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[172879_x_at] collagen /// collagen

Description F15H10.1 /REP_DB=WormBase Gene ID /WP=CE05638 /GEN=col-12 /TR=SW:P20630 /GB=CAA98257.1 /SUBMIT=HINXTON /CHR=5 /FEA=Sanger Annotation /DEF=collagen
Cluster 6grp_highest_10_10 > 08      6grp_high1_10_10 > 80      4grp_highest_8_8 > 09      4grp_high_8_8 > 54      6grp_highest_nonorm > 18      6grp_total > 72      4grp_total > 57      6grp_cgc > 74      6grp_high1_sub > 02_03_04_05      6grp_cgc_sub > 02_03_04_05      6grp_total_sub > Hat      6grp_rule_based > S2      4grp_rule_based > L3      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 25899
1 2 3 4 range
A 5434.1
(-1.7)
P 		23287.7
(3)
P 		21749.9
(2.6)
P 		541.4
(-3)
P 		22746
B 5542.3
(-1.8)
P 		22171.8
(2)
P 		26293.5
(3)
P 		394.4
(-3)
P 		25899
C 4980.8
(-1.7)
P 		20295.5
(3)
P 		18969.8
(2.6)
P 		592.8
(-3)
P 		19703
avr 5319.1
(-1.7) 		21918.3
(2.9) 		22337.7
(3) 		509.5
(-3) 		21828

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 14722
1 2 3 4 5 6 range
A 6811
(-3)
P 		21268
(3)
P 		17997.4
(1.6)
P 		17851.3
(1.6)
P 		16348.4
(1)
P 		13814.6
(-0.1)
P 		14457
B 6545.6
(-3)
P 		17812.8
(3)
P 		17617.9
(2.9)
P 		16041
(2.1)
P 		14066.1
(1)
P 		11612.9
(-0.3)
P 		11267
C 8030.8
(-3)
P 		18531
(2.1)
P 		17965
(1.8)
P 		16766.6
(1.2)
P 		20389.5
(3)
P 		10199.9
(-1.9)
P 		12359
avr 7129.1
(-3) 		19203.9
(3) 		17860.1
(2.3) 		16886.3
(1.8) 		16934.7
(1.9) 		11875.8
(-0.6) 		12075
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 6532
1 2 3 4 range
A 1978.6
(-1)
P 		5055.1
(2.3)
P 		5685.9
(3)
P 		79.3
(-3)
P 		5607
B 1767.4
(-1.3)
P 		5475.9
(2.4)
P 		6092.8
(3)
P 		84
(-3)
P 		6009
C 1648.8
(-1.6)
P 		5835.1
(2.3)
P 		6611.6
(3)
P 		100
(-3)
P 		6512
avr 1798.3
(-1.3) 		5455.4
(2.3) 		6130.1
(3) 		87.8
(-3) 		6042

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 6309
1 2 3 4 5 6 range
A 1255.5
(-3)
P 		7564
(3)
P 		3919.5
(-0.5)
P 		4527.5
(0.1)
P 		4933.2
(0.5)
P 		3363.4
(-1)
P 		6309
B 2277.5
(-3)
P 		5929.1
(3)
P 		4278.2
(0.3)
P 		4248.7
(0.2)
P 		5714.9
(2.6)
P 		4330.4
(0.4)
P 		3652
C 2976.7
(-3)
P 		5654.4
(1.4)
P 		4572.4
(-0.4)
P 		3371.8
(-2.3)
P 		6597.8
(3)
P 		3414.5
(-2.3)
P 		3621
avr 2169.9
(-3) 		6382.5
(3) 		4256.7
(-0) 		4049.3
(-0.3) 		5748.6
(2.1) 		3702.8
(-0.8) 		4213
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 172879_x_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.11670
Sequence Type Exemplar sequence
Representative Public ID F15H10.1 NCBI
Target Description F15H10.1 /REP_DB=WormBase Gene ID /WP=CE05638 /GEN=col-12 /TR=SW:P20630 /GB=CAA98257.1 /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_073276(10), NM_073277(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_073276 NCBI Caenorhabditis elegans F15H10.2 (collagen) mRNA, complete cds. 10/11 A 
NM_073277 NCBI Caenorhabditis elegans F15H10.1 (collagen) mRNA, complete cds. 11/11 A 
SNAP00000002816 ENSEMBL cdna:SNAP chromosome:CEL140:V:10423472:10424474:-1 10/11 None
SNAP00000002817 ENSEMBL cdna:SNAP chromosome:CEL140:V:10426590:10427592:-1 11/11 None
GENEFINDER00000002822 ENSEMBL cdna:GeneFinder chromosome:CEL140:V:10426590:10427592:-1 11/11 None
GENEFINDER00000002824 ENSEMBL cdna:GeneFinder chromosome:CEL140:V:10423472:10424474:-1 10/11 None
F15H10.2 ENSEMBL cdna:known chromosome:CEL140:V:10423472:10424474:-1 gene:F15H10.2 10/11 A 
F15H10.1.2 ENSEMBL cdna:known chromosome:CEL140:V:10426489:10427598:-1 gene:F15H10.1 11/11 A 
F15H10.1.1 ENSEMBL cdna:known chromosome:CEL140:V:10426489:10427674:-1 gene:F15H10.1 11/11 A 
Annotation Notes
Cross Hybridizing mRNA Matched Probes Nature of Assignment Related Probesets by Grade
NM_067008 1/11 Cross Hyb Matching Probes A 
NM_067009 1/11 Cross Hyb Matching Probes A 
NM_067504 2/11 Cross Hyb Matching Probes A 
NM_073882 1/11 Cross Hyb Matching Probes A 
NM_073883 2/11 Cross Hyb Matching Probes A 
NM_072673 1/11 Cross Hyb Matching Probes A 
SNAP00000036391 1/11 Cross Hyb Matching Probes None
GENEFINDER00000036400 1/11 Cross Hyb Matching Probes None
SNAP00000036392 1/11 Cross Hyb Matching Probes None
GENEFINDER00000036395 1/11 Cross Hyb Matching Probes None
SNAP00000015232 2/11 Cross Hyb Matching Probes None
GENEFINDER00000015234 2/11 Cross Hyb Matching Probes None
SNAP00000007051 1/11 Cross Hyb Matching Probes None
SNAP00000007052 2/11 Cross Hyb Matching Probes None
GENEFINDER00000007058 1/11 Cross Hyb Matching Probes None
GENEFINDER00000007063 2/11 Cross Hyb Matching Probes None
SNAP00000025313 1/11 Cross Hyb Matching Probes None
GENEFINDER00000025319 1/11 Cross Hyb Matching Probes None
W05B2.5 1/11 Cross Hyb Matching Probes A 
W05B2.1 1/11 Cross Hyb Matching Probes A 
K02D7.3 2/11 Cross Hyb Matching Probes A 
ZC513.8 1/11 Cross Hyb Matching Probes A 
F57B1.3 1/11 Cross Hyb Matching Probes A 
F57B1.4.1 2/11 Cross Hyb Matching Probes A 
F57B1.4.3 2/11 Cross Hyb Matching Probes None
F57B1.4.2 2/11 Cross Hyb Matching Probes A 
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrV:10426589-10427592(-) 91.48 100.0
chrV:10423471-10424468(-) 90.54 99.05
Public Domain and Genome References
Gene Title collagen
collagen
Gene Symbol col-12
col-13
Ensembl F15H10.2
F15H10.1
Entrez Gene 179452 Entrez gene
179453 Entrez gene
SwissProt P20630 EMBL-EBI
P20631 EMBL-EBI
WormBase CE05638 Wormbase
CE05639 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 CAA98257 Hypothetical protein F15H10.1 [Caenorhabditis elegans] ref|NP_505678.1| F15H10.1 [Caenorhabditis elegans] sp|P20630|COL12_CAEEL Cuticle collagen 12 precursor emb|CAA35954.1| collagen [Caenorhabditis elegans] 4.0E-60
blast CAA98258 Hypothetical protein F15H10.2 [Caenorhabditis elegans] ref|NP_505677.1| F15H10.2 [Caenorhabditis elegans] sp|P20631|COL13_CAEEL Cuticle collagen 13 precursor emb|CAA35955.1| collagen [Caenorhabditis elegans] 1.0E-59
blast CAA98257 Hypothetical protein F15H10.1 [Caenorhabditis elegans] ref|NP_505678.1| F15H10.1 [Caenorhabditis elegans] sp|P20630|COL12_CAEEL Cuticle collagen 12 precursor emb|CAA35954.1| collagen [Caenorhabditis elegans] 2.0E-58
Protein Domains
Database ID Description E-Value
Pfam IPR002486 EMBL-EBI Nematode cuticle collagen, N-terminal 2.3E-14
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 4.6E-4
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 2.0E-13
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 6.0E-7
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_505677.1 1 19-41
NP_505678.1 1 19-41
F15H10.2 1 19-41
F15H10.1.2 1 19-41
F15H10.1.1 1 19-41
SNAP00000002816 1 19-41
SNAP00000002817 1 19-41
GENEFINDER00000002822 1 19-41
GENEFINDER00000002824 1 19-41
Sequence
Target Sequence 
>C. ELEGANS:172879_X_AT
cgctgctgtcggaggattcggtggatcatctggaggatcatgctgctcatgcggatctgg
agctgctggaccagctggatcaccaggacaagatggagcaccaggaaacgatggagctcc
aggagcaccaggaaacccaggacaagatgcttctgaggatcaaactgctggaccagacag
cttctgcttcgattgcccagctggaccaccaggaccatcaggagcaccaggacaaaaggg
accatcaggagctccaggagccccaggacaatctggaggagctgctcttccaggaccacc
aggaccagctggaccaccaggaccagccggacaaccaggatccaacggaaacgccggagc
tccaggagccccaggacaagtcgtcgatgttccaggaactccaggaccagctggaccacc
aggatcaccaggaccagccggagctccaggacaaccaggacaagccggatcttcccaacc
aggaggcccaggaccacaaggagatgc

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
CGCTGCTGTCGGAGGATTCGGTGGA 346 255 336 Antisense
GAGGATCATGCTGCTCATGCGGATC 306 403 368 Antisense
GCGGATCTGGAGCTGCTGGACCAGC 129 293 386 Antisense
ACCAGACAGCTTCTGCTTCGATTGC 180 87 507 Antisense
TCAGGAGCTCCAGGAGCCCCAGGAC 264 621 580 Antisense
GACAATCTGGAGGAGCTGCTCTTCC 188 365 602 Antisense
GATCCAACGGAAACGCCGGAGCTCC 1 397 674 Antisense
GCCCCAGGACAAGTCGTCGATGTTC 621 285 703 Antisense
ATGTTCCAGGAACTCCAGGACCAGC 343 47 722 Antisense
GACAACCAGGACAAGCCGGATCTTC 502 365 785 Antisense
GAGGCCCAGGACCACAAGGAGATGC 266 405 818 Antisense
Sequence Source Affymetrix Proprietary Database