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[172561_x_at]

Description F52E1.12 /REP_DB=WormBase Gene ID /WP=CE04640 /TR=P90881 /GB=AAB37045.1 /SUBMIT=ST.LOUIS /CHR=5 /FEA=Sanger Annotation
Cluster 6grp_total > 50      4grp_total > 03      6grp_total_sub > Hat      4grp_rule_based > L4      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 79
1 2 3 4 range
A 1.3
(-3)
A 		1.9
(-2.9)
A 		1.1
(-3)
A 		78.9
(3)
A 		78
B 19.2
(3)
A 		2.4
(-2.9)
A 		2.1
(-3)
A 		16.9
(2.2)
A 		17
C 4.5
(-2.6)
A 		1.9
(-2.8)
A 		0.3
(-3)
A 		62.6
(3)
P 		62
avr 8.3
(-2.2) 		2.1
(-2.9) 		1.2
(-3) 		52.8
(3) 		52

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 27
1 2 3 4 5 6 range
A 2.8
(-2.5)
A 		0.6
(-3)
A 		27.9
(3)
A 		21.4
(1.6)
A 		2
(-2.7)
A 		2.5
(-2.6)
A 		27
B 4
(0.8)
A 		0.9
(-2.6)
A 		0.5
(-3)
A 		0.6
(-2.9)
A 		6.1
(3)
A 		0.8
(-2.7)
A 		6
C 19.3
(3)
A 		17.3
(2.4)
A 		2.1
(-2.6)
A 		7.1
(-1)
A 		0.9
(-3)
A 		0.8
(-3)
A 		19
avr 8.7
(2) 		6.3
(0.3) 		10.2
(3) 		9.7
(2.7) 		3
(-1.9) 		1.4
(-3) 		9
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 12
1 2 3 4 range
A 0.5
(-2.9)
A 		0.4
(-2.9)
A 		0.3
(-3)
A 		11.6
(3)
A 		11
B 6.1
(3)
A 		0.6
(-2.9)
A 		0.5
(-3)
A 		3.6
(0.3)
A 		6
C 1.5
(-2.2)
A 		0.5
(-2.8)
A 		0.1
(-3)
A 		10.6
(3)
P 		11
avr 2.7
(-1.3) 		0.5
(-2.9) 		0.3
(-3) 		8.6
(3) 		8

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 7
1 2 3 4 5 6 range
A 0.5
(-2.7)
A 		0.2
(-3)
A 		6.1
(3)
A 		5.4
(2.3)
A 		0.6
(-2.6)
A 		0.6
(-2.6)
A 		6
B 1.4
(0.3)
A 		0.3
(-2.5)
A 		0.1
(-3)
A 		0.2
(-2.8)
A 		2.5
(3)
A 		0.3
(-2.5)
A 		2
C 7.2
(3)
A 		5.3
(1.3)
A 		0.5
(-2.8)
A 		1.4
(-2)
A 		0.3
(-3)
A 		0.3
(-3)
A 		7
avr 3
(3) 		1.9
(0.5) 		2.2
(1.2) 		2.3
(1.4) 		1.1
(-1.4) 		0.4
(-3) 		3
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 172561_x_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.12520
Sequence Type Exemplar sequence
Representative Public ID F52E1.12 NCBI
Target Description F52E1.12 /REP_DB=WormBase Gene ID /WP=CE04640 /TR=P90881 /GB=AAB37045.1 /SUBMIT=ST.LOUIS /CHR=5 /FEA=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_072761(11), NM_062865(9), NM_072760(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_072761 NCBI Caenorhabditis elegans F52E1.12 (F52E1.12) mRNA, complete cds. 11/11 None
NM_062865 NCBI Caenorhabditis elegans C29F5.6 (C29F5.6) mRNA, complete cds. 9/11 A 
NM_072760 NCBI Caenorhabditis elegans F38E1.2 (F38E1.2) mRNA, complete cds. 11/11 None
SNAP00000032522 ENSEMBL cdna:SNAP chromosome:CEL140:II:6301814:6302842:-1 9/11 None
C29F5.6 ENSEMBL cdna:known chromosome:CEL140:II:6301814:6302842:-1 gene:C29F5.6 9/11 A 
F38E1.2 ENSEMBL cdna:known chromosome:CEL140:V:8383372:8385513:1 gene:F38E1.2 11/11 A 
F52E1.12 ENSEMBL cdna:known chromosome:CEL140:V:8384485:8385540:1 gene:F52E1.12 11/11 None
Annotation Notes
Cross Hybridizing mRNA Matched Probes Nature of Assignment Related Probesets by Grade
NM_063332 4/11 Cross Hyb Matching Probes A 
NM_075927 7/11 Cross Hyb Matching Probes A 
NM_058704 3/11 Cross Hyb Matching Probes A 
NM_058536 7/11 Cross Hyb Matching Probes A 
NM_062489 6/11 Cross Hyb Matching Probes A 
NM_067826 7/11 Cross Hyb Matching Probes A 
NM_069210 5/11 Cross Hyb Matching Probes A 
SNAP00000001197 5/11 Cross Hyb Matching Probes None
GENEFINDER00000035332 3/11 Cross Hyb Matching Probes None
SNAP00000018816 5/11 Cross Hyb Matching Probes None
GENEFINDER00000018837 7/11 Cross Hyb Matching Probes None
Y37E3.18 7/11 Cross Hyb Matching Probes A 
K09H9.4 3/11 Cross Hyb Matching Probes A 
R05F9.4 6/11 Cross Hyb Matching Probes A 
M110.6 4/11 Cross Hyb Matching Probes A 
Y69A2AR.10 7/11 Cross Hyb Matching Probes A 
Y11D7A.6 5/11 Cross Hyb Matching Probes A 
Y60A3A.11 3/11 Cross Hyb Matching Probes A 
Y113G7A.2 7/11 Cross Hyb Matching Probes A 
F31A9.6 7/11 Cross Hyb Matching Probes A 
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrIV:2590989-2591226(+) 97.89 97.89
chrIV:9246502-9246739(+) 97.05 97.05
chrII:4898105-4898342(+) 97.89 97.89
chrV:8385304-8385541(+) 100.0 100.0
chrV:20042168-20042405(+) 97.89 97.89
chrIII:8347986-8348223(+) 95.78 95.78
chrIII:8339791-8340028(+) 95.78 95.78
chrIV:722457-722694(-) 97.47 97.47
chrII:6301810-6302047(-) 99.16 99.16
chrX:1789006-1789243(-) 97.47 97.47
chrI:2130471-2130708(-) 97.89 97.89
Public Domain and Genome References
Ensembl C29F5.6
F38E1.2
F52E1.12
Functional Annotations
Protein Similarities
Method ID Description E-Value
blast NP_495266 C29F5.6 [Caenorhabditis elegans] gb|AAC46825.1| Hypothetical protein C29F5.6 [Caenorhabditis elegans] 0.0
blast NP_505161 F38E1.2 [Caenorhabditis elegans] 0.0
blast NP_494890 R05F9.4 [Caenorhabditis elegans] gb|AAA83167.1| Hypothetical protein R05F9.4 [Caenorhabditis elegans] 1.0E-167
blast NP_490937 Y37E3.18 [Caenorhabditis elegans] gb|AAK27868.1| Hypothetical protein Y37E3.18 [Caenorhabditis elegans] 1.0E-167
Protein Domains
Database ID Description E-Value
Pfam IPR000477 EMBL-EBI RNA-directed DNA polymerase (Reverse transcriptase) 5.2E-6
Pfam IPR000477 EMBL-EBI RNA-directed DNA polymerase (Reverse transcriptase) 8.6E-22
Sequence
Target Sequence 
>C. ELEGANS:172561_X_AT
tggaacgtaacgaactattcgacctccaaaccttaagcacgagacgtaaaataattgaca
gaatccaagtaaccagaatgaatactggtaaagtagacttaaaaacatctgagttttttg
agcaacaagagacccaaactcgttctaaaaagaaatatatctggagcacaggaaaatcta
aacttaggagacacttttttg

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
TGGAACGTAACGAACTATTCGACCT 343 543 14 Antisense
TTCGACCTCCAAACCTTAAGCACGA 209 695 31 Antisense
GACCTCCAAACCTTAAGCACGAGAC 261 383 34 Antisense
TCCAAACCTTAAGCACGAGACGTAA 524 273 38 Antisense
GCACGAGACGTAAAATAATTGACAG 316 313 50 Antisense
GACAGAATCCAAGTAACCAGAATGA 675 365 70 Antisense
AAGTAGACTTAAAAACATCTGAGTT 478 157 104 Antisense
ACATCTGAGTTTTTTGAGCAACAAG 662 105 118 Antisense
GCAACAAGAGACCCAAACTCGTTCT 526 317 135 Antisense
GGAGCACAGGAAAATCTAAACTTAG 61 521 176 Antisense
TCTAAACTTAGGAGACACTTTTTTG 152 601 190 Antisense
Sequence Source Affymetrix Proprietary Database