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[188364_s_at] collagen

Description F08G5.4 /REP_DB=WormBase Gene ID /WP=CE05574 /TR=Q19218 /GB=CAA94581.1 /SUBMIT=HINXTON /CHR=4 /FEA=Sanger Annotation /DEF=collagen
Cluster 6grp_highest_10_10 > 09      6grp_high1_10_10 > 90      6grp_highest_nonorm > 54      6grp_total > 0      4grp_total > 57      6grp_total_sub > Hat      6grp_cgc > 64      4grp_rule_based > L3      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 3379
1 2 3 4 range
A 55.3
(-2.9)
A 		3127.6
(2.5)
P 		3389.3
(3)
P 		10.4
(-3)
A 		3379
B 21.3
(-3)
A 		2602.1
(1.6)
P 		3357.2
(3)
P 		43.6
(-3)
A 		3336
C 91.9
(-3)
A 		2250.6
(1.4)
P 		3018.7
(3)
P 		85.3
(-3)
A 		2933
avr 56.2
(-3) 		2660.1
(1.9) 		3255.1
(3) 		46.4
(-3) 		3209

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 2066
1 2 3 4 5 6 range
A 226.4
(-3)
P 		2292.6
(3)
P 		1099.7
(-0.5)
P 		1373.3
(0.3)
P 		1621.5
(1.1)
P 		1078.4
(-0.5)
P 		2066
B 246.1
(-3)
P 		1879.6
(3)
P 		1114.8
(0.2)
P 		1378.1
(1.2)
P 		1495.7
(1.6)
P 		1083.6
(0.1)
P 		1634
C 362.1
(-3)
P 		1676.9
(1.9)
P 		1233.5
(0.3)
P 		1107.8
(-0.2)
P 		1968.9
(3)
P 		828.4
(-1.3)
P 		1607
avr 278.2
(-3) 		1949.7
(3) 		1149.3
(0.1) 		1286.4
(0.6) 		1695.4
(2.1) 		996.8
(-0.4) 		1672
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 1051
1 2 3 4 range
A 20.1
(-2.9)
A 		678.9
(1.6)
P 		886
(3)
P 		1.5
(-3)
A 		885
B 6.8
(-3)
A 		642.7
(1.9)
P 		777.9
(3)
P 		9.3
(-3)
A 		771
C 30.4
(-2.9)
A 		647.1
(0.7)
P 		1052.1
(3)
P 		14.4
(-3)
A 		1038
avr 19.1
(-2.9) 		656.2
(1.3) 		905.3
(3) 		8.4
(-3) 		897

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 774
1 2 3 4 5 6 range
A 41.7
(-3)
P 		815.4
(3)
P 		239.5
(-1.5)
P 		348.3
(-0.6)
P 		489.3
(0.5)
P 		262.6
(-1.3)
P 		774
B 85.6
(-3)
P 		625.6
(3)
P 		270.7
(-0.9)
P 		365
(0.1)
P 		607.7
(2.8)
P 		404.1
(0.5)
P 		540
C 134.2
(-3)
P 		511.7
(1.5)
P 		314
(-0.9)
P 		222.8
(-1.9)
P 		637.1
(3)
P 		277.3
(-1.3)
P 		503
avr 87.2
(-3) 		650.9
(3) 		274.7
(-1) 		312
(-0.6) 		578
(2.2) 		314.7
(-0.6) 		564
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 188364_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.8770
Sequence Type Exemplar sequence
Representative Public ID F08G5.4 NCBI
Target Description F08G5.4 /REP_DB=WormBase Gene ID /WP=CE05574 /TR=Q19218 /GB=CAA94581.1 /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_069971(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_069971 NCBI Caenorhabditis elegans F08G5.4 (collagen) mRNA, complete cds. 11/11 None
SNAP00000043808 ENSEMBL cdna:SNAP chromosome:CEL140:IV:12427516:12428467:-1 11/11 None
GENEFINDER00000043818 ENSEMBL cdna:GeneFinder chromosome:CEL140:IV:12427516:12428467:-1 11/11 None
F08G5.4 ENSEMBL cdna:known chromosome:CEL140:IV:12427476:12428486:-1 gene:F08G5.4 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
chrIV:12427521-12428473(-) 83.89 100.0
Public Domain and Genome References
Gene Title collagen
Gene Symbol col-130
Ensembl F08G5.4
Entrez Gene 178193 Entrez gene
SwissProt Q19218 EMBL-EBI
WormBase CE05574 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 CAA94581 Hypothetical protein F08G5.4 [Caenorhabditis elegans] ref|NP_502372.1| F08G5.4 [Caenorhabditis elegans] 4.0E-55
blast CAE59859 Hypothetical protein CBG03334 [Caenorhabditis briggsae] 6.0E-52
blast CAE62622 Hypothetical protein CBG06744 [Caenorhabditis briggsae] 8.0E-20
Protein Domains
Database ID Description E-Value
Pfam IPR002486 EMBL-EBI Nematode cuticle collagen, N-terminal 4.2E-32
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 1.2E-4
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 5.7E-12
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 1.5E-13
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_502372.1 1 7-29
F08G5.4 1 7-29
SNAP00000043808 1 7-29
GENEFINDER00000043818 1 7-29
Sequence
Target Sequence 
>C. ELEGANS:188364_S_AT
gagaggctggaaagaccggaattaatggaatttcactcatcagccatgaaggagagtccg
gatgcattaaatgcccagccggagaagccggaccagctggaccagatggagctccaggag
caccaggaccagacggacagccaggacaagatggaccagccggacagccaggagccccag
gaccagctggaccagaaggagatgctggagcaccaggagacgccggagcaccaggagccc
caggagccccaggacaagacggacaacgcggaaccggacttccaggagcaccaggagccc
caggaccacagggaccatctggaaacccaggacaagacggagccgctggagccccaggac
aagctggaccagctggaccagccggaccagacggacaaccaggacaagctggacaagacg
gagaggctggaccagaaggaaatgctggacaaccaggagctgatgctgcctactgtccat
gcccagccagaactggagcagttgagaacaagccagagaccagtg

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GAGAGGCTGGAAAGACCGGAATTAA 665 391 356 Antisense
GACCGGAATTAATGGAATTTCACTC 114 383 369 Antisense
GGAATTTCACTCATCAGCCATGAAG 431 533 382 Antisense
CATCAGCCATGAAGGAGAGTCCGGA 57 213 393 Antisense
AGGAGAGTCCGGATGCATTAAATGC 284 55 405 Antisense
CATTAAATGCCCAGCCGGAGAAGCC 349 207 420 Antisense
CCAGCCGGAGAAGCCGGACCAGCTG 46 273 430 Antisense
GTCCATGCCCAGCCAGAACTGGAGC 402 477 830 Antisense
TGCCCAGCCAGAACTGGAGCAGTTG 186 585 835 Antisense
GGAGCAGTTGAGAACAAGCCAGAGA 224 521 850 Antisense
GTTGAGAACAAGCCAGAGACCAGTG 254 437 856 Antisense
Sequence Source Affymetrix Proprietary Database