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[190408_s_at] reverse transcriptase /// reverse transcriptase

Description K09H9.4 /REP_DB=WormBase Gene ID /WP=CE18039 /TR=O44988 /GB=AAB97571.1 /SUBMIT=ST.LOUIS /CHR=1 /FEA=Sanger Annotation /DEF=reverse transcriptase
Cluster 6grp_total > 35      4grp_total > 02      6grp_total_sub > Cup      4grp_rule_based > L4      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 114
1 2 3 4 range
A 5.1
(-2.7)
A 		1.9
(-2.9)
A 		0.5
(-3)
A 		89.5
(3)
P 		89
B 2.1
(-2.9)
A 		12
(-0.8)
A 		1.7
(-3)
A 		29.3
(3)
A 		28
C 16.6
(-2.2)
A 		1.9
(-2.9)
A 		0.6
(-3)
A 		114.5
(3)
P 		114
avr 7.9
(-2.5) 		5.3
(-2.7) 		0.9
(-3) 		77.8
(3) 		77

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 29
1 2 3 4 5 6 range
A 2.2
(-3)
A 		5.8
(-2.1)
A 		26.7
(3)
A 		9.6
(-1.2)
A 		2
(-3)
A 		25.4
(2.7)
A 		25
B 12.3
(3)
P 		8.2
(0.9)
A 		3.3
(-1.7)
A 		1.6
(-2.5)
A 		11.7
(2.7)
A 		0.7
(-3)
A 		12
C 21.2
(1.3)
A 		29.1
(3)
A 		1.9
(-2.7)
A 		0.4
(-3)
A 		1.6
(-2.7)
A 		1
(-2.9)
A 		29
avr 11.9
(1.6) 		14.4
(3) 		10.6
(0.8) 		3.9
(-3) 		5.1
(-2.3) 		9
(-0.1) 		11
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 19
1 2 3 4 range
A 1.8
(-2.2)
A 		0.4
(-2.9)
A 		0.1
(-3)
A 		13.1
(3)
P 		13
B 0.7
(-2.7)
A 		3
(-0.4)
A 		0.4
(-3)
A 		6.3
(3)
A 		6
C 5.5
(-1.3)
A 		0.6
(-2.9)
A 		0.2
(-3)
A 		19.3
(3)
P 		19
avr 2.7
(-1.8) 		1.3
(-2.5) 		0.2
(-3) 		12.9
(3) 		13

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 9
1 2 3 4 5 6 range
A 0.4
(-3)
A 		2.1
(-1.2)
A 		5.8
(2.6)
A 		2.4
(-0.9)
A 		0.6
(-2.8)
A 		6.2
(3)
A 		6
B 4.3
(2.3)
P 		2.7
(0.3)
A 		0.8
(-2.2)
A 		0.4
(-2.7)
A 		4.8
(3)
A 		0.2
(-3)
A 		5
C 7.9
(2.3)
A 		8.9
(3)
A 		0.5
(-2.7)
A 		0.1
(-3)
A 		0.5
(-2.7)
A 		0.3
(-2.9)
A 		9
avr 4.2
(2.3) 		4.6
(3) 		2.4
(-0.7) 		1
(-3) 		2
(-1.3) 		2.2
(-1) 		4
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 190408_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.111
Sequence Type Exemplar sequence
Representative Public ID K09H9.4 NCBI
Target Description K09H9.4 /REP_DB=WormBase Gene ID /WP=CE18039 /TR=O44988 /GB=AAB97571.1 /SUBMIT=ST.LOUIS /CHR=1 /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_063332(11), NM_058704(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_063332 NCBI Caenorhabditis elegans M110.6 (M110.6) mRNA, complete cds. 11/11 None
NM_058704 NCBI Caenorhabditis elegans K09H9.4 (K09H9.4) mRNA, complete cds. 11/11 None
K09H9.4 ENSEMBL cdna:known chromosome:CEL140:I:3133797:3135234:-1 gene:K09H9.4 11/11 None
M110.6 ENSEMBL cdna:known chromosome:CEL140:II:8229053:8230557:1 gene:M110.6 11/11 None
Annotation Notes
Cross Hybridizing mRNA Matched Probes Nature of Assignment Related Probesets by Grade
GENEFINDER00000035332 5/11 Cross Hyb Matching Probes None
Y60A3A.11 7/11 Cross Hyb Matching Probes A 
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrII:8229812-8230554(+) 80.59 80.59
chrV:19937163-19937989(+) 89.58 89.58
chrI:3133796-3135234(-) 100.0 100.0
chrII:1261068-1261865(-) 84.98 84.98
Public Domain and Genome References
Gene Title reverse transcriptase
reverse transcriptase
Ensembl K09H9.4
M110.6
Entrez Gene 187240 Entrez gene
187473 Entrez gene
SwissProt O44988 EMBL-EBI
Q21533 EMBL-EBI
WormBase CE36702 Wormbase
CE02279 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
GO Molecular Function (view graph)
ID Description Evidence Links
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 NP_491105 K09H9.4 [Caenorhabditis elegans] gb|AAB97571.2| Hypothetical protein K09H9.4 [Caenorhabditis elegans] 1.0E-162
blast CAA90263 Hypothetical protein M110.6 [Caenorhabditis elegans] ref|NP_495733.1| M110.6 [Caenorhabditis elegans] 1.0E-141
blast NP_494890 R05F9.4 [Caenorhabditis elegans] gb|AAA83167.1| Hypothetical protein R05F9.4 [Caenorhabditis elegans] 1.0E-130
blast NP_495266 C29F5.6 [Caenorhabditis elegans] gb|AAC46825.1| Hypothetical protein C29F5.6 [Caenorhabditis elegans] 1.0E-129
blast NP_491105 K09H9.4 [Caenorhabditis elegans] gb|AAB97571.2| Hypothetical protein K09H9.4 [Caenorhabditis elegans] 1.0E-127
Protein Domains
Database ID Description E-Value
Pfam IPR000477 EMBL-EBI RNA-directed DNA polymerase (Reverse transcriptase) 9.2E-5
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_491105.2 1 2-24
K09H9.4 1 2-24
Sequence
Target Sequence 
>C. ELEGANS:190408_S_AT
tcacgtcacagtagggagatgtagaaaagattttaaataccaccttgacggttaccctat
agagcgaaaaacaattaccagagaccttggatttctaatatcagaaaaactggatttctc
ggagcattggaagaaatctatcaatctggcgaaatttcagctggccaacatttttaacca
gtacagtacctccaataaaaaactaatgattcttttatacaaaactttcattcgtcctcg
tctagaatatggaacagtagtgtcttctccgacgaaaaaatcggatgagaaagcaataga
gtctgtgcaaaacgcgttcactaggcgcctttatagtagaatcaaaaaaaggtatattaa
tccaacagataaagattacaaaacatccatggaacgtaacgaactattcaaccttcaaac
cttaagcacgagacgtaaaataattgacagaatccaagtaatcagaatgaatactggtaa
agtagacttaaaaacatctgagttttttgagcaacaagagacccacactcgttctaaaaa
gaaatatgtgtggcgcacaggaaaaactaaacttag

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
TCACGTCACAGTAGGGAGATGTAGA 64 625 300 Antisense
CCACCTTGACGGTTACCCTATAGAG 494 271 339 Antisense
GCGAAAAACAATTACCAGAGACCTT 572 287 363 Antisense
GAGACCTTGGATTTCTAATATCAGA 230 395 380 Antisense
AGAAATCTATCAATCTGGCGAAATT 126 73 431 Antisense
GCGAAATTTCAGCTGGCCAACATTT 404 287 448 Antisense
TGGCCAACATTTTTAACCAGTACAG 540 541 461 Antisense
TACAAAACTTTCATTCGTCCTCGTC 46 641 517 Antisense
CATTCGTCCTCGTCTAGAATATGGA 301 217 528 Antisense
GAGTCTGTGCAAAACGCGTTCACTA 480 399 598 Antisense
GGCGCACAGGAAAAACTAAACTTAG 405 539 851 Antisense
Sequence Source Affymetrix Proprietary Database