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[172930_x_at] POL Polyprotein (reverse transcriptase)

Description K02A2.6 /REP_DB=WormBase Gene ID /WP=CE02792 /TR=SW:Q09575 /GB=AAC46707.1 /SUBMIT=ST.LOUIS /CHR=2 /FEA=Sanger Annotation /DEF=POL Polyprotein (reverse transcriptase)
Cluster 6grp_total > 92      4grp_total > 09      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 36
1 2 3 4 range
A 4.2
(-3)
A 		18.5
(3)
A 		13.4
(0.9)
A 		11.5
(0.1)
A 		14
B 15.2
(-0.6)
A 		4.6
(-3)
A 		15.1
(-0.7)
A 		31.6
(3)
A 		27
C 2.9
(-3)
A 		9.3
(-1.9)
A 		7.3
(-2.3)
A 		38.9
(3)
A 		36
avr 7.4
(-3) 		10.8
(-2) 		11.9
(-1.6) 		27.3
(3) 		20

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 39
1 2 3 4 5 6 range
A 6.4
(-3)
A 		13.2
(-1.8)
A 		11.5
(-2.1)
A 		41.4
(3)
A 		9.7
(-2.4)
A 		21.9
(-0.3)
A 		35
B 15.8
(1)
A 		6.5
(-1.8)
A 		7.4
(-1.5)
A 		3.7
(-2.6)
A 		22.7
(3)
A 		2.4
(-3)
A 		20
C 13.2
(-1.7)
A 		39.3
(3)
A 		12.9
(-1.8)
A 		11.4
(-2.1)
A 		27.1
(0.8)
A 		6.3
(-3)
A 		33
avr 11.8
(-2) 		19.7
(2.9) 		10.6
(-2.8) 		18.8
(2.4) 		19.8
(3) 		10.2
(-3) 		10
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 6
1 2 3 4 range
A 1.5
(-3)
A 		4
(3)
A 		3.5
(1.8)
A 		1.7
(-2.5)
A 		3
B 4.8
(1)
A 		1.1
(-3)
A 		3.5
(-0.4)
A 		6.7
(3)
A 		6
C 1
(-3)
A 		2.7
(-1.2)
A 		2.6
(-1.3)
A 		6.6
(3)
A 		6
avr 2.4
(-3) 		2.6
(-2.5) 		3.2
(-1.2) 		5
(3) 		3

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 11
1 2 3 4 5 6 range
A 1.2
(-3)
A 		4.7
(-0.7)
A 		2.5
(-2.2)
A 		10.5
(3)
A 		2.9
(-1.9)
A 		5.3
(-0.4)
A 		9
B 5.5
(0.3)
A 		2.2
(-2.1)
A 		1.8
(-2.3)
A 		1
(-2.9)
A 		9.2
(3)
A 		0.9
(-3)
A 		8
C 4.9
(-1.3)
A 		12
(3)
A 		3.3
(-2.3)
A 		2.3
(-2.9)
A 		8.8
(1.1)
A 		2.1
(-3)
A 		10
avr 3.9
(-1.1) 		6.3
(2.1) 		2.5
(-3) 		4.6
(-0.2) 		7
(3) 		2.8
(-2.6) 		5
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 172930_x_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.5854
Sequence Type Exemplar sequence
Representative Public ID K02A2.6 NCBI
Target Description K02A2.6 /REP_DB=WormBase Gene ID /WP=CE02792 /TR=SW:Q09575 /GB=AAC46707.1 /SUBMIT=ST.LOUIS /CHR=2 /FEA=Sanger Annotation /DEF=POL Polyprotein (reverse transcriptase)
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_063156(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_063156 NCBI Caenorhabditis elegans K02A2.6 (K02A2.6) mRNA, complete cds. 11/11 None
K02A2.6 ENSEMBL cdna:known chromosome:CEL140:II:7439448:7443909:-1 gene:K02A2.6 11/11 None
Annotation Notes
Cross Hybridizing mRNA Matched Probes Nature of Assignment Related Probesets by Grade
NM_077928 4/11 Cross Hyb Matching Probes A 
NM_078442 2/11 Cross Hyb Matching Probes A 
NM_058839 7/11 Cross Hyb Matching Probes A 
SNAP00000013113 7/11 Cross Hyb Matching Probes None
GENEFINDER00000013124 5/11 Cross Hyb Matching Probes None
SNAP00000027025 3/11 Cross Hyb Matching Probes None
GENEFINDER00000027034 2/11 Cross Hyb Matching Probes None
SNAP00000016726 2/11 Cross Hyb Matching Probes None
GENEFINDER00000016739 2/11 Cross Hyb Matching Probes None
T03F1.4 7/11 Cross Hyb Matching Probes A 
C31E10.2 4/11 Cross Hyb Matching Probes A 
F39B3.3 2/11 Cross Hyb Matching Probes A 
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Public Domain and Genome References
Gene Title POL Polyprotein (reverse transcriptase)
Ensembl K02A2.6
Entrez Gene 186858 Entrez gene
SwissProt Q09575 EMBL-EBI
WormBase CE02792 Wormbase
Functional Annotations
Gene Ontology
GO Biological Process (view graph)
ID Description Evidence Links
6278 RNA-dependent DNA replication inferred from electronic annotation QuickGO AmiGO
6310 DNA recombination inferred from electronic annotation QuickGO AmiGO
GO Molecular Function (view graph)
ID Description Evidence Links
3676 nucleic acid binding inferred from electronic annotation QuickGO AmiGO
3677 DNA binding inferred from electronic annotation QuickGO AmiGO
3723 RNA binding inferred from electronic annotation QuickGO AmiGO
3964 RNA-directed DNA polymerase activity inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast AAC46707 Hypothetical protein K02A2.6 [Caenorhabditis elegans] ref|NP_495557.1| K02A2.6 [Caenorhabditis elegans] sp|Q09575|YRD6_CAEEL Hypothetical protein K02A2.6 in chromosome II 0.0
blast NP_491240 T03F1.4 [Caenorhabditis elegans] gb|AAB42240.2| Hypothetical protein T03F1.4 [Caenorhabditis elegans] 0.0
blast AAB71256 Hypothetical protein T23E7.1 [Caenorhabditis elegans] ref|NP_510849.1| T23E7.1 [Caenorhabditis elegans] 1.0E-165
Protein Domains
Database ID Description E-Value
Pfam IPR001584 EMBL-EBI Integrase, catalytic domain 5.5E-47
Pfam IPR001878 EMBL-EBI Zn-finger, CCHC type 2.0E-6
Pfam IPR000477 EMBL-EBI RNA-directed DNA polymerase (Reverse transcriptase) 3.3E-39
Sequence
Target Sequence 
>C. ELEGANS:172930_X_AT
aagtttggtggtgttctctacgaagttcaagtcggagacagaatgcaaaagtctcacgtt
aatcagattcggactcgttatggtgactacagtcgctcgtctgttaatcctagattgtct
tccgatcctttgggttttgtgggggagagtggcggtgatgagatgtcccgcaatgatgat
ccagttgttacttcgaatggttccagtactgatgtcaatcgtggaagccgaatcacaagt
gaactaaagaagaaagaaagcaatgcagtcagaggacagccatgtggatcctgctctcca
accaacaacgacgtctcggcgcccggatacgcctcacgttctcacccgaccaccgaccca
agccattccgtaagacgaagttcgcgaattcgacgagtactggacagatatggttcatct
gtggagcacccttcaacctccaccggaactccgcgaggatcgacatccacccagctcggt
caagcctccactcgcaacggaagtcgatatacagcttctggtcgaaacccctcttgccaa
gggaatcg

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
AAGTTTGGTGGTGTTCTCTACGAAG 90 155 3205 Antisense
GATTCGGACTCGTTATGGTGACTAC 293 431 3270 Antisense
GACTACAGTCGCTCGTCTGTTAATC 536 373 3289 Antisense
TAATCCTAGATTGTCTTCCGATCCT 149 635 3309 Antisense
TCTTCCGATCCTTTGGGTTTTGTGG 324 613 3322 Antisense
GATGTCCCGCAATGATGATCCAGTT 230 409 3366 Antisense
GAGGACAGCCATGTGGATCCTGCTC 520 403 3476 Antisense
TATGGTTCATCTGTGGAGCACCCTT 658 655 3613 Antisense
CCTCCACTCGCAACGGAAGTCGATA 329 267 3689 Antisense
TATACAGCTTCTGGTCGAAACCCCT 332 659 3712 Antisense
GAAACCCCTCTTGCCAAGGGAATCG 256 355 3728 Antisense
Sequence Source Affymetrix Proprietary Database