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[171770_x_at]

Description CEK068B9R_rc /REP_DB=TREMBL Accession /5_PRIME_EXT_ID=W05B2.5 /5_PRIME_EXT_DB=WormBase Gene ID /GB=D65750 /WB_GENE_ID=W05B2.5 /WP=CE20147 /CHR=3 /FEA=Genomic Cluster /DEF=C.elegans cDNA clone yk68b9 : 3prime end, single read.
Cluster 6grp_highest_10_10 > 25      6grp_high1_10_10 > 41      4grp_highest_8_8 > 16      4grp_high_8_8 > 60      6grp_highest_nonorm > 09      6grp_total > 52      4grp_total > 59      6grp_highest_sub > 03      6grp_cgc > 82      6grp_high1_sub > 03      6grp_cgc_sub > 03      6grp_total_sub > Hat      6grp_rule_based > S3      4grp_rule_based > L3      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 44580
1 2 3 4 range
A 28186.7
(0.5)
P 		46412.7
(3)
P 		41501.3
(2.3)
P 		2847
(-3)
P 		43566
B 30948.1
(0.8)
P 		36215.1
(1.5)
P 		47426.9
(3)
P 		3445.1
(-3)
P 		43982
C 26849.7
(1.9)
P 		32198.1
(3)
P 		31738.8
(2.9)
P 		3740.1
(-3)
P 		28458
avr 28661.5
(1.1) 		38275.3
(2.7) 		40222.3
(3) 		3344.1
(-3) 		36878

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 20839
1 2 3 4 5 6 range
A 34516.8
(-0.8)
P 		34864.8
(-0.7)
P 		45802.3
(3)
P 		34367
(-0.9)
P 		29396.8
(-2.5)
P 		28039.3
(-3)
P 		17763
B 29950.2
(-1.4)
P 		36937.2
(0.8)
P 		43659.6
(3)
P 		34127.8
(-0.1)
P 		24963.4
(-3)
P 		26197.1
(-2.6)
P 		18696
C 28925.3
(-2.3)
P 		37198.7
(3)
P 		36699.3
(2.7)
P 		36563.3
(2.6)
P 		31461.3
(-0.7)
P 		27848.7
(-3)
P 		9350
avr 31130.8
(-1.5) 		36333.6
(0.7) 		42053.7
(3) 		35019.4
(0.1) 		28607.2
(-2.5) 		27361.7
(-3) 		14692
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 10645
1 2 3 4 range
A 10262.8
(2.7)
P 		10074.9
(2.6)
P 		10849.2
(3)
P 		416.7
(-3)
P 		10433
B 9869.1
(2.3)
P 		8944.3
(1.8)
P 		10989.9
(3)
P 		734.1
(-3)
P 		10256
C 8888
(1.7)
P 		9257.1
(2)
P 		11062
(3)
P 		630.6
(-3)
P 		10431
avr 9673.3
(2.3) 		9425.4
(2.1) 		10967
(3) 		593.8
(-3) 		10373

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 6037
1 2 3 4 5 6 range
A 6362.9
(-3)
P 		12399.6
(3)
P 		9974.8
(0.6)
P 		8716.3
(-0.7)
P 		8870.7
(-0.5)
P 		6826.7
(-2.5)
P 		6037
B 10421.2
(-0.5)
P 		12294.8
(3)
P 		10601.8
(-0.1)
P 		9039.3
(-3)
P 		10142.3
(-1)
P 		9768.8
(-1.7)
P 		3256
C 10721.4
(2.1)
P 		11350.5
(3)
P 		9340.6
(-0)
P 		7352.9
(-3)
P 		10180.4
(1.2)
P 		9322.6
(-0)
P 		3998
avr 9168.5
(-1.7) 		12015
(3) 		9972.4
(-0.4) 		8369.5
(-3) 		9731.1
(-0.8) 		8639.4
(-2.6) 		3646
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 171770_x_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.24227
Sequence Type Exemplar sequence
Representative Public ID CEK068B9R NCBI
Target Description CEK068B9R_rc /REP_DB=TREMBL Accession /5_PRIME_EXT_ID=W05B2.5 /5_PRIME_EXT_DB=WormBase Gene ID /GB=D65750 /WB_GENE_ID=W05B2.5 /WP=CE20147 /CHR=3 /FEA=Genomic Cluster /DEF=C.elegans cDNA clone yk68b9 : 3prime end, single read.
Cluster Evidence This cluster is supported by a Genomic Cluster.
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_067008(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_067008 NCBI Caenorhabditis elegans COLlagen family member (col-93) (col-93) mRNA, complete cds. 11/11 A 
SNAP00000036391 ENSEMBL cdna:SNAP chromosome:CEL140:III:10984490:10985461:-1 11/11 None
GENEFINDER00000036400 ENSEMBL cdna:GeneFinder chromosome:CEL140:III:10984490:10985461:-1 11/11 None
W05B2.5 ENSEMBL cdna:known chromosome:CEL140:III:10984415:10985485:-1 gene:W05B2.5 11/11 A 
Annotation Notes
Cross Hybridizing mRNA Matched Probes Nature of Assignment Related Probesets by Grade
NM_067009 7/11 Cross Hyb Matching Probes A 
NM_181982 2/11 Cross Hyb Matching Probes None
NM_182467 1/11 Cross Hyb Matching Probes A 
NM_069466 1/11 Cross Hyb Matching Probes A 
NM_064730 1/11 Cross Hyb Matching Probes A 
NM_069125 3/11 Cross Hyb Matching Probes A 
NM_069126 3/11 Cross Hyb Matching Probes A 
NM_072337 1/11 Cross Hyb Matching Probes A 
NM_069160 1/11 Cross Hyb Matching Probes A 
NM_072974 2/11 Cross Hyb Matching Probes A 
NM_070299 1/11 Cross Hyb Matching Probes A 
NM_075994 1/11 Cross Hyb Matching Probes A 
NM_073882 2/11 Cross Hyb Matching Probes A 
NM_073883 1/11 Cross Hyb Matching Probes A 
NM_073501 1/11 Cross Hyb Matching Probes A 
NM_072335 1/11 Cross Hyb Matching Probes A 
NM_067007 7/11 Cross Hyb Matching Probes A 
NM_069706 3/11 Cross Hyb Matching Probes A 
NM_068118 1/11 Cross Hyb Matching Probes A 
NM_077559 1/11 Cross Hyb Matching Probes A 
SNAP00000036390 7/11 Cross Hyb Matching Probes None
GENEFINDER00000036401 7/11 Cross Hyb Matching Probes None
SNAP00000036392 7/11 Cross Hyb Matching Probes None
GENEFINDER00000036395 7/11 Cross Hyb Matching Probes None
SNAP00000017782 1/11 Cross Hyb Matching Probes None
SNAP00000034887 3/11 Cross Hyb Matching Probes None
GENEFINDER00000034916 2/11 Cross Hyb Matching Probes None
SNAP00000003708 1/11 Cross Hyb Matching Probes None
GENEFINDER00000003712 1/11 Cross Hyb Matching Probes None
SNAP00000005654 3/11 Cross Hyb Matching Probes None
SNAP00000005655 3/11 Cross Hyb Matching Probes None
GENEFINDER00000005663 3/11 Cross Hyb Matching Probes None
GENEFINDER00000005664 3/11 Cross Hyb Matching Probes None
SNAP00000023158 1/11 Cross Hyb Matching Probes None
GENEFINDER00000023159 1/11 Cross Hyb Matching Probes None
SNAP00000035582 1/11 Cross Hyb Matching Probes None
GENEFINDER00000035589 1/11 Cross Hyb Matching Probes None
SNAP00000037122 3/11 Cross Hyb Matching Probes None
GENEFINDER00000037126 3/11 Cross Hyb Matching Probes None
SNAP00000043526 1/11 Cross Hyb Matching Probes None
GENEFINDER00000043530 1/11 Cross Hyb Matching Probes None
SNAP00000007051 1/11 Cross Hyb Matching Probes None
SNAP00000007052 1/11 Cross Hyb Matching Probes None
GENEFINDER00000007058 2/11 Cross Hyb Matching Probes None
GENEFINDER00000007063 1/11 Cross Hyb Matching Probes None
SNAP00000018332 1/11 Cross Hyb Matching Probes None
GENEFINDER00000018334 1/11 Cross Hyb Matching Probes None
SNAP00000023008 1/11 Cross Hyb Matching Probes None
SNAP00000023009 2/11 Cross Hyb Matching Probes None
SNAP00000023010 1/11 Cross Hyb Matching Probes None
GENEFINDER00000023016 1/11 Cross Hyb Matching Probes None
GENEFINDER00000023017 2/11 Cross Hyb Matching Probes None
SNAP00000035388 1/11 Cross Hyb Matching Probes None
SNAP00000035390 1/11 Cross Hyb Matching Probes None
GENEFINDER00000035395 1/11 Cross Hyb Matching Probes None
GENEFINDER00000035407 1/11 Cross Hyb Matching Probes None
SNAP00000029186 1/11 Cross Hyb Matching Probes None
GENEFINDER00000029192 1/11 Cross Hyb Matching Probes None
SNAP00000037973 1/11 Cross Hyb Matching Probes None
GENEFINDER00000037983 1/11 Cross Hyb Matching Probes None
SNAP00000008502 1/11 Cross Hyb Matching Probes None
GENEFINDER00000008503 1/11 Cross Hyb Matching Probes None
W05G11.3.1 1/11 Cross Hyb Matching Probes None
W05G11.3.2 1/11 Cross Hyb Matching Probes None
W05B2.6 7/11 Cross Hyb Matching Probes A 
W05B2.1 7/11 Cross Hyb Matching Probes A 
Y41C4A.19 2/11 Cross Hyb Matching Probes None
F30B5.1 1/11 Cross Hyb Matching Probes A 
T28C6.4 3/11 Cross Hyb Matching Probes A 
T28C6.6 3/11 Cross Hyb Matching Probes A 
C53B4.5 1/11 Cross Hyb Matching Probes A 
C24F3.6 1/11 Cross Hyb Matching Probes None
C29F4.1.2 3/11 Cross Hyb Matching Probes None
C29F4.1.1 3/11 Cross Hyb Matching Probes None
F52B11.4 1/11 Cross Hyb Matching Probes A 
T15B7.4 1/11 Cross Hyb Matching Probes A 
T15B7.3 1/11 Cross Hyb Matching Probes A 
B0222.7 2/11 Cross Hyb Matching Probes A 
F57B7.3 1/11 Cross Hyb Matching Probes A 
F57B1.3 2/11 Cross Hyb Matching Probes A 
F57B1.4.1 1/11 Cross Hyb Matching Probes A 
F57B1.4.3 1/11 Cross Hyb Matching Probes None
F57B1.4.2 1/11 Cross Hyb Matching Probes A 
EGAP7.1.1 1/11 Cross Hyb Matching Probes None
EGAP7.1.2 1/11 Cross Hyb Matching Probes None
T10E10.6 1/11 Cross Hyb Matching Probes A 
C44C10.1 1/11 Cross Hyb Matching Probes A 
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrIII:10984441-10985458(-) 100.0 100.0
chrIII:10982054-10983087(-) 94.27 94.27
chrIII:10986721-10987693(-) 94.27 94.27
Public Domain and Genome References
Gene Title
Gene Symbol col-93
Ensembl W05B2.5
Entrez Gene 259335 Entrez gene
SwissProt Q9U348 EMBL-EBI
WormBase CE20147 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 CAB63321 Hypothetical protein W05B2.5 [Caenorhabditis elegans] ref|NP_499409.1| COLlagen family member (col-93) [Caenorhabditis elegans] 4.0E-35
blast CAB03475 Hypothetical protein W05B2.1 [Caenorhabditis elegans] ref|NP_499410.1| COLlagen family member (col-94) [Caenorhabditis elegans] 2.0E-34
blast CAB03474 Hypothetical protein W05B2.6 [Caenorhabditis elegans] ref|NP_499408.1| COLlagen family member (col-92) [Caenorhabditis elegans] 3.0E-34
Protein Domains
Database ID Description E-Value
Pfam IPR002486 EMBL-EBI Nematode cuticle collagen, N-terminal 4.8E-10
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 8.6E-8
Pfam IPR008160 EMBL-EBI Collagen triple helix repeat 3.1E-12
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_499409.1 1 12-34
W05B2.5 1 12-34
SNAP00000036391 1 12-34
GENEFINDER00000036400 1 12-34
Sequence
Target Sequence 
>C. ELEGANS:171770_X_AT
aagaccaggacgtccaggagcagctggacttccaggaaacccaggacgcccaccagcaca
accatgtgagccaatcaccccaccaccatgcaagccatgcccacaaggaccagctggagc
cccaggagccccaggaccacaaggagatgccggagcaccaggacaagccgggcaaggatc
aggagccggagccccaggaccagccggaccaaagggagccccaggagccccaggaaaccc
aggacaagctggagccccaggacaaccaggatccgacgctcaatccgagtcttctccagg
agccccaggacaagccggaccacaaggaccaccaggaccagctggatccccaggagcccc
aggaggaccaggacaagccggagccccaggaccaaagggaccatcaggagccccaggaca
gccaggagccgacggaaacccaggagccccaggacagccaggacaatctggaggtgccgg
agagaagggaatctgtccaaagtactgcgccatcgacggaggagtatt

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
AAGACCAGGACGTCCAGGAGCAGCT 657 151 373 Antisense
AGCCCCAGGACCACAAGGAGATGCC 356 83 499 Antisense
GCCGGAGCACCAGGACAAGCCGGGC 154 283 521 Antisense
GGCAAGGATCAGGAGCCGGAGCCCC 71 535 543 Antisense
AGCCCCAGGAAACCCAGGACAAGCT 361 83 598 Antisense
AGGACCACCAGGACCAGCTGGATCC 33 57 697 Antisense
CAGGAGGACCAGGACAAGCCGGAGC 652 207 732 Antisense
GAGCCCCAGGACCAAAGGGACCATC 629 385 753 Antisense
GCCAGGAGCCGACGGAAACCCAGGA 552 277 793 Antisense
GGGAATCTGTCCAAAGTACTGCGCC 623 493 859 Antisense
ACTGCGCCATCGACGGAGGAGTATT 646 97 876 Antisense
Sequence Source Affymetrix Proprietary Database