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[188339_at] collagen

Description W08D2.6 /REP_DB=WormBase Gene ID /WP=CE06561 /TR=Q23222 /GB=CAA94234.1 /SUBMIT=HINXTON /CHR=4 /FEA=Sanger Annotation /DEF=collagen
Cluster 6grp_highest_10_10 > 29      6grp_high1_10_10 > 81      4grp_high_8_8 > 45      6grp_highest_nonorm > 45      6grp_total > 81      4grp_total > 50      6grp_highest_sub > 04_05      6grp_cgc > 86      6grp_high1_sub > 04      6grp_cgc_sub > 04      6grp_total_sub > Hat      6grp_rule_based > S4      4grp_rule_based > L2      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 151
1 2 3 4 range
A 56.5
(-2.3)
P 		176.7
(3)
P 		172.3
(2.8)
P 		40.7
(-3)
A 		136
B 71.9
(-2.8)
P 		191.9
(3)
P 		121.6
(-0.4)
P 		67.5
(-3)
P 		124
C 86.1
(-2.1)
P 		180.8
(3)
P 		135.5
(0.6)
P 		68.6
(-3)
M 		112
avr 71.5
(-2.4) 		183.1
(3) 		143.1
(1.1) 		58.9
(-3) 		124

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 6341
1 2 3 4 5 6 range
A 113.7
(-3)
P 		130.7
(-3)
P 		653.5
(-2.5)
P 		6448.7
(3)
P 		3807.3
(0.5)
P 		221.7
(-2.9)
P 		6335
B 125.7
(-3)
P 		126.9
(-3)
P 		621.2
(-2.5)
P 		5531.5
(3)
P 		4415.7
(1.8)
P 		176.9
(-2.9)
P 		5406
C 121.7
(-3)
P 		107.5
(-3)
P 		739
(-2.3)
P 		5643.6
(3)
P 		4463.1
(1.7)
P 		162.4
(-2.9)
P 		5536
avr 120.4
(-3) 		121.7
(-3) 		671.2
(-2.4) 		5874.6
(3) 		4228.7
(1.3) 		187
(-2.9) 		5754
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 46
1 2 3 4 range
A 20.6
(-0.8)
P 		38.4
(2)
P 		45
(3)
P 		6
(-3)
A 		39
B 22.9
(-1.5)
P 		47.4
(3)
P 		28.2
(-0.5)
P 		14.4
(-3)
P 		33
C 28.5
(-0.5)
P 		52
(3)
P 		47.2
(2.3)
P 		11.6
(-3)
M 		40
avr 24
(-0.7) 		45.9
(3) 		40.1
(2) 		10.7
(-3) 		35

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 1773
1 2 3 4 5 6 range
A 21
(-3)
P 		46.5
(-2.9)
P 		142.3
(-2.5)
P 		1635.5
(3)
P 		1148.9
(1.2)
P 		54
(-2.9)
P 		1615
B 43.7
(-3)
P 		42.2
(-3)
P 		150.8
(-2.6)
P 		1465.1
(1.9)
P 		1794
(3)
P 		66
(-2.9)
P 		1752
C 45.1
(-2.9)
P 		32.8
(-3)
P 		188.1
(-2.3)
P 		1134.9
(1.7)
P 		1444.2
(3)
P 		54.4
(-2.9)
P 		1411
avr 36.6
(-3) 		40.5
(-3) 		160.4
(-2.5) 		1411.8
(2.8) 		1462.4
(3) 		58.1
(-2.9) 		1426
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 188339_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.8979
Sequence Type Exemplar sequence
Representative Public ID W08D2.6 NCBI
Target Description W08D2.6 /REP_DB=WormBase Gene ID /WP=CE06561 /TR=Q23222 /GB=CAA94234.1 /SUBMIT=HINXTON /CHR=4 /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_069355(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_069355 NCBI Caenorhabditis elegans W08D2.6 (collagen) mRNA, complete cds. 11/11 None
SNAP00000011773 ENSEMBL cdna:SNAP chromosome:CEL140:IV:9821899:9823369:1 11/11 None
GENEFINDER00000011780 ENSEMBL cdna:GeneFinder chromosome:CEL140:IV:9821899:9823040:1 11/11 None
W08D2.6 ENSEMBL cdna:known chromosome:CEL140:IV:9821869:9823086:1 gene:W08D2.6 11/11 None
Annotation Notes
Cross Hybridizing mRNA Matched Probes Nature of Assignment Related Probesets by Grade
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrIV:9821874-9823046(+) 100.0 100.0
Public Domain and Genome References
Gene Title collagen
Gene Symbol col-123
Ensembl W08D2.6
Entrez Gene 177823 Entrez gene
SwissProt Q23222 EMBL-EBI
WormBase CE06561 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 CAA94234 Hypothetical protein W08D2.6 [Caenorhabditis elegans] ref|NP_501756.1| W08D2.6 [Caenorhabditis elegans] 1.0E-102
blast CAA94234 Hypothetical protein W08D2.6 [Caenorhabditis elegans] ref|NP_501756.1| W08D2.6 [Caenorhabditis elegans] 2.0E-96
blast CAA94234 Hypothetical protein W08D2.6 [Caenorhabditis elegans] ref|NP_501756.1| W08D2.6 [Caenorhabditis elegans] 3.0E-93
blast CAE59983 Hypothetical protein CBG03475 [Caenorhabditis briggsae] 3.0E-76
blast CAE59983 Hypothetical protein CBG03475 [Caenorhabditis briggsae] 7.0E-73
blast CAA88865 Hypothetical protein K12D12.3 [Caenorhabditis elegans] ref|NP_496535.1| COLlagen family member (col-84) [Caenorhabditis elegans] 2.0E-35
Protein Domains
Database ID Description E-Value
Pfam IPR002486 EMBL-EBI Nematode cuticle collagen, N-terminal 1.1E-20
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 5.6E-11
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 2.0E-8
Pfam IPR002486 EMBL-EBI Nematode cuticle collagen, N-terminal 1.1E-20
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 5.6E-11
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 2.0E-8
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_501756.1 1 15-37
W08D2.6 1 15-37
SNAP00000011773 1 7-29
GENEFINDER00000011780 1 7-29
Sequence
Target Sequence 
>C. ELEGANS:188339_AT
caccaggactaccagggccaaatggagttcctggacttgatggtaaaccgggactggact
cactagatgtggaaccacaagcacagggaactggaacgtgcttccattgtccacagggac
cgccgggatctcctggaccaatgggacatccaggagcacgtggaatgaagggatccgatg
gacaaccaggacaaccaggaaaagacggggatccaggaaaaccaggagagatgggaccta
atggattccaaggaaaggtaggaccagatggattccctggagaaaaaggaggtgatggac
gaaggcttattggaagacctggaccaaagggacagaaaggagagacaggacatccaggtg
cacaaggaactccaggccacaatggaccaactgggccccctggagatgcgggaccagatg
gaggaccagggccccaaggagagcaaggagcggatggaggtccaggatcagaaggaaaag
ttggaagaccggggagggatgccgaatactgtcattgcccagcacgtggatctcatggtg
gttcatctggaggtgga

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
CACCAGGACTACCAGGGCCAAATGG 19 201 470 Antisense
GGGCCAAATGGAGTTCCTGGACTTG 145 405 484 Antisense
AACCGGGACTGGACTCACTAGATGT 293 147 515 Antisense
GGAACTGGAACGTGCTTCCATTGTC 517 527 556 Antisense
TGCTTCCATTGTCCACAGGGACCGC 222 577 568 Antisense
GGACCAATGGGACATCCAGGAGCAC 208 523 604 Antisense
GAGACAGGACATCCAGGTGCACAAG 359 393 811 Antisense
GGAACTCCAGGCCACAATGGACCAA 545 529 835 Antisense
GGATGCCGAATACTGTCATTGCCCA 657 511 966 Antisense
CCCAGCACGTGGATCTCATGGTGGT 121 257 987 Antisense
TCATGGTGGTTCATCTGGAGGTGGA 241 619 1002 Antisense
Sequence Source Affymetrix Proprietary Database