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[188301_at] collagen

Description C12D8.8 /REP_DB=WormBase Gene ID /WP=CE05271 /TR=Q17939 /GB=CAA98236.1 /SUBMIT=HINXTON /CHR=5 /FEA=Sanger Annotation /DEF=collagen
Cluster 6grp_total > 92      4grp_total > 35      6grp_cgc > 64      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 152
1 2 3 4 range
A 61
(0.2)
A 		94.2
(3)
A 		22.4
(-3)
A 		80.6
(1.9)
A 		72
B 64.5
(-3)
A 		73.6
(0.2)
A 		79.3
(2.2)
A 		81.5
(3)
A 		17
C 40.9
(-3)
A 		173.9
(3)
A 		46.7
(-2.7)
A 		51.1
(-2.5)
A 		133
avr 55.5
(-2.4) 		113.9
(3) 		49.5
(-3) 		71.1
(-1) 		64

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 108
1 2 3 4 5 6 range
A 82
(2.9)
A 		75.5
(2.3)
A 		61.5
(1.1)
A 		83.1
(3)
A 		54.3
(0.5)
A 		14.8
(-3)
A 		68
B 18.7
(-3)
A 		107.9
(3)
A 		87
(1.6)
A 		37.9
(-1.7)
A 		94.1
(2.1)
P 		60.1
(-0.2)
A 		89
C 70.9
(-0.9)
A 		86.6
(0.2)
A 		66.7
(-1.3)
A 		64.2
(-1.5)
A 		123.1
(3)
A 		43.7
(-3)
A 		79
avr 57.2
(-0.9) 		90
(2.9) 		71.7
(0.8) 		61.7
(-0.4) 		90.5
(3) 		39.5
(-3) 		51
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 44
1 2 3 4 range
A 22.2
(3)
A 		20.4
(2.3)
A 		5.9
(-3)
A 		11.8
(-0.8)
A 		16
B 20.6
(3)
A 		18.2
(-1.5)
A 		18.4
(-1.1)
A 		17.4
(-3)
A 		3
C 13.5
(-2.3)
A 		50
(3)
A 		16.3
(-1.9)
A 		8.6
(-3)
A 		41
avr 18.8
(-0.8) 		29.5
(3) 		13.5
(-2.7) 		12.6
(-3) 		17

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 36
1 2 3 4 5 6 range
A 15.1
(-0)
A 		26.9
(3)
A 		13.4
(-0.5)
A 		21.1
(1.5)
A 		16.4
(0.3)
A 		3.6
(-3)
A 		23
B 6.5
(-3)
A 		35.9
(2.6)
A 		21.1
(-0.2)
A 		10
(-2.3)
A 		38.2
(3)
P 		22.4
(0)
A 		32
C 26.3
(-0)
A 		26.4
(0)
A 		17
(-2.1)
A 		12.9
(-3)
A 		39.8
(3)
A 		14.6
(-2.6)
A 		27
avr 16
(-2.2) 		29.7
(2.4) 		17.2
(-1.8) 		14.7
(-2.6) 		31.5
(3) 		13.5
(-3) 		18
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 188301_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.11772
Sequence Type Exemplar sequence
Representative Public ID C12D8.8 NCBI
Target Description C12D8.8 /REP_DB=WormBase Gene ID /WP=CE05271 /TR=Q17939 /GB=CAA98236.1 /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_073234(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_073234 NCBI Caenorhabditis elegans C12D8.8 (collagen) mRNA, complete cds. 11/11 None
SNAP00000021006 ENSEMBL cdna:SNAP chromosome:CEL140:V:10244365:10245299:1 11/11 None
GENEFINDER00000021011 ENSEMBL cdna:GeneFinder chromosome:CEL140:V:10244365:10245299:1 11/11 None
C12D8.8 ENSEMBL cdna:known chromosome:CEL140:V:10244365:10245299:1 gene:C12D8.8 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:10244364-10245299(+) 100.0 100.0
Public Domain and Genome References
Gene Title collagen
Gene Symbol col-148
Ensembl C12D8.8
Entrez Gene 182542 Entrez gene
SwissProt Q17939 EMBL-EBI
WormBase CE05271 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 CAA98236 Hypothetical protein C12D8.8 [Caenorhabditis elegans] ref|NP_505635.1| C12D8.8 [Caenorhabditis elegans] 1.0E-120
blast CAE64772 Hypothetical protein CBG09563 [Caenorhabditis briggsae] 1.0E-75
blast CAE72121 Hypothetical protein CBG19217 [Caenorhabditis briggsae] 2.0E-63
Protein Domains
Database ID Description E-Value
Pfam IPR002486 EMBL-EBI Nematode cuticle collagen, N-terminal 2.6E-23
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 1.1E-10
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 7.1E-10
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_505635.1 1 7-26
C12D8.8 1 7-26
SNAP00000021006 1 7-26
GENEFINDER00000021011 1 7-26
Sequence
Target Sequence 
>C. ELEGANS:188301_AT
gccaaccaaaccaatttgtccacctggcccaccgggacaaccgggacaacaaggacagaa
aggcccgccaggagttccagggcaacgtggacaagattgtacaattgtttatgctccaat
catctgccctcctgtttctcaagaatgtgttaaatgtcctccgggaccagtaggagcaat
aggaccaatgggcccaataggatctatgggtagagctggtcaaccgggatactccggacc
acgtggaaatgacggatttcctggacttcctgggccaccaggagaaaatggacaaccagg
acaatcaggaaaagatggtcaaccaggaagaaacggagctgatggtaagagaggatacgg
agccccaggtgcacctggagctcaaggaaagccaggaccatctggaccccctggaattga
tggatatcctgggcaaaatggttggaaaggacaacaaggagtaccagggcaagacgattt
tccaggaacatttggagaaccaggtgcagctggaaaacaaggatatcctggacttccagg
atcagatgcatctt

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GCCAACCAAACCAATTTGTCCACCT 476 275 303 Antisense
GACAGAAAGGCCCGCCAGGAGTTCC 173 367 356 Antisense
ATTGTTTATGCTCCAATCATCTGCC 221 5 406 Antisense
GCCCTCCTGTTTCTCAAGAATGTGT 68 287 428 Antisense
GAATGTGTTAAATGTCCTCCGGGAC 472 329 445 Antisense
CAACCGGGATACTCCGGACCACGTG 398 1 523 Antisense
AATGACGGATTTCCTGGACTTCCTG 137 163 550 Antisense
GCCCCAGGTGCACCTGGAGCTCAAG 629 285 664 Antisense
TCTGGACCCCCTGGAATTGATGGAT 418 607 703 Antisense
GTACCAGGGCAAGACGATTTTCCAG 525 457 763 Antisense
GGACTTCCAGGATCAGATGCATCTT 289 525 832 Antisense
Sequence Source Affymetrix Proprietary Database