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[190530_s_at] collagen

Description F11G11.11 /REP_DB=WormBase Gene ID /WP=CE09353 /GEN=col-20 /TR=P91249 /GB=AAB37842.1 /SUBMIT=ST.LOUIS /CHR=2 /FEA=Sanger Annotation /DEF=collagen
Cluster 6grp_total > 94      4grp_total > 57      6grp_cgc > 89      6grp_total_sub > Hat      6grp_rule_based > S5      4grp_rule_based > L3      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 109
1 2 3 4 range
A 27
(-3)
A 		104.3
(1.9)
A 		122
(3)
P 		45.5
(-1.8)
A 		95
B 20.6
(-3)
A 		116.5
(3)
P 		79.9
(0.7)
P 		26.4
(-2.6)
A 		96
C 43.3
(-0.6)
A 		53.8
(0.2)
A 		88.2
(3)
P 		13.2
(-3)
A 		75
avr 30.3
(-2.8) 		91.5
(2.5) 		96.7
(3) 		28.4
(-3) 		68

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 1764
1 2 3 4 5 6 range
A 37.3
(-3)
A 		168.6
(-2.4)
P 		121.9
(-2.6)
P 		241.8
(-2)
P 		1294.9
(3)
P 		894.8
(1.1)
P 		1258
B 45.2
(-3)
A 		267.8
(-2.2)
P 		112.4
(-2.7)
A 		247.8
(-2.2)
P 		1627.6
(3)
P 		779.6
(-0.2)
P 		1582
C 47.4
(-3)
A 		249.5
(-2.3)
A 		174.7
(-2.6)
P 		258.8
(-2.3)
P 		1801.4
(3)
P 		585.8
(-1.2)
P 		1754
avr 43.3
(-3) 		228.6
(-2.3) 		136.3
(-2.6) 		249.5
(-2.2) 		1574.6
(3) 		753.4
(-0.2) 		1531
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 30
1 2 3 4 range
A 9.8
(-2.3)
A 		22.6
(0.8)
A 		31.9
(3)
P 		6.7
(-3)
A 		25
B 6.6
(-2.7)
A 		28.8
(3)
P 		18.5
(0.3)
P 		5.6
(-3)
A 		23
C 14.3
(-0.5)
A 		15.5
(-0.2)
A 		30.7
(3)
P 		2.2
(-3)
A 		29
avr 10.2
(-1.5) 		22.3
(1.7) 		27
(3) 		4.8
(-3) 		22

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 654
1 2 3 4 5 6 range
A 6.9
(-3)
A 		59.9
(-2.2)
P 		26.5
(-2.7)
P 		61.3
(-2.1)
P 		390.7
(3)
P 		217.8
(0.3)
P 		384
B 15.7
(-3)
A 		89.1
(-2.3)
P 		27.3
(-2.9)
A 		65.6
(-2.5)
P 		661.3
(3)
P 		290.7
(-0.4)
P 		646
C 17.6
(-3)
A 		76.1
(-2.4)
A 		44.5
(-2.7)
P 		52
(-2.6)
P 		582.9
(3)
P 		196.1
(-1.1)
P 		565
avr 13.4
(-3) 		75
(-2.3) 		32.8
(-2.8) 		59.6
(-2.5) 		545
(3) 		234.9
(-0.5) 		532
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 190530_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.5221
Sequence Type Exemplar sequence
Representative Public ID F11G11.11 NCBI
Target Description F11G11.11 /REP_DB=WormBase Gene ID /WP=CE09353 /GEN=col-20 /TR=P91249 /GB=AAB37842.1 /SUBMIT=ST.LOUIS /CHR=2 /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_062478(9)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_062478 NCBI Caenorhabditis elegans F11G11.11 (collagen) mRNA, complete cds. 9/11 None
F11G11.11.2 ENSEMBL cdna:known chromosome:CEL140:II:4869263:4870757:-1 gene:F11G11.11 9/11 None
F11G11.11.1 ENSEMBL cdna:known chromosome:CEL140:II:4869593:4870762:-1 gene:F11G11.11 11/11 None
Annotation Notes
Cross Hybridizing mRNA Matched Probes Nature of Assignment Related Probesets by Grade
SNAP00000005485 6/11 Cross Hyb Matching Probes None
GENEFINDER00000005498 6/11 Cross Hyb Matching Probes None
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrII:4869589-4870755(-) 94.99 100.0
Public Domain and Genome References
Gene Title collagen
Gene Symbol col-20
Ensembl F11G11.11
Entrez Gene 173840 Entrez gene
SwissProt P91249 EMBL-EBI
WormBase CE36533 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 NP_494879 F11G11.11 [Caenorhabditis elegans] gb|AAB37842.2| Collagen protein 20 [Caenorhabditis elegans] 5.0E-56
blast CAE56955 Hypothetical protein CBG24805 [Caenorhabditis briggsae] 7.0E-34
blast NP_494880 F11G11.12 [Caenorhabditis elegans] gb|AAB37843.1| Collagen protein 73 [Caenorhabditis elegans] 1.0E-27
Protein Domains
Database ID Description E-Value
Pfam IPR002486 EMBL-EBI Nematode cuticle collagen, N-terminal 3.8E-6
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 4.1E-4
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 7.7E-7
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 2.2E-13
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_494879.2 1 20-42
F11G11.11.2 1 20-42
F11G11.11.1 1 20-42
Sequence
Target Sequence 
>C. ELEGANS:190530_S_AT
aagatggaggagccggaaacccaggaactccaggacaagttcgttctcttccatccccac
caggagagccaggacaaccaggagagccaggaggtccaggagagccaggagccgatggac
gaccaggacacccaggaagagccggacctccaggaccaccaggagacaatggaccaaacg
gagagccaggaaaggacggggaggatggagctccaggagccgcaggaaacgccggagcca
agggatcttgcgatcactgcccaccaccaagaactgctccaggatattagattgtctttc
tatgtttttaaattcttcttttctttctggtcgtttatgtttttcactcaaaatgaagaa
ctttcgagtatattagttgattcgaattatcatataagtgtgttttcaaa

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
AAGATGGAGGAGCCGGAAACCCAGG 415 153 589 Antisense
ACTCCAGGACAAGTTCGTTCTCTTC 417 99 615 Antisense
CCAGGACAAGTTCGTTCTCTTCCAT 304 265 618 Antisense
CCAGGAGACAATGGACCAAACGGAG 394 271 747 Antisense
GGAAAGGACGGGGAGGATGGAGCTC 632 523 777 Antisense
AACGCCGGAGCCAAGGGATCTTGCG 636 143 816 Antisense
TTCTTTTCTTTCTGGTCGTTTATGT 37 691 904 Antisense
TCTTTCTGGTCGTTTATGTTTTTCA 522 615 910 Antisense
GTTTATGTTTTTCACTCAAAATGAA 595 449 921 Antisense
GAGTATATTAGTTGATTCGAATTAT 231 399 954 Antisense
ATTATCATATAAGTGTGTTTTCAAA 700 13 974 Antisense
Sequence Source Affymetrix Proprietary Database