCTGGTCCAGATGGCGGTTATCCC 439 281 714 Antisense
GGTTATCCCATGTCTGGGGAGCCTG 682 503 730 Antisense
TCAACCGGGTGGACCTGGAGTCGAT 79 629 783 Antisense
GTCGATGGGCATCCTGGAAGGCCTG 90 473 802 Antisense
CTGGGCCGGATTCTGGATACTGCAA 168 239 842 Antisense
ATACGAAGGCATCCACGCCAACAGA 301 23 908 Antisense
Sequence Source Affymetrix Proprietary Database