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[187886_at] ATP-dependent RNA helicase

Description C06E1.10 /REP_DB=WormBase Gene ID /WP=CE00055 /SUBMIT=ST.LOUIS /CHR=3 /FEA=Sanger Annotation /DEF=ATP-dependent RNA helicase
Cluster 6grp_highest_10_10 > 83      6grp_high1_10_10 > 48      4grp_highest_8_8 > 50      4grp_high_8_8 > 40      6grp_highest_nonorm > 80      6grp_total > 37      4grp_total > 55      6grp_highest_sub > Cu      6grp_cgc > 16      6grp_high1_sub > Cu      6grp_cgc_sub > Cu      6grp_total_sub > Cup      4grp_rule_based > L1      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 230
1 2 3 4 range
A 424
(3)
P 		204.2
(-3)
P 		240.6
(-2)
P 		246.2
(-1.9)
P 		220
B 301.1
(3)
P 		244.4
(-0.2)
P 		194.1
(-3)
P 		213.2
(-1.9)
P 		107
C 419.2
(3)
P 		231
(-2.1)
P 		311.6
(0.1)
P 		197.6
(-3)
P 		222
avr 381.4
(3) 		226.5
(-2.7) 		248.8
(-1.9) 		219
(-3) 		162

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 208
1 2 3 4 5 6 range
A 241.9
(1.1)
P 		279
(2.7)
P 		145
(-3)
P 		165.9
(-2.1)
P 		181.5
(-1.4)
P 		285.8
(3)
P 		141
B 273.2
(3)
P 		218.9
(0.5)
P 		191.1
(-0.8)
P 		143.1
(-3)
P 		166.3
(-1.9)
P 		246.7
(1.8)
P 		130
C 350.8
(3)
P 		233.6
(-1.2)
P 		189.6
(-2.8)
P 		185.1
(-3)
P 		203.3
(-2.3)
P 		267.6
(-0)
P 		166
avr 288.6
(3) 		243.8
(0.8) 		175.2
(-2.5) 		164.7
(-3) 		183.7
(-2.1) 		266.7
(1.9) 		124
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 121
1 2 3 4 range
A 154.4
(3)
P 		44.3
(-2.6)
P 		62.9
(-1.6)
P 		36
(-3)
P 		118
B 96
(3)
P 		60.4
(-1.2)
P 		45
(-3)
P 		45.4
(-3)
P 		51
C 138.8
(3)
P 		66.4
(-1.1)
P 		108.6
(1.3)
P 		33.3
(-3)
P 		106
avr 129.7
(3) 		57
(-1.8) 		72.2
(-0.8) 		38.2
(-3) 		92

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 98
1 2 3 4 5 6 range
A 44.6
(-1.8)
P 		99.2
(3)
P 		31.6
(-3)
P 		42.1
(-2.1)
P 		54.8
(-0.9)
P 		69.6
(0.4)
P 		68
B 95.1
(3)
P 		72.9
(0.7)
P 		46.4
(-2.1)
P 		37.9
(-3)
P 		67.5
(0.1)
P 		92
(2.7)
P 		57
C 130
(3)
P 		71.3
(-0.8)
P 		48.2
(-2.3)
P 		37.2
(-3)
P 		65.8
(-1.2)
P 		89.6
(0.4)
P 		93
avr 89.9
(3) 		81.1
(2) 		42.1
(-2.6) 		39.1
(-3) 		62.7
(-0.2) 		83.7
(2.3) 		51
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 187886_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.7431
Sequence Type Exemplar sequence
Representative Public ID C06E1.10 NCBI
Target Description C06E1.10 /REP_DB=WormBase Gene ID /WP=CE00055 /SUBMIT=ST.LOUIS /CHR=3 /FEA=Sanger Annotation /DEF=ATP-dependent RNA 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_066494(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_066494 NCBI Caenorhabditis elegans C06E1.10 (C06E1.10) mRNA, complete cds. 11/11 None
SNAP00000034823 ENSEMBL cdna:SNAP chromosome:CEL140:III:8609967:8614459:-1 11/11 None
GENEFINDER00000034825 ENSEMBL cdna:GeneFinder chromosome:CEL140:III:8609967:8614459:-1 11/11 None
C06E1.10 ENSEMBL cdna:known chromosome:CEL140:III:8609967:8614459:-1 gene:C06E1.10 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:8609961-8614454(-) 99.28 100.0
Public Domain and Genome References
Gene Title ATP-dependent RNA helicase
Gene Symbol rha-2
Ensembl C06E1.10
Entrez Gene 176207 Entrez gene
SwissProt P34305 EMBL-EBI
WormBase CE29563 Wormbase
Functional Annotations
Ortholog
ID Title Organism
ATH1-121501:256511_AT helicase domain-containing protein at
CANINE_2:CFAAFFX.11316.1.S1_AT similar to DEAH (Asp-Glu-Ala-His) box polypeptide 37 cfa
DROSOPHILA_2:1623496_AT kurz dm
DROSGENOME1:143210_AT kurz dm
CHICKEN:GGA.17012.1.S1_S_AT DEAH (Asp-Glu-Ala-His) box polypeptide 37 gga
CHICKEN:GGAAFFX.1887.1.S1_AT DEAH (Asp-Glu-Ala-His) box polypeptide 37 gga
CHICKEN:GGAAFFX.25699.1.S1_AT DEAH (Asp-Glu-Ala-His) box polypeptide 37 gga
CHICKEN:GGAAFFX.25699.1.S1_S_AT DEAH (Asp-Glu-Ala-His) box polypeptide 37 gga
HU35KSUBA:RC_AA357204_S_AT DEAH (Asp-Glu-Ala-His) box polypeptide 37 hs
HU35KSUBC:RC_AA027833_I_AT DEAH (Asp-Glu-Ala-His) box polypeptide 37 hs
HG-U133B:223364_S_AT DEAH (Asp-Glu-Ala-His) box polypeptide 37 hs
HG-U133_PLUS_2:223364_S_AT DEAH (Asp-Glu-Ala-His) box polypeptide 37 hs
HG-U133B:223365_AT DEAH (Asp-Glu-Ala-His) box polypeptide 37 hs
HG-U133_PLUS_2:223365_AT DEAH (Asp-Glu-Ala-His) box polypeptide 37 hs
U133_X3P:G13325300_3P_X_AT DEAH (Asp-Glu-Ala-His) box polypeptide 37 hs
U133_X3P:G13325300_3P_AT DEAH (Asp-Glu-Ala-His) box polypeptide 37 hs
U133_X3P:G13325300_3P_A_AT DEAH (Asp-Glu-Ala-His) box polypeptide 37 hs
HG-U95C:58500_AT DEAH (Asp-Glu-Ala-His) box polypeptide 37 hs
HG-U95E:69913_AT DEAH (Asp-Glu-Ala-His) box polypeptide 37 hs
MOUSE430_2:1443493_AT MKIAA1517 protein mm
MOE430B:1443493_AT MKIAA1517 protein mm
MG-U74CV2:166764_AT MKIAA1517 protein mm
RAE230B:1378031_AT DEAH (Asp-Glu-Ala-His) box polypeptide 37 (predicted) rn
RAT230_2:1378031_AT DEAH (Asp-Glu-Ala-His) box polypeptide 37 (predicted) rn
YEAST_2:1769871_AT Essential DEAH-box ATP-dependent RNA helicase specific to the U3 snoRNP, predominantly nucleolar in distribution, required for 18S rRNA synthesis Sc
Gene Ontology
GO Molecular Function (view graph)
ID Description Evidence Links
3676 nucleic acid binding inferred from electronic annotation QuickGO AmiGO
4386 helicase 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
Protein Similarities
Method ID Description E-Value
blast AAA27928 Hypothetical protein C06E1.10 [Caenorhabditis elegans] ref|NP_498895.1| C06E1.10 [Caenorhabditis elegans] sp|P34305|YKQ0_CAEEL Putative ATP-dependent RNA helicase C06E1.10 in chromosome III 0.0
blast H88533 probable ATP-dependent RNA helicase C06E1.10 - Caenorhabditis elegans 0.0
blast CAE69279 Hypothetical protein CBG15333 [Caenorhabditis briggsae] 0.0
Protein Domains
Database ID Description E-Value
Pfam IPR007502 EMBL-EBI Helicase-associated region 4.7E-14
Pfam IPR001650 EMBL-EBI Helicase, C-terminal 2.3E-11
Sequence
Target Sequence 
>C. ELEGANS:187886_AT
gacacgttttcattgatccatgctcagtcgtattcacagaagaaccagaatttgtgatct
atcaagaattggttcaagtaaatgagaagaagctgatgacgtcagtgtgtgcagttgata
aagaatggctcagtagattggctgaatcatattgcaattatggagaacaggacaagaatc
aggaaccgatttacgatccagtcaaagatatggttgtgaaaacagtgaaagtgacatttg
gaccgttgaattgggaattgccgaacgaaaatcgaagtgtaccacatgatatcatgatgt
atagatattttgcactattcctcctcgatggattggtttttgaaaaactcaaagaatata
ctccgaagctactagcaccgccatcaacaatggtcaagtcttgggcaaaattgcagaaac
gaacggagatgttgttgaataagttaatcgagaaggaggtaacaacgcgatcatcactga
aagagcaatggttgaaaaatgagaattggttgctggaagaatatttggaatgggttccag
aatccgtgcatcaacaaatttcccttatgtggccaccgcttgaagatcatga

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GACACGTTTTCATTGATCCATGCTC 671 367 2843 Antisense
ATCCATGCTCAGTCGTATTCACAGA 677 39 2858 Antisense
GATGACGTCAGTGTGTGCAGTTGAT 657 411 2937 Antisense
GGAACCGATTTACGATCCAGTCAAA 268 529 3024 Antisense
GTGACATTTGGACCGTTGAATTGGG 709 465 3073 Antisense
CACTATTCCTCCTCGATGGATTGGT 197 197 3155 Antisense
GAATATACTCCGAAGCTACTAGCAC 491 325 3196 Antisense
GGAGGTAACAACGCGATCATCACTG 469 515 3297 Antisense
GAATGGGTTCCAGAATCCGTGCATC 578 331 3370 Antisense
CAACAAATTTCCCTTATGTGGCCAC 199 185 3394 Antisense
TGTGGCCACCGCTTGAAGATCATGA 168 555 3410 Antisense
Sequence Source Affymetrix Proprietary Database