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[188389_at] collagen

Description B0024.2 /REP_DB=WormBase Gene ID /WP=CE05147 /TR=Q17418 /GB=CAA94875.1 /SUBMIT=HINXTON /CHR=5 /FEA=Sanger Annotation /DEF=collagen
Cluster 6grp_total > 94      4grp_total > 49      6grp_cgc > 88      6grp_total_sub > Hat      6grp_rule_based > S5      4grp_rule_based > L3      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 304
1 2 3 4 range
A 4.7
(-3)
A 		162.6
(0.9)
A 		246.5
(3)
A 		5.3
(-3)
A 		242
B 6.1
(-3)
A 		182.2
(1.3)
A 		251.7
(3)
A 		6.8
(-3)
A 		246
C 12.2
(-3)
A 		281
(2.4)
A 		308.5
(3)
A 		43.4
(-2.4)
A 		296
avr 7.7
(-3) 		208.6
(1.6) 		268.9
(3) 		18.5
(-2.8) 		261

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 2158
1 2 3 4 5 6 range
A 130.9
(-2.8)
A 		57.3
(-3)
A 		698.9
(-0.9)
P 		1004.1
(0)
P 		1933.5
(3)
P 		1238.6
(0.8)
P 		1876
B 93.7
(-2.9)
A 		57.6
(-3)
A 		594.4
(-1.5)
P 		861.7
(-0.7)
P 		2201
(3)
P 		1202.7
(0.2)
P 		2143
C 92
(-3)
A 		80
(-3)
A 		512.6
(-1.8)
P 		1130.7
(-0)
P 		2215.3
(3)
P 		1161.8
(0)
P 		2135
avr 105.5
(-2.9) 		65
(-3) 		602
(-1.4) 		998.8
(-0.3) 		2116.6
(3) 		1201
(0.3) 		2052
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 107
1 2 3 4 range
A 1.7
(-2.9)
A 		35.3
(0.3)
A 		64.4
(3)
A 		0.8
(-3)
A 		64
B 2
(-2.9)
A 		45
(1.6)
A 		58.3
(3)
A 		1.4
(-3)
A 		57
C 4
(-3)
A 		80.8
(1.5)
A 		107.5
(3)
A 		7.3
(-2.8)
A 		104
avr 2.6
(-3) 		53.7
(1.1) 		76.7
(3) 		3.2
(-3) 		74

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 875
1 2 3 4 5 6 range
A 24.1
(-3)
A 		20.4
(-3)
A 		152.2
(-1.6)
P 		254.7
(-0.5)
P 		583.5
(3)
P 		301.6
(-0)
P 		563
B 32.6
(-2.9)
A 		19.2
(-3)
A 		144.3
(-2.1)
P 		228.2
(-1.6)
P 		894.2
(3)
P 		448.5
(-0.1)
P 		875
C 34.1
(-2.9)
A 		24.4
(-3)
A 		130.5
(-2.1)
P 		227.4
(-1.2)
P 		716.9
(3)
P 		388.9
(0.2)
P 		693
avr 30.3
(-2.9) 		21.3
(-3) 		142.3
(-2) 		236.8
(-1.2) 		731.5
(3) 		379.7
(0) 		710
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 188389_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.12213
Sequence Type Exemplar sequence
Representative Public ID B0024.2 NCBI
Target Description B0024.2 /REP_DB=WormBase Gene ID /WP=CE05147 /TR=Q17418 /GB=CAA94875.1 /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_073246(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_073246 NCBI Caenorhabditis elegans B0024.2 (collagen) mRNA, complete cds. 11/11 None
SNAP00000027128 ENSEMBL cdna:SNAP chromosome:CEL140:V:10296215:10297274:-1 11/11 None
GENEFINDER00000027145 ENSEMBL cdna:GeneFinder chromosome:CEL140:V:10296215:10297274:-1 11/11 None
B0024.2 ENSEMBL cdna:known chromosome:CEL140:V:10296215:10297187:-1 gene:B0024.2 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:10296214-10297187(-) 100.0 100.0
Public Domain and Genome References
Gene Title collagen
Gene Symbol col-150
Ensembl B0024.2
Entrez Gene 181814 Entrez gene
SwissProt Q17418 EMBL-EBI
WormBase CE05147 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 CAA94875 Hypothetical protein B0024.2 [Caenorhabditis elegans] ref|NP_505647.1| B0024.2 [Caenorhabditis elegans] 1.0E-115
blast CAE64784 Hypothetical protein CBG09577 [Caenorhabditis briggsae] 4.0E-99
blast CAA94874 Hypothetical protein B0024.1 [Caenorhabditis elegans] ref|NP_505646.1| B0024.1 [Caenorhabditis elegans] 6.0E-83
Protein Domains
Database ID Description E-Value
Pfam IPR002486 EMBL-EBI Nematode cuticle collagen, N-terminal 3.3E-26
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 8.0E-4
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 2.9E-5
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 1.7E-9
Pfam IPR002486 EMBL-EBI Nematode cuticle collagen, N-terminal 3.3E-26
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 8.0E-4
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 2.9E-5
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 1.7E-9
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_505647.1 1 7-29
B0024.2 1 7-29
SNAP00000027128 1 35-57
GENEFINDER00000027145 1 35-57
Sequence
Target Sequence 
>C. ELEGANS:188389_AT
aatgtgagccggcgaagccacgttgtccacggggaccaccaggacctccaggtcgtccag
gacaacgtggaacttctggatcaccaggaccccgtggacaggacaatcatcaggtgcatg
ctccaattcaatgtccacgacaacaaccaggatgtgttaaatgcccacgaggaccagcag
gcccaacaggttcaattggacaagcaggaagaccaggtccagatggacgtccaggacaac
ctggaagaaaaggaaataatggtagaccaggtcaaccggcaccacaaggaaatgctggac
atcctggaagagacggagaacccgggcaaccaggaaatccaggaaaagacggaagaaagg
gacgtgggcatccaggaacagctggaagaccaggacaaccaggaaagcaaggaagtgcag
gaaatccaggaagaaaaggagaaagaggacaagatggtcaaccaggaccaggaggaagac
cagggcaaccaggaaacagaggatccgatggacatccaggtactccaggaggtagaggcc
ttccaggaccagatgctgcatattgtgcatgcccacca

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
AATGTGAGCCGGCGAAGCCACGTTG 550 161 296 Antisense
GGAACTTCTGGATCACCAGGACCCC 130 529 364 Antisense
ACCCCGTGGACAGGACAATCATCAG 674 89 384 Antisense
CAATCATCAGGTGCATGCTCCAATT 346 181 399 Antisense
TGCTCCAATTCAATGTCCACGACAA 5 583 414 Antisense
TAAATGCCCACGAGGACCAGCAGGC 462 639 453 Antisense
GACCAGGTCCAGATGGACGTCCAGG 351 381 506 Antisense
TGGTAGACCAGGTCAACCGGCACCA 538 547 555 Antisense
AAGGGACGTGGGCATCCAGGAACAG 253 159 652 Antisense
CCAGGAGGTAGAGGCCTTCCAGGAC 308 267 820 Antisense
TGCTGCATATTGTGCATGCCCACCA 660 581 849 Antisense
Sequence Source Affymetrix Proprietary Database