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[188350_at] collagen

Description B0024.1 /REP_DB=WormBase Gene ID /WP=CE05146 /TR=Q17417 /GB=CAA94874.1 /SUBMIT=HINXTON /CHR=5 /FEA=Sanger Annotation /DEF=collagen
Cluster 6grp_total > 42      4grp_total > 58      6grp_cgc > 91      6grp_cgc_sub > 03      6grp_total_sub > Hat      4grp_rule_based > L2      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 3582
1 2 3 4 range
A 849.9
(-1.6)
P 		2495.8
(1.2)
P 		3588.7
(3)
P 		20.4
(-3)
A 		3568
B 599.6
(-1.9)
P 		3123.7
(3)
P 		2708.9
(2.2)
P 		6.3
(-3)
A 		3117
C 790.3
(-1.6)
P 		3395.8
(3)
P 		2612.9
(1.6)
P 		15.2
(-3)
A 		3381
avr 746.6
(-1.5) 		3005.1
(3) 		2970.2
(2.9) 		14
(-3) 		2991

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 9734
1 2 3 4 5 6 range
A 4775.7
(0.3)
P 		2683.8
(-1.2)
P 		8539.1
(3)
P 		4433.5
(0.1)
P 		2247.1
(-1.5)
P 		179
(-3)
A 		8360
B 4942.4
(-0.1)
P 		2372.4
(-1.7)
P 		9912.7
(3)
P 		4311.4
(-0.5)
P 		2231.8
(-1.8)
P 		285
(-3)
A 		9628
C 5148.4
(0.7)
P 		2070
(-1.6)
P 		8137.8
(3)
P 		3927.2
(-0.2)
P 		2686.4
(-1.1)
P 		227.3
(-3)
A 		7911
avr 4955.5
(0.3) 		2375.4
(-1.5) 		8863.2
(3) 		4224
(-0.2) 		2388.4
(-1.5) 		230.4
(-3) 		8633
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 975
1 2 3 4 range
A 309.5
(-1)
P 		541.8
(0.5)
P 		938.1
(3)
P 		3
(-3)
A 		935
B 191.2
(-1.5)
P 		771.5
(3)
P 		627.7
(1.9)
P 		1.3
(-3)
A 		770
C 261.6
(-1.4)
P 		976.3
(3)
P 		910.7
(2.6)
P 		2.6
(-3)
A 		974
avr 254.1
(-1.2) 		763.2
(2.5) 		825.5
(3) 		2.3
(-3) 		823

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 2364
1 2 3 4 5 6 range
A 880.4
(-0.2)
P 		954.5
(0)
P 		1859.6
(3)
P 		1124.4
(0.6)
P 		678.1
(-0.9)
P 		43.6
(-3)
A 		1816
B 1719.7
(1.2)
P 		789.7
(-1.2)
P 		2407.1
(3)
P 		1141.9
(-0.3)
P 		906.8
(-0.9)
P 		106.3
(-3)
A 		2301
C 1908.3
(2.5)
P 		631.6
(-1.3)
P 		2071.2
(3)
P 		789.8
(-0.9)
P 		869.3
(-0.6)
P 		76.1
(-3)
A 		1995
avr 1502.8
(1.2) 		791.9
(-0.9) 		2112.6
(3) 		1018.7
(-0.2) 		818.1
(-0.8) 		75.3
(-3) 		2037
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 188350_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.12095
Sequence Type Exemplar sequence
Representative Public ID B0024.1 NCBI
Target Description B0024.1 /REP_DB=WormBase Gene ID /WP=CE05146 /TR=Q17417 /GB=CAA94874.1 /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_073245(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_073245 NCBI Caenorhabditis elegans B0024.1 (collagen) mRNA, complete cds. 11/11 None
SNAP00000027127 ENSEMBL cdna:SNAP chromosome:CEL140:V:10294375:10295393:-1 11/11 None
GENEFINDER00000027152 ENSEMBL cdna:GeneFinder chromosome:CEL140:V:10294375:10295393:-1 11/11 None
B0024.1 ENSEMBL cdna:known chromosome:CEL140:V:10294291:10295449:-1 gene:B0024.1 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:10294374-10295393(-) 100.0 100.0
Public Domain and Genome References
Gene Title collagen
Gene Symbol col-149
Ensembl B0024.1
Entrez Gene 179431 Entrez gene
SwissProt Q17417 EMBL-EBI
WormBase CE05146 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 CAA94874 Hypothetical protein B0024.1 [Caenorhabditis elegans] ref|NP_505646.1| B0024.1 [Caenorhabditis elegans] 1.0E-107
blast CAE64783 Hypothetical protein CBG09576 [Caenorhabditis briggsae] 4.0E-92
blast CAA94875 Hypothetical protein B0024.2 [Caenorhabditis elegans] ref|NP_505647.1| B0024.2 [Caenorhabditis elegans] 2.0E-75
Protein Domains
Database ID Description E-Value
Pfam IPR002486 EMBL-EBI Nematode cuticle collagen, N-terminal 6.9E-27
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 6.2E-5
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 3.6E-8
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 2.9E-11
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_505646.1 1 7-29
B0024.1 1 7-29
SNAP00000027127 1 7-29
GENEFINDER00000027152 1 7-29
Sequence
Target Sequence 
>C. ELEGANS:188350_AT
gccaaaatgtccacgaggaccaccaggaccaccagggcatccaggacagagaggaattcc
aggaattccaggacgcaatggacaagataattataacacaattcgtgctcccgcctgtcc
accgcgtaatcaagactgtattaaatgcccggccggaccaccaggaccatccggtacatg
cggacaggttggaagaccgggtccagacggacgtccaggacaaccaggaagacgaggaaa
tgatggaagaccaggacaaccaggaccacaaggaaatgctggacaaccaggaagagatgg
aaatccaggacaaccaggacatccaggaaaggatgggcgtcgcggacacggatctccagg
agcaccaggaagagctggacaaccaggacgtcaaggagcacctggaaacccaggaagacc
aggagagagaggaccaagtggaccatgtggaccagctggaagatcaggtcaaccaggaaa
ccgaggatccgatggtcatccaggagctcc

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GCCAAAATGTCCACGAGGACCACCA 254 277 315 Antisense
TTATAACACAATTCGTGCTCCCGCC 19 675 405 Antisense
CCTGTCCACCGCGTAATCAAGACTG 146 267 428 Antisense
CTGTATTAAATGCCCGGCCGGACCA 373 239 450 Antisense
ACCAGGACCATCCGGTACATGCGGA 55 87 474 Antisense
GGTACATGCGGACAGGTTGGAAGAC 339 499 487 Antisense
TGGAAGACCGGGTCCAGACGGACGT 396 525 504 Antisense
GGAAAGGATGGGCGTCGCGGACACG 511 525 640 Antisense
GACAACCAGGACGTCAAGGAGCACC 500 365 692 Antisense
GGAAACCGAGGATCCGATGGTCATC 705 527 790 Antisense
GATCCGATGGTCATCCAGGAGCTCC 592 415 800 Antisense
Sequence Source Affymetrix Proprietary Database