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[192371_s_at] Double-stranded RNA binding motif

Description T20G5.11 /REP_DB=WormBase Gene ID /WP=CE00630 /TR=Q22617 /GB=CAA83012.1 /SUBMIT=HINXTON /CHR=3 /FEA=Sanger Annotation /DEF=Double-stranded RNA binding motif
Cluster 6grp_highest_10_10 > 86      6grp_high1_10_10 > 77      4grp_highest_8_8 > 35      4grp_high_8_8 > 56      6grp_highest_nonorm > 96      6grp_total > 78      4grp_total > 63      6grp_highest_sub > Da      6grp_cgc > 49      6grp_high1_sub > Da      6grp_cgc_sub > Da      6grp_total_sub > Increase      6grp_rule_based > S6      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 470
1 2 3 4 range
A 933.3
(0.6)
P 		915
(0.3)
P 		1052.2
(3)
P 		751.4
(-3)
P 		301
B 1105.9
(3)
P 		762.8
(-3)
P 		1003.3
(1.2)
P 		850.8
(-1.5)
P 		343
C 960
(3)
P 		635.9
(-3)
P 		880.4
(1.5)
P 		801.9
(0.1)
P 		324
avr 999.7
(3) 		771.2
(-3) 		978.6
(2.4) 		801.4
(-2.2) 		229

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 774
1 2 3 4 5 6 range
A 853.9
(-0.9)
P 		790.3
(-1.8)
P 		697.9
(-3)
P 		873.7
(-0.7)
P 		950.2
(0.4)
P 		1149.1
(3)
P 		451
B 846.1
(-3)
P 		888
(-2.5)
P 		938.2
(-1.8)
P 		857.6
(-2.9)
P 		915
(-2.1)
P 		1309.7
(3)
P 		464
C 785
(-1.9)
P 		905.2
(-0.9)
P 		639.7
(-3)
P 		761.3
(-2.1)
P 		885.4
(-1.1)
P 		1413.7
(3)
P 		774
avr 828.3
(-2.2) 		861.2
(-1.8) 		758.6
(-3) 		830.9
(-2.2) 		916.9
(-1.2) 		1290.8
(3) 		532
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 243
1 2 3 4 range
A 339.8
(3)
P 		198.6
(-0.7)
P 		275.1
(1.3)
P 		110
(-3)
P 		230
B 352.7
(3)
P 		188.4
(-2.8)
P 		232.5
(-1.2)
P 		181.3
(-3)
P 		171
C 317.8
(3)
P 		182.8
(-1.4)
P 		306.8
(2.6)
P 		135.2
(-3)
P 		183
avr 336.8
(3) 		189.9
(-1.5) 		271.5
(1) 		142.2
(-3) 		195

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 336
1 2 3 4 5 6 range
A 157.4
(-2.8)
P 		281.1
(2.8)
P 		152
(-3)
P 		221.6
(0.1)
P 		286.7
(3)
P 		279.8
(2.7)
P 		135
B 294.4
(-1.5)
P 		295.6
(-1.4)
P 		227.8
(-3)
P 		227.2
(-3)
P 		371.7
(0.3)
P 		488.4
(3)
P 		261
C 291
(-0.4)
P 		276.2
(-0.7)
P 		162.8
(-2.8)
P 		153.1
(-3)
P 		286.5
(-0.5)
P 		473.2
(3)
P 		320
avr 247.6
(-1.3) 		284.3
(-0.3) 		180.9
(-3) 		200.6
(-2.5) 		315
(0.5) 		413.8
(3) 		233
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 192371_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.6735
Sequence Type Exemplar sequence
Representative Public ID T20G5.11 NCBI
Target Description T20G5.11 /REP_DB=WormBase Gene ID /WP=CE00630 /TR=Q22617 /GB=CAA83012.1 /SUBMIT=HINXTON /CHR=3 /FEA=Sanger Annotation /DEF=Double-stranded RNA binding motif
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_066864(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_066864 NCBI Caenorhabditis elegans RNAi DEfective family member (rde-4) (rde-4) mRNA, complete cds. 11/11 None
SNAP00000033308 ENSEMBL cdna:SNAP chromosome:CEL140:III:10217235:10218533:-1 11/11 None
GENEFINDER00000033343 ENSEMBL cdna:GeneFinder chromosome:CEL140:III:10217235:10218533:-1 11/11 None
T20G5.11 ENSEMBL cdna:known chromosome:CEL140:III:10216665:10218533:-1 gene:T20G5.11 11/11 None
Annotation Notes
There are no noteworthy cross hybridizing mRNAs found for this probe set.
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrIII:10217230-10218529(-) 100.0 100.0
Public Domain and Genome References
Gene Title Double-stranded RNA binding motif
Gene Symbol rde-4
Ensembl T20G5.11
Entrez Gene 176438 Entrez gene
SwissProt Q22617 EMBL-EBI
WormBase CE00630 Wormbase
Functional Annotations
Gene Ontology
GO Cellular Component (view graph)
ID Description Evidence Links
5622 intracellular inferred from electronic annotation QuickGO AmiGO
GO Molecular Function (view graph)
ID Description Evidence Links
3725 double-stranded RNA binding inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast CAA83012 Hypothetical protein T20G5.11 [Caenorhabditis elegans] ref|NP_499265.1| RNAi DEfective family member (rde-4) [Caenorhabditis elegans] gb|AAL61544.1| RNA interference promoting factor [Caenorhabditis elegans] 0.0
blast CAE64977 Hypothetical protein CBG09811 [Caenorhabditis briggsae] 1.0E-103
Protein Domains
Database ID Description E-Value
Pfam IPR001159 EMBL-EBI Double-stranded RNA binding (DsRBD) domain 6.6E-11
Pfam IPR001159 EMBL-EBI Double-stranded RNA binding (DsRBD) domain 5.8E-15
Sequence
Target Sequence 
>C. ELEGANS:192371_S_AT
gctgcaagccccaatctatgaagattccaagaatgagagaaccgagcgtttcttggttat
atgcacgatgtgcaatcaaaaaaccagaggaatcagaagtaagaagaaggacgcaaagaa
tcttgcagcatggttgatgtggaaagcgttggaagacggtatcgaatctctggaatcata
tgatatggttgatgtgattgaaaatttggaagaagctgaacatttactcgaaattcagga
tcaagcatccaagattaaagacaagcattccgcactgattgatatactctcggacaagaa
aagattttcagactacagcatggatttcaacgtattatcagtgagcacaatgggaataca
tcaggtgctattggaaatctcgttccggcgtctagtttctccagaccccgacgatttgga
aatgggagcagaacacacccagactgaagaaattatgaaggctactgccgagaaggaaaa
gctacggaagaagaatatgccagattccgggccgctagtgtttgctggacatggttcatc
ggcggaagaggc

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GCTGCAAGCCCCAATCTATGAAGAT 375 297 558 Antisense
CCGAGCGTTTCTTGGTTATATGCAC 64 265 599 Antisense
GACGGTATCGAATCTCTGGAATCAT 158 377 712 Antisense
AAGACAAGCATTCCGCACTGATTGA 269 153 815 Antisense
GCACTGATTGATATACTCTCGGACA 1 313 829 Antisense
CAGACTACAGCATGGATTTCAACGT 188 205 866 Antisense
TATTGGAAATCTCGTTCCGGCGTCT 307 665 926 Antisense
TTCTCCAGACCCCGACGATTTGGAA 627 693 954 Antisense
GAAGAATATGCCAGATTCCGGGCCG 79 341 1047 Antisense
GCCGCTAGTGTTTGCTGGACATGGT 383 285 1068 Antisense
GACATGGTTCATCGGCGGAAGAGGC 664 369 1085 Antisense
Sequence Source Affymetrix Proprietary Database