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[177140_s_at] dead box helicase

Description K12H4.8 /REP_DB=WormBase Gene ID /WP=CE25057 /SUBMIT=ST.LOUIS /CHR=3 /FEA=Sanger Annotation /DEF=dead box helicase
Cluster 6grp_highest_10_10 > 74      6grp_high1_10_10 > 56      4grp_highest_8_8 > 50      4grp_high_8_8 > 40      6grp_highest_nonorm > 84      6grp_total > 56      4grp_total > 54      6grp_highest_sub > Cu      6grp_cgc > 36      6grp_high1_sub > Cu      4grp_rule_based > L1      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 467
1 2 3 4 range
A 658.4
(3)
P 		466.7
(-0.4)
P 		384.3
(-1.8)
P 		316.3
(-3)
P 		342
B 755.8
(3)
P 		438.8
(-1.9)
P 		414.4
(-2.2)
P 		364.4
(-3)
P 		391
C 782.8
(3)
P 		412.8
(-1.9)
P 		489.2
(-0.9)
P 		329.5
(-3)
P 		453
avr 732.3
(3) 		439.4
(-1.4) 		429.3
(-1.6) 		336.7
(-3) 		396

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 349
1 2 3 4 5 6 range
A 760.8
(3)
P 		614.6
(0.1)
P 		584.7
(-0.5)
P 		540.4
(-1.4)
P 		457
(-3)
P 		691.9
(1.6)
P 		304
B 603.2
(0.4)
P 		553.1
(-0.5)
P 		642.3
(1.1)
P 		571.9
(-0.2)
P 		418.5
(-3)
P 		742.9
(3)
P 		324
C 553
(-0.7)
P 		574.1
(-0.3)
P 		603.5
(0.2)
P 		596.2
(0.1)
P 		416.9
(-3)
P 		766
(3)
P 		349
avr 639
(1.1) 		580.6
(-0) 		610.2
(0.6) 		569.5
(-0.3) 		430.8
(-3) 		733.6
(3) 		303
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 213
1 2 3 4 range
A 239.7
(3)
P 		101.3
(-1.3)
P 		100.5
(-1.3)
P 		46.3
(-3)
P 		193
B 241
(3)
P 		108.4
(-1.9)
P 		96
(-2.3)
P 		77.7
(-3)
P 		163
C 259.1
(3)
P 		118.7
(-1.1)
P 		170.5
(0.4)
P 		55.6
(-3)
P 		204
avr 246.6
(3) 		109.5
(-1.4) 		122.3
(-1) 		59.9
(-3) 		187

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 157
1 2 3 4 5 6 range
A 140.2
(-2.2)
P 		218.6
(3)
P 		127.3
(-3)
P 		137.1
(-2.4)
P 		137.9
(-2.3)
P 		168.5
(-0.3)
P 		91
B 209.9
(-0.2)
P 		184.1
(-1.4)
P 		156
(-2.8)
P 		151.5
(-3)
P 		170
(-2.1)
P 		277
(3)
P 		126
C 205
(0.7)
P 		175.2
(-0.6)
P 		153.6
(-1.5)
P 		119.9
(-3)
P 		134.9
(-2.3)
P 		256.4
(3)
P 		137
avr 185
(-0) 		192.6
(0.5) 		145.6
(-2.4) 		136.2
(-3) 		147.6
(-2.3) 		234
(3) 		98
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 177140_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.6325
Sequence Type Exemplar sequence
Representative Public ID K12H4.8 NCBI
Target Description K12H4.8 /REP_DB=WormBase Gene ID /WP=CE25057 /SUBMIT=ST.LOUIS /CHR=3 /FEA=Sanger Annotation /DEF=dead box helicase
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_066360(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_066360 NCBI Caenorhabditis elegans DiCer Related family member (dcr-1) (dcr-1) mRNA, complete cds. 11/11 None
SNAP00000000461 ENSEMBL cdna:SNAP chromosome:CEL140:III:8072031:8080195:-1 11/11 None
GENEFINDER00000000470 ENSEMBL cdna:GeneFinder chromosome:CEL140:III:8072031:8073951:-1 11/11 None
K12H4.8 ENSEMBL cdna:known chromosome:CEL140:III:8071837:8080195:-1 gene:K12H4.8 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:8072028-8080193(-) 100.0 100.0
Public Domain and Genome References
Gene Title dead box helicase
Gene Symbol dcr-1
Ensembl K12H4.8
Entrez Gene 176138 Entrez gene
SwissProt P34529 EMBL-EBI
WormBase CE25057 Wormbase
Functional Annotations
Ortholog
ID Title Organism
CANINE:1601171_AT similar to dicer1 cfa
CANINE_2:CFA.4679.1.A1_AT similar to dicer1 cfa
CANINE_2:CFA.4679.1.A1_S_AT similar to dicer1 cfa
CANINE_2:CFAAFFX.27100.1.S1_AT similar to dicer1 cfa
DROSOPHILA_2:1627580_AT Dicer-1 dm
DROSGENOME1:142974_AT Dicer-1 dm
CHICKEN:GGA.12004.1.S1_S_AT similar to dicer1; helicase-moi; K12H4.8-LIKE; helicase with RNAse motif gga
CHICKEN:GGAAFFX.23420.2.S1_S_AT similar to dicer1; helicase-moi; K12H4.8-LIKE; helicase with RNAse motif gga
HG-U133_PLUS_2:206061_S_AT Dicer1, Dcr-1 homolog (Drosophila) hs
HG-U133A:206061_S_AT Dicer1, Dcr-1 homolog (Drosophila) hs
HG-U133A_2:206061_S_AT Dicer1, Dcr-1 homolog (Drosophila) hs
HU35KSUBA:R54534_AT Dicer1, Dcr-1 homolog (Drosophila) hs
HU35KSUBA:RC_AA481525_AT Dicer1, Dcr-1 homolog (Drosophila) hs
HU35KSUBC:RC_AA521474_AT Dicer1, Dcr-1 homolog (Drosophila) hs
HU35KSUBC:RC_AA251552_AT Dicer1, Dcr-1 homolog (Drosophila) hs
HU35KSUBD:RC_W45302_AT Dicer1, Dcr-1 homolog (Drosophila) hs
U133_X3P:HS.87889.2.S1_3P_AT Dicer1, Dcr-1 homolog (Drosophila) hs
U133_X3P:HS.87889.1.A1_3P_A_AT Dicer1, Dcr-1 homolog (Drosophila) hs
U133_X3P:HS.325625.0.A1_3P_AT Dicer1, Dcr-1 homolog (Drosophila) hs
HG-U133A_2:212888_AT Dicer1, Dcr-1 homolog (Drosophila) hs
HG-U133_PLUS_2:212888_AT Dicer1, Dcr-1 homolog (Drosophila) hs
HG-U133A:212888_AT Dicer1, Dcr-1 homolog (Drosophila) hs
HG-U133A_2:213229_AT Dicer1, Dcr-1 homolog (Drosophila) hs
HG-FOCUS:213229_AT Dicer1, Dcr-1 homolog (Drosophila) hs
HG-U133_PLUS_2:213229_AT Dicer1, Dcr-1 homolog (Drosophila) hs
HG-U133A:213229_AT Dicer1, Dcr-1 homolog (Drosophila) hs
HG-U133A_2:216260_AT Dicer1, Dcr-1 homolog (Drosophila) hs
HG-U133_PLUS_2:216260_AT Dicer1, Dcr-1 homolog (Drosophila) hs
HG-U133A:216260_AT Dicer1, Dcr-1 homolog (Drosophila) hs
HG-U95AV2:38764_AT Dicer1, Dcr-1 homolog (Drosophila) hs
HG-U95AV2:38765_AT Dicer1, Dcr-1 homolog (Drosophila) hs
HG-U133A_2:216280_S_AT Dicer1, Dcr-1 homolog (Drosophila) hs
HG-U133_PLUS_2:216280_S_AT Dicer1, Dcr-1 homolog (Drosophila) hs
HG-U133A:216280_S_AT Dicer1, Dcr-1 homolog (Drosophila) hs
HG-U133A_2:216281_AT Dicer1, Dcr-1 homolog (Drosophila) hs
HG-U133_PLUS_2:216281_AT Dicer1, Dcr-1 homolog (Drosophila) hs
HG-U133A:216281_AT Dicer1, Dcr-1 homolog (Drosophila) hs
HU35KSUBA:RC_AA057341_AT Dicer1, Dcr-1 homolog (Drosophila) hs
MOE430A:1427941_AT Dicer1, Dcr-1 homolog (Drosophila) mm
MOUSE430A_2:1427941_AT Dicer1, Dcr-1 homolog (Drosophila) mm
MOUSE430_2:1427941_AT Dicer1, Dcr-1 homolog (Drosophila) mm
MG-U74BV2:113757_AT Dicer1, Dcr-1 homolog (Drosophila) mm
MU11KSUBA:C76324_RC_S_AT Double-strand-specific ribonuclease MDCR mm
MG-U74AV2:160957_AT Double-strand-specific ribonuclease MDCR mm
MOE430A:1460571_AT Double-strand-specific ribonuclease MDCR mm
MOUSE430A_2:1460571_AT Double-strand-specific ribonuclease MDCR mm
MOUSE430_2:1460571_AT Double-strand-specific ribonuclease MDCR mm
MG-U74CV2:137716_AT Double-strand-specific ribonuclease MDCR mm
MU19KSUBC:TC36176_AT Double-strand-specific ribonuclease MDCR mm
MU19KSUBC:TC36176_G_AT Double-strand-specific ribonuclease MDCR mm
RAE230B:1394715_AT Dicer1, Dcr-1 homolog (Drosophila) (predicted) rn
RAT230_2:1394715_AT Dicer1, Dcr-1 homolog (Drosophila) (predicted) rn
RAE230B:1398643_AT Dicer1, Dcr-1 homolog (Drosophila) (predicted) rn
RAT230_2:1398643_AT Dicer1, Dcr-1 homolog (Drosophila) (predicted) rn
Gene Ontology
GO Biological Process (view graph)
ID Description Evidence Links
6396 RNA processing inferred from electronic annotation QuickGO AmiGO
7186 G-protein coupled receptor protein signaling pathway inferred from electronic annotation QuickGO AmiGO
9307 DNA restriction-modification system inferred from electronic annotation QuickGO AmiGO
GO Cellular Component (view graph)
ID Description Evidence Links
5622 intracellular inferred from electronic annotation QuickGO AmiGO
16021 integral to membrane inferred from electronic annotation QuickGO AmiGO
GO Molecular Function (view graph)
ID Description Evidence Links
1584 rhodopsin-like receptor activity inferred from electronic annotation QuickGO AmiGO
3676 nucleic acid binding inferred from electronic annotation QuickGO AmiGO
3723 RNA binding inferred from electronic annotation QuickGO AmiGO
3725 double-stranded RNA binding inferred from electronic annotation QuickGO AmiGO
4386 helicase activity inferred from electronic annotation QuickGO AmiGO
4525 ribonuclease III activity inferred from electronic annotation QuickGO AmiGO
5524 ATP binding inferred from electronic annotation QuickGO AmiGO
8026 ATP-dependent helicase activity inferred from electronic annotation QuickGO AmiGO
15668 type III site-specific deoxyribonuclease activity inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast NP_498761 DiCer Related family member (dcr-1) [Caenorhabditis elegans] gb|AAA28101.2| Dicer related protein 1 [Caenorhabditis elegans] sp|P34529|DCR1_CAEEL Endoribonuclease dcr-1 0.0
blast S44849 K12H4.8 protein - Caenorhabditis elegans 0.0
blast CAE75060 Hypothetical protein CBG22974 [Caenorhabditis briggsae] 0.0
Protein Domains
Database ID Description E-Value
Pfam IPR001410 EMBL-EBI DEAD/DEAH box helicase 5.2E-9
Pfam IPR001650 EMBL-EBI Helicase, C-terminal 4.2E-18
Pfam IPR005034 EMBL-EBI Protein of unknown function DUF283 1.1E-62
Pfam IPR000999 EMBL-EBI Ribonuclease III 4.8E-58
Pfam IPR000999 EMBL-EBI Ribonuclease III 8.4E-55
Pfam IPR001159 EMBL-EBI Double-stranded RNA binding (DsRBD) domain 1.1E-8
Pfam IPR001410 EMBL-EBI DEAD/DEAH box helicase 1.8E-7
Pfam IPR001650 EMBL-EBI Helicase, C-terminal 4.2E-18
Pfam IPR005034 EMBL-EBI Protein of unknown function DUF283 2.6E-64
Pfam IPR000999 EMBL-EBI Ribonuclease III 4.8E-58
Pfam IPR000999 EMBL-EBI Ribonuclease III 8.4E-55
Pfam IPR001159 EMBL-EBI Double-stranded RNA binding (DsRBD) domain 1.1E-8
Pfam IPR000999 EMBL-EBI Ribonuclease III 4.8E-58
Pfam IPR000999 EMBL-EBI Ribonuclease III 8.4E-55
Pfam IPR001159 EMBL-EBI Double-stranded RNA binding (DsRBD) domain 1.1E-8
Sequence
Target Sequence 
>C. ELEGANS:177140_S_AT
gtcaatacagtccgggtgttctcactgatttacgatcagctctcgtcaataatacaattt
tcgcgtcgttagcagtgaaattcgagtttcaaaagcacttcatcgctatgtgcccagggc
tttatcacatgattgagaaatttgttaagctgtgctcggagcgcaatttcgatactaatt
tcaatgctgagatgtatatggtgactactgaggaagaaatagatgaaggccaagaagagg
atattgaagttccaaaagcgatgggtgacatatttgaatcagtagctggcgccatttatc
tcgactctggacgtaatttggataccacttggcaagtgattttccacatgatgcgcggga
ctattgaattgtgctgtgcgaacccaccaagatcaccgattcgagagcttatggagttcg
agcagagcaaagttcgattcagtaaaatggaacgaattctcgagagtggaaaagttcgag
ttacagtcgaggttgttaataacatgagattcactggaatgggaaggaactatcgaatcg
cgaaagctactgctgc

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GTCAATACAGTCCGGGTGTTCTCAC 542 463 4922 Antisense
ACAATTTTCGCGTCGTTAGCAGTGA 257 115 4975 Antisense
AAAGCACTTCATCGCTATGTGCCCA 386 123 5013 Antisense
TGCCCAGGGCTTTATCACATGATTG 673 583 5032 Antisense
GTGCTCGGAGCGCAATTTCGATACT 73 479 5073 Antisense
TCAGTAGCTGGCGCCATTTATCTCG 634 623 5200 Antisense
ATTTATCTCGACTCTGGACGTAATT 154 15 5215 Antisense
CCACATGATGCGCGGGACTATTGAA 446 275 5265 Antisense
TTGAATTGTGCTGTGCGAACCCACC 704 703 5285 Antisense
CCCACCAAGATCACCGATTCGAGAG 115 259 5304 Antisense
ATCGAATCGCGAAAGCTACTGCTGC 325 37 5453 Antisense
Sequence Source Affymetrix Proprietary Database