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[190331_s_at]

Description T05F1.12 /REP_DB=WormBase Gene ID /WP=CE20038 /TR=Q9XUR0 /GB=CAB04698.1 /SUBMIT=HINXTON /CHR=1 /FEA=Sanger Annotation /DEF=reverse transcriptase
Cluster 6grp_total > 02      4grp_total > 06      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 56
1 2 3 4 range
A 7
(-2.1)
A 		2.3
(-3)
A 		25.7
(1.6)
A 		32.6
(3)
A 		30
B 43.2
(3)
A 		31.6
(0.6)
A 		29.5
(0.2)
A 		13.7
(-3)
A 		30
C 34.2
(-1.6)
A 		32.7
(-1.9)
A 		27.1
(-3)
A 		58.2
(3)
A 		31
avr 28.1
(-0.2) 		22.2
(-3) 		27.4
(-0.5) 		34.8
(3) 		13

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 36
1 2 3 4 5 6 range
A 4.5
(-2.6)
A 		38.6
(3)
A 		33.2
(2.1)
M 		26.4
(1)
A 		20.9
(0.1)
A 		2.2
(-3)
A 		36
B 25.2
(2.6)
A 		5.3
(-3)
A 		14.3
(-0.5)
A 		23.4
(2.1)
A 		26.7
(3)
A 		15.2
(-0.2)
A 		21
C 20.4
(1.7)
A 		24.8
(3)
A 		5.8
(-2.5)
A 		4.2
(-3)
A 		9.1
(-1.6)
A 		16.8
(0.7)
A 		21
avr 16.7
(-0.2) 		22.9
(3) 		17.8
(0.3) 		18
(0.4) 		18.9
(0.9) 		11.4
(-3) 		12
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 13
1 2 3 4 range
A 2.6
(-1)
A 		0.5
(-3)
A 		6.7
(3)
A 		4.8
(1.2)
A 		6
B 13.8
(3)
A 		7.8
(-0.3)
A 		6.8
(-0.9)
A 		2.9
(-3)
A 		11
C 11.3
(3)
A 		9.4
(-3)
A 		9.4
(-3)
A 		9.8
(-1.7)
A 		2
avr 9.2
(3) 		5.9
(-2.8) 		7.6
(0.2) 		5.8
(-3) 		3

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 13
1 2 3 4 5 6 range
A 0.8
(-2.9)
A 		13.7
(3)
A 		7.2
(0)
M 		6.7
(-0.2)
A 		6.3
(-0.4)
A 		0.5
(-3)
A 		13
B 8.8
(1.6)
A 		1.8
(-3)
A 		3.5
(-1.9)
A 		6.2
(-0.1)
A 		10.9
(3)
A 		5.7
(-0.4)
A 		9
C 7.6
(3)
A 		7.6
(3)
A 		1.5
(-2.4)
A 		0.8
(-3)
A 		2.9
(-1.1)
A 		5.6
(1.2)
A 		7
avr 5.7
(-0.2) 		7.7
(3) 		4.1
(-2.7) 		4.6
(-1.9) 		6.7
(1.4) 		3.9
(-3) 		4
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 190331_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.542
Sequence Type Exemplar sequence
Representative Public ID T05F1.12 NCBI
Target Description T05F1.12 /REP_DB=WormBase Gene ID /WP=CE20038 /TR=Q9XUR0 /GB=CAB04698.1 /SUBMIT=HINXTON /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_076204(11), NM_068671(11), NM_001027290(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_076204 NCBI Caenorhabditis elegans C12D12.6 (C12D12.6) mRNA, complete cds. 11/11 A 
NM_068671 NCBI Caenorhabditis elegans B0478.2 (B0478.2) mRNA, complete cds. 11/11 None
NM_001027290 NCBI Caenorhabditis elegans Y52E8A.6 (Y52E8A.6) mRNA, complete cds. 11/11 None
SNAP00000031641 ENSEMBL cdna:SNAP chromosome:CEL140:I:4121295:4123037:1 10/11 None
GENEFINDER00000031644 ENSEMBL cdna:GeneFinder chromosome:CEL140:I:4121295:4123037:1 10/11 None
SNAP00000038114 ENSEMBL cdna:SNAP chromosome:CEL140:I:10907232:10910149:1 10/11 None
SNAP00000040246 ENSEMBL cdna:SNAP chromosome:CEL140:II:4316791:4319889:-1 11/11 None
SNAP00000002696 ENSEMBL cdna:SNAP chromosome:CEL140:IV:6947709:6950421:-1 11/11 None
GENEFINDER00000002700 ENSEMBL cdna:GeneFinder chromosome:CEL140:IV:6948127:6950421:-1 11/11 None
SNAP00000040499 ENSEMBL cdna:SNAP chromosome:CEL140:X:3514813:3515817:-1 11/11 None
GENEFINDER00000040500 ENSEMBL cdna:GeneFinder chromosome:CEL140:X:3514813:3515619:-1 11/11 None
H31G24.2 ENSEMBL cdna:pseudogene chromosome:CEL140:I:4120408:4123037:1 gene:H31G24.2 10/11 None
T05F1.11 ENSEMBL cdna:known chromosome:CEL140:I:9661222:9665161:1 gene:T05F1.11 11/11 None
Y52E8A.6 ENSEMBL cdna:known chromosome:CEL140:II:4316791:4319961:-1 gene:Y52E8A.6 11/11 None
B0478.2 ENSEMBL cdna:known chromosome:CEL140:IV:6947709:6950421:-1 gene:B0478.2 11/11 None
C12D12.6 ENSEMBL cdna:known chromosome:CEL140:X:3514429:3515722:-1 gene:C12D12.6 11/11 A 
Annotation Notes
There are no noteworthy cross hybridizing mRNAs found for this probe set.
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Public Domain and Genome References
Gene Title
Ensembl H31G24.2
T05F1.11
Y52E8A.6
B0478.2
C12D12.6
Entrez Gene 3565213 Entrez gene
SwissProt Q86FN2 EMBL-EBI
WormBase CE33880 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_501072 B0478.2 [Caenorhabditis elegans] 0.0
blast AAC71186 Hypothetical protein C49D10.1 [Caenorhabditis elegans] ref|NP_494683.1| C49D10.1 [Caenorhabditis elegans] 0.0
blast AAP13750 Hypothetical protein Y52E8A.6 [Caenorhabditis elegans] ref|NP_001022461.1| Y52E8A.6 [Caenorhabditis elegans] 0.0
blast CAB04699 Hypothetical protein T05F1.11 [Caenorhabditis elegans] ref|NP_492564.2| T05F1.11 [Caenorhabditis elegans] 0.0
blast NP_508294 H02F09.4 [Caenorhabditis elegans] 0.0
blast NP_510671 F38E9.3 [Caenorhabditis elegans] 0.0
blast AAA21080 Hypothetical protein T07E3.1 [Caenorhabditis elegans] ref|NP_498506.1| T07E3.1 [Caenorhabditis elegans] 0.0
Protein Domains
Database ID Description E-Value
Pfam IPR005135 EMBL-EBI Endonuclease/exonuclease/phosphatase 1.4E-13
Pfam IPR000477 EMBL-EBI RNA-directed DNA polymerase (Reverse transcriptase) 1.5E-8
Pfam IPR000477 EMBL-EBI RNA-directed DNA polymerase (Reverse transcriptase) 1.7E-30
Pfam IPR000477 EMBL-EBI RNA-directed DNA polymerase (Reverse transcriptase) 4.6E-19
Pfam IPR010291 EMBL-EBI Eukaryotic protein of unknown function DUF895 1.0E-78
Pfam IPR000477 EMBL-EBI RNA-directed DNA polymerase (Reverse transcriptase) 1.4E-12
Pfam IPR000477 EMBL-EBI RNA-directed DNA polymerase (Reverse transcriptase) 2.3E-71
Pfam IPR000477 EMBL-EBI RNA-directed DNA polymerase (Reverse transcriptase) 3.8E-35
Pfam IPR000477 EMBL-EBI RNA-directed DNA polymerase (Reverse transcriptase) 2.6E-71
Pfam IPR000477 EMBL-EBI RNA-directed DNA polymerase (Reverse transcriptase) 4.6E-19
Pfam IPR000477 EMBL-EBI RNA-directed DNA polymerase (Reverse transcriptase) 4.6E-19
Pfam IPR010291 EMBL-EBI Eukaryotic protein of unknown function DUF895 3.6E-65
Pfam IPR000477 EMBL-EBI RNA-directed DNA polymerase (Reverse transcriptase) 1.4E-12
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_001022461.1 12 13-30,50-72,79-96,100-119,139-161,192-211,495-517,532-554,566-585,605-627,640-658,668-690
Y52E8A.6 12 13-30,50-72,79-96,100-119,139-161,192-211,495-517,532-554,566-585,605-627,640-658,668-690
SNAP00000038114 7 24-46,59-81,96-115,238-260,286-308,321-343,358-380
SNAP00000040246 11 26-48,55-72,76-95,115-137,152-171,398-420,440-462,474-493,513-535,548-566,576-598
Sequence
Target Sequence 
>C. ELEGANS:190331_S_AT
ggactcagtgaaagaccttggaatcttcgtcgacgacaagctgaacttccagaagcacat
aaacatcatttcgaacttagcccttctcaaatgccggcagttacttcgatccttccgctc
aacaaatgccagcctttacttcaaattgtacaatatctatgtgcagccaatattaaa

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GGACTCAGTGAAAGACCTTGGAATC 192 525 204 Antisense
TCGTCGACGACAAGCTGAACTTCCA 129 605 230 Antisense
CGACAAGCTGAACTTCCAGAAGCAC 17 253 237 Antisense
CTTCCAGAAGCACATAAACATCATT 253 219 249 Antisense
AAACATCATTTCGAACTTAGCCCTT 222 129 264 Antisense
TTTCGAACTTAGCCCTTCTCAAATG 644 669 272 Antisense
AACTTAGCCCTTCTCAAATGCCGGC 399 137 277 Antisense
TTAGCCCTTCTCAAATGCCGGCAGT 585 681 280 Antisense
GCCCTTCTCAAATGCCGGCAGTTAC 702 285 283 Antisense
CAAATGCCGGCAGTTACTTCGATCC 701 191 291 Antisense
ATATCTATGTGCAGCCAATATTAAA 134 21 356 Antisense
Sequence Source Affymetrix Proprietary Database