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[172831_x_at] reverse transcriptase

Description Y11D7A.6 /REP_DB=WormBase Gene ID /WP=CE20189 /TR=Q9U2R8 /GB=CAB63343.1 /SUBMIT=HINXTON /CHR=4 /FEA=Sanger Annotation /DEF=reverse transcriptase
Cluster 6grp_total > 44      4grp_total > 02      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 1585
1 2 3 4 range
A 55.2
(-2.6)
A 		31.3
(-3)
A 		53.5
(-2.6)
A 		409.2
(3)
P 		378
B 52.8
(-1)
A 		4.4
(-3)
A 		81.7
(0.3)
A 		146.3
(3)
A 		142
C 51.8
(-2.8)
A 		7.3
(-3)
A 		10
(-3)
A 		1589
(3)
P 		1582
avr 53.3
(-2.7) 		14.3
(-3) 		48.4
(-2.7) 		714.8
(3) 		701

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 109
1 2 3 4 5 6 range
A 116.5
(3)
A 		47.3
(-1.3)
A 		99
(1.9)
A 		19.5
(-3)
A 		41.4
(-1.6)
A 		44.6
(-1.4)
A 		97
B 58.7
(-2.9)
A 		64.4
(-2.4)
A 		128.1
(3)
A 		67.7
(-2.2)
A 		68
(-2.1)
A 		57.8
(-3)
A 		70
C 38.6
(-2.6)
A 		124.9
(3)
A 		69.7
(-0.6)
A 		33.4
(-2.9)
A 		32.3
(-3)
A 		51.2
(-1.8)
A 		93
avr 71.3
(0.2) 		78.9
(1) 		98.9
(3) 		40.2
(-3) 		47.2
(-2.3) 		51.2
(-1.9) 		59
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 267
1 2 3 4 range
A 20.1
(-1.5)
A 		6.8
(-3)
A 		14
(-2.2)
A 		59.9
(3)
P 		53
B 16.8
(0.1)
A 		1.1
(-3)
A 		18.9
(0.5)
A 		31.2
(3)
A 		30
C 17.2
(-2.7)
A 		2.1
(-3)
A 		3.5
(-3)
A 		267.9
(3)
P 		266
avr 18
(-2.2) 		3.3
(-3) 		12.1
(-2.5) 		119.7
(3) 		116

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 33
1 2 3 4 5 6 range
A 21.5
(3)
A 		16.8
(1.3)
A 		21.6
(3)
A 		5
(-3)
A 		12.5
(-0.3)
A 		10.9
(-0.9)
A 		17
B 20.4
(-1.9)
A 		21.4
(-1.4)
A 		31.1
(3)
A 		17.9
(-3)
A 		27.6
(1.4)
A 		21.6
(-1.3)
A 		13
C 14.3
(-1.5)
A 		38.1
(3)
A 		17.7
(-0.9)
A 		6.7
(-3)
A 		10.4
(-2.3)
A 		17.1
(-1)
A 		31
avr 18.7
(0.4) 		25.4
(3) 		23.5
(2.3) 		9.9
(-3) 		16.8
(-0.3) 		16.5
(-0.4) 		16
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 172831_x_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.10024
Sequence Type Exemplar sequence
Representative Public ID Y11D7A.6 NCBI
Target Description Y11D7A.6 /REP_DB=WormBase Gene ID /WP=CE20189 /TR=Q9U2R8 /GB=CAB63343.1 /SUBMIT=HINXTON /CHR=4 /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_058536(9), NM_062489(9), NM_069210(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_058536 NCBI Caenorhabditis elegans Y37E3.18 (Y37E3.18) mRNA, complete cds. 9/11 A 
NM_062489 NCBI Caenorhabditis elegans R05F9.4 (R05F9.4) mRNA, complete cds. 9/11 A 
NM_069210 NCBI Caenorhabditis elegans Y11D7A.6 (Y11D7A.6) mRNA, complete cds. 11/11 None
Y37E3.18 ENSEMBL cdna:known chromosome:CEL140:I:2130472:2131902:-1 gene:Y37E3.18 9/11 A 
R05F9.4 ENSEMBL cdna:known chromosome:CEL140:II:4896914:4898344:1 gene:R05F9.4 9/11 A 
Y11D7A.6 ENSEMBL cdna:known chromosome:CEL140:IV:9246278:9246733:1 gene:Y11D7A.6 11/11 None
Annotation Notes
Cross Hybridizing mRNA Matched Probes Nature of Assignment Related Probesets by Grade
NM_063332 1/11 Cross Hyb Matching Probes A 
NM_075927 6/11 Cross Hyb Matching Probes A 
NM_072761 7/11 Cross Hyb Matching Probes None
NM_058704 5/11 Cross Hyb Matching Probes A 
NM_067826 8/11 Cross Hyb Matching Probes A 
NM_062865 8/11 Cross Hyb Matching Probes A 
NM_072760 7/11 Cross Hyb Matching Probes None
SNAP00000001197 7/11 Cross Hyb Matching Probes None
GENEFINDER00000035332 3/11 Cross Hyb Matching Probes None
SNAP00000032522 8/11 Cross Hyb Matching Probes None
SNAP00000018816 6/11 Cross Hyb Matching Probes None
GENEFINDER00000018837 8/11 Cross Hyb Matching Probes None
K09H9.4 5/11 Cross Hyb Matching Probes A 
C29F5.6 8/11 Cross Hyb Matching Probes A 
M110.6 1/11 Cross Hyb Matching Probes A 
Y69A2AR.10 8/11 Cross Hyb Matching Probes A 
F38E1.2 7/11 Cross Hyb Matching Probes A 
F38E1.1 3/11 Cross Hyb Matching Probes None
F52E1.12 7/11 Cross Hyb Matching Probes A 
Y60A3A.11 3/11 Cross Hyb Matching Probes A 
Y113G7A.2 8/11 Cross Hyb Matching Probes A 
F31A9.6 6/11 Cross Hyb Matching Probes A 
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrII:4897886-4898342(+) 98.46 98.46
chrIV:9246283-9246739(+) 100.0 100.0
chrIV:2590770-2591226(+) 98.46 98.46
chrV:8385086-8385541(+) 98.25 98.25
chrV:20041949-20042405(+) 97.59 97.59
chrI:2130471-2130927(-) 97.81 97.81
chrII:6301810-6302266(-) 98.46 98.46
chrX:1789006-1789462(-) 97.37 97.37
Public Domain and Genome References
Gene Title reverse transcriptase
Ensembl Y37E3.18
R05F9.4
Y11D7A.6
Entrez Gene 189431 Entrez gene
SwissProt Q9U2R8 EMBL-EBI
WormBase CE20189 Wormbase
Functional Annotations
Protein Similarities
Method ID Description E-Value
blast NP_490937 Y37E3.18 [Caenorhabditis elegans] gb|AAK27868.1| Hypothetical protein Y37E3.18 [Caenorhabditis elegans] 0.0
blast NP_494890 R05F9.4 [Caenorhabditis elegans] gb|AAA83167.1| Hypothetical protein R05F9.4 [Caenorhabditis elegans] 0.0
blast NP_500227 Y69A2AR.10 [Caenorhabditis elegans] 0.0
Protein Domains
Database ID Description E-Value
Pfam IPR000477 EMBL-EBI RNA-directed DNA polymerase (Reverse transcriptase) 3.2E-55
Pfam IPR000477 EMBL-EBI RNA-directed DNA polymerase (Reverse transcriptase) 4.8E-55
Sequence
Target Sequence 
>C. ELEGANS:172831_X_AT
gttcaaccagtacagtacctccaataagaaactaatgattctcttatacaaaactttcat
ccgccctcgtttagaatatggaacagtagtgtcttctccgacaaaaaaatcggatgagaa
agcaatagagtctgtacaaaacgcattcactaggcgcctttatagtagaatcaaaaaaag
atatattaatccaactgataaagattacaaaactgccatggaacgtaacgaactattcga
tttccaaaccttaagcacgagacgtaaaataattgacagaatccaagtaatcagaatgaa
taatggtaaattagacttaaaaacatctgagttttttgagcaacaagagacccacactcg
ttctaaaaaga

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GTTCAACCAGTACAGTACCTCCAAT 552 443 15 Antisense
GAAACTAATGATTCTCTTATACAAA 200 357 42 Antisense
CTTATACAAAACTTTCATCCGCCCT 440 221 57 Antisense
TCATCCGCCCTCGTTTAGAATATGG 609 621 71 Antisense
ATGGAACAGTAGTGTCTTCTCCGAC 562 51 92 Antisense
TAGAGTCTGTACAAAACGCATTCAC 283 653 140 Antisense
AACGCATTCACTAGGCGCCTTTATA 130 145 154 Antisense
AAACTGCCATGGAACGTAACGAACT 96 123 224 Antisense
GATTTCCAAACCTTAAGCACGAGAC 78 427 253 Antisense
AGCAACAAGAGACCCACACTCGTTC 609 75 353 Antisense
GAGACCCACACTCGTTCTAAAAAGA 160 393 361 Antisense
Sequence Source Affymetrix Proprietary Database