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[172828_x_at] reverse transcriptase

Description B0302.3 /REP_DB=WormBase Gene ID /WP=CE03868 /TR=Q17470 /GB=AAA82369.1 /SUBMIT=ST.LOUIS /CHR=X /FEA=Sanger Annotation /DEF=reverse transcriptase
Cluster 6grp_total > 17      4grp_total > 11      6grp_total_sub > Decrease      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 607
1 2 3 4 range
A 103.4
(-2.1)
A 		112.4
(-1.8)
A 		76.2
(-3)
A 		253.6
(3)
A 		177
B 118
(3)
A 		106.3
(1.7)
A 		63.5
(-2.9)
A 		62.2
(-3)
A 		56
C 105.6
(-2.7)
A 		143.4
(-2.4)
A 		79.7
(-3)
A 		669.3
(3)
P 		590
avr 109
(-2.2) 		120.7
(-1.9) 		73.1
(-3) 		328.4
(3) 		255

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 100
1 2 3 4 5 6 range
A 107.1
(3)
A 		14.2
(-3)
A 		97.2
(2.4)
A 		53.5
(-0.5)
A 		30.1
(-2)
A 		53.1
(-0.5)
A 		93
B 91
(3)
A 		72.1
(1.3)
A 		66.1
(0.8)
A 		24.2
(-3)
A 		42.4
(-1.4)
A 		51.9
(-0.5)
A 		67
C 45.1
(0)
A 		81.5
(3)
A 		8.3
(-2.9)
A 		7.5
(-3)
A 		12.3
(-2.6)
A 		30.2
(-1.2)
A 		74
avr 81.1
(3) 		55.9
(0.1) 		57.2
(0.3) 		28.4
(-3) 		28.3
(-3) 		45.1
(-1.1) 		53
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 100
1 2 3 4 range
A 37.7
(3)
A 		24.4
(-1.5)
A 		19.9
(-3)
A 		37.1
(2.8)
A 		18
B 37.6
(3)
A 		26.3
(0.2)
A 		14.7
(-2.7)
A 		13.3
(-3)
A 		24
C 35
(-2.5)
A 		41.2
(-2.1)
A 		27.8
(-3)
A 		112.8
(3)
P 		85
avr 36.8
(-0.1) 		30.6
(-1.3) 		20.8
(-3) 		54.4
(3) 		34

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 30
1 2 3 4 5 6 range
A 19.7
(2.4)
A 		5.1
(-3)
A 		21.2
(3)
A 		13.6
(0.2)
A 		9.1
(-1.5)
A 		12.9
(-0.1)
A 		16
B 31.7
(3)
A 		24
(1.2)
A 		16.1
(-0.7)
A 		6.4
(-3)
A 		17.2
(-0.4)
A 		19.4
(0.1)
A 		25
C 16.7
(0.9)
A 		24.9
(3)
A 		2.1
(-2.8)
A 		1.5
(-3)
A 		4
(-2.4)
A 		10.1
(-0.8)
A 		23
avr 22.7
(3) 		18
(1.2) 		13.1
(-0.7) 		7.2
(-3) 		10.1
(-1.9) 		14.1
(-0.3) 		16
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 172828_x_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.17367
Sequence Type Exemplar sequence
Representative Public ID B0302.3 NCBI
Target Description B0302.3 /REP_DB=WormBase Gene ID /WP=CE03868 /TR=Q17470 /GB=AAA82369.1 /SUBMIT=ST.LOUIS /CHR=X /FEA=Sanger Annotation /DEF=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_078379(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_078379 NCBI Caenorhabditis elegans B0302.3 (B0302.3) mRNA, complete cds. 11/11 None
SNAP00000034055 ENSEMBL cdna:SNAP chromosome:CEL140:X:17168539:17170147:1 11/11 None
B0302.3 ENSEMBL cdna:known chromosome:CEL140:X:17169308:17170147:1 gene:B0302.3 11/11 None
Annotation Notes
Cross Hybridizing mRNA Matched Probes Nature of Assignment Related Probesets by Grade
NM_077119 6/11 Cross Hyb Matching Probes A 
NM_064793 8/11 Cross Hyb Matching Probes A 
NM_071125 3/11 Cross Hyb Matching Probes None
NM_066128 7/11 Cross Hyb Matching Probes A 
NM_075970 5/11 Cross Hyb Matching Probes A 
NM_078455 7/11 Cross Hyb Matching Probes A 
NM_058672 7/11 Cross Hyb Matching Probes A 
NM_061681 5/11 Cross Hyb Matching Probes A 
NM_059054 7/11 Cross Hyb Matching Probes A 
GENEFINDER00000005898 7/11 Cross Hyb Matching Probes None
GENEFINDER00000043553 4/11 Cross Hyb Matching Probes None
SNAP00000043540 8/11 Cross Hyb Matching Probes None
SNAP00000039702 7/11 Cross Hyb Matching Probes None
GENEFINDER00000039704 7/11 Cross Hyb Matching Probes None
SNAP00000012049 5/11 Cross Hyb Matching Probes None
GENEFINDER00000012051 5/11 Cross Hyb Matching Probes None
SNAP00000043894 6/11 Cross Hyb Matching Probes None
GENEFINDER00000043904 4/11 Cross Hyb Matching Probes None
SNAP00000008916 1/11 Cross Hyb Matching Probes None
SNAP00000030989 7/11 Cross Hyb Matching Probes None
GENEFINDER00000030995 4/11 Cross Hyb Matching Probes None
SNAP00000031879 8/11 Cross Hyb Matching Probes None
GENEFINDER00000031882 8/11 Cross Hyb Matching Probes None
SNAP00000000198 6/11 Cross Hyb Matching Probes None
GENEFINDER00000000200 4/11 Cross Hyb Matching Probes None
SNAP00000006732 8/11 Cross Hyb Matching Probes None
GENEFINDER00000006742 8/11 Cross Hyb Matching Probes None
SNAP00000028592 7/11 Cross Hyb Matching Probes None
GENEFINDER00000028599 7/11 Cross Hyb Matching Probes None
SNAP00000033705 5/11 Cross Hyb Matching Probes None
GENEFINDER00000033772 3/11 Cross Hyb Matching Probes None
SNAP00000037693 3/11 Cross Hyb Matching Probes None
GENEFINDER00000037709 3/11 Cross Hyb Matching Probes None
SNAP00000039289 5/11 Cross Hyb Matching Probes None
GENEFINDER00000039297 5/11 Cross Hyb Matching Probes None
SNAP00000043497 6/11 Cross Hyb Matching Probes None
GENEFINDER00000043506 6/11 Cross Hyb Matching Probes None
SNAP00000001526 5/11 Cross Hyb Matching Probes None
GENEFINDER00000001539 5/11 Cross Hyb Matching Probes None
SNAP00000003414 3/11 Cross Hyb Matching Probes None
GENEFINDER00000003424 3/11 Cross Hyb Matching Probes None
SNAP00000028144 3/11 Cross Hyb Matching Probes None
GENEFINDER00000028157 3/11 Cross Hyb Matching Probes None
SNAP00000032429 5/11 Cross Hyb Matching Probes None
GENEFINDER00000032435 5/11 Cross Hyb Matching Probes None
SNAP00000012632 1/11 Cross Hyb Matching Probes None
GENEFINDER00000034063 6/11 Cross Hyb Matching Probes None
SNAP00000007929 7/11 Cross Hyb Matching Probes None
GENEFINDER00000007942 3/11 Cross Hyb Matching Probes None
GENEFINDER00000009534 8/11 Cross Hyb Matching Probes None
SNAP00000009529 8/11 Cross Hyb Matching Probes None
SNAP00000043287 5/11 Cross Hyb Matching Probes None
GENEFINDER00000043303 5/11 Cross Hyb Matching Probes None
SNAP00000003534 6/11 Cross Hyb Matching Probes None
GENEFINDER00000003544 6/11 Cross Hyb Matching Probes None
SNAP00000035247 6/11 Cross Hyb Matching Probes None
GENEFINDER00000035253 6/11 Cross Hyb Matching Probes None
SNAP00000022302 8/11 Cross Hyb Matching Probes None
GENEFINDER00000022354 8/11 Cross Hyb Matching Probes None
SNAP00000022319 2/11 Cross Hyb Matching Probes None
Y71F9AL.3 7/11 Cross Hyb Matching Probes A 
F54D7.1 7/11 Cross Hyb Matching Probes A 
C08F1.9 5/11 Cross Hyb Matching Probes A 
Y53C12A.5 4/11 Cross Hyb Matching Probes None
K10F12.5 8/11 Cross Hyb Matching Probes A 
C06E8.4 7/11 Cross Hyb Matching Probes A 
Y105C5A.7 5/11 Cross Hyb Matching Probes None
Y32G9A.9 3/11 Cross Hyb Matching Probes None
F44G3.3 3/11 Cross Hyb Matching Probes A 
Y102A11A.4 5/11 Cross Hyb Matching Probes A 
C24A3.7 6/11 Cross Hyb Matching Probes A 
C33E10.4 6/11 Cross Hyb Matching Probes None
F20B4.7 7/11 Cross Hyb Matching Probes A 
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Public Domain and Genome References
Gene Title reverse transcriptase
Ensembl B0302.3
Entrez Gene 181912 Entrez gene
SwissProt Q17470 EMBL-EBI
WormBase CE03868 Wormbase
Functional Annotations
Protein Similarities
Method ID Description E-Value
blast H88671 protein F28E10.3 [imported] - Caenorhabditis elegans 0.0
blast C87861 protein F43G9.7 [imported] - Caenorhabditis elegans 0.0
blast AAB71003 Hypothetical protein K10F12.5 [Caenorhabditis elegans] ref|NP_497194.1| K10F12.5 [Caenorhabditis elegans] 0.0
blast AAA82369 Hypothetical protein B0302.3 [Caenorhabditis elegans] ref|NP_510780.1| B0302.3 [Caenorhabditis elegans] 1.0E-161
blast H88671 protein F28E10.3 [imported] - Caenorhabditis elegans 1.0E-161
blast T24639 hypothetical protein T07C12.2 - Caenorhabditis elegans 1.0E-160
Protein Domains
Database ID Description E-Value
Pfam IPR000477 EMBL-EBI RNA-directed DNA polymerase (Reverse transcriptase) 7.3E-15
Pfam IPR000477 EMBL-EBI RNA-directed DNA polymerase (Reverse transcriptase) 2.0E-25
Sequence
Target Sequence 
>C. ELEGANS:172828_X_AT
gtcgacgagtacatctaccttggtcgtcaaatcaacgcccaaaacaacttgatgccggaa
atccaccgaagacgtcgagcagcctgggctgcattcaatggaatcaagaacaccaccgac
tccatcaccgacaagaagattcgtgcgaatctgttcgactcaattgtccttccagcgctc
acctacggttcagaagcctggacattcaccaaagctctatccgaacgagtacgaatcaca
catgcctccctagaaagacggcttgttgggataacactcacccaacaacgagagcgagat
ctccatcgagaagacattcgtacgatgtctctagtcagggatccgctcaatttcgtgaaa
aagaggaagctaggatgggctggacacgttgcgagaaggaaagacggaagatggaccacg
ttgatgacagaatggcgcccatatggatggaaaaggcctgttggaaggccgccgatgcga
tggactgattcgctgcgaaaggagatcaccactcgcgacgcagacggagaa

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GTCGACGAGTACATCTACCTTGGTC 95 475 241 Antisense
ACCTTGGTCGTCAAATCAACGCCCA 401 85 257 Antisense
ATCTGTTCGACTCAATTGTCCTTCC 195 35 389 Antisense
GCTCACCTACGGTTCAGAAGCCTGG 215 301 417 Antisense
GAAGCCTGGACATTCACCAAAGCTC 259 345 433 Antisense
GAACGAGTACGAATCACACATGCCT 577 347 463 Antisense
ATTCGTACGATGTCTCTAGTCAGGG 127 3 556 Antisense
TAGTCAGGGATCCGCTCAATTTCGT 611 653 572 Antisense
GCTAGGATGGGCTGGACACGTTGCG 442 299 609 Antisense
GGCCGCCGATGCGATGGACTGATTC 94 543 707 Antisense
CACCACTCGCGACGCAGACGGAGAA 368 201 747 Antisense
Sequence Source Affymetrix Proprietary Database