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[175076_s_at] ATP-dependent RNA helicase

Description C58962_rc /REP_DB=TREMBL Accession /GB=C58962 /CHR=2 /FEA=Genomic Cluster /REVCOMP /DEF=C.elegans cDNA clone yk384b11 : 3prime end, single read.
Cluster 6grp_highest_10_10 > 62      6grp_high1_10_10 > 36      4grp_highest_8_8 > 41      4grp_high_8_8 > 49      6grp_highest_nonorm > 81      6grp_total > 37      4grp_total > 54      6grp_highest_sub > Cu      6grp_cgc > 05      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.
4 291
1 2 3 4 range
A 259.6
(1.4)
P 		256.1
(1.2)
P 		291.7
(3)
P 		170.6
(-3)
P 		121
B 457.6
(3)
P 		275.3
(-0.9)
P 		247.4
(-1.5)
P 		177.4
(-3)
P 		280
C 419.3
(3)
P 		280.5
(-0.3)
P 		242.1
(-1.2)
P 		166.6
(-3)
P 		253
avr 378.8
(3) 		270.6
(-0.1) 		260.4
(-0.4) 		171.5
(-3) 		207

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 200
1 2 3 4 5 6 range
A 298.5
(1.2)
P 		329.3
(2.2)
P 		167.9
(-3)
P 		235.3
(-0.8)
P 		236.6
(-0.8)
P 		354.2
(3)
P 		186
B 305.7
(3)
P 		292.5
(2)
P 		255.8
(-0.7)
P 		253.2
(-0.9)
P 		224.5
(-3)
P 		257.1
(-0.6)
P 		81
C 367.9
(3)
P 		281.7
(0.2)
P 		258.1
(-0.5)
P 		180.3
(-3)
P 		240.5
(-1.1)
P 		243.7
(-1)
P 		188
avr 324
(3) 		301.2
(1.6) 		227.3
(-2.7) 		222.9
(-3) 		233.9
(-2.3) 		285
(0.7) 		101
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 121
1 2 3 4 range
A 94.5
(3)
P 		55.6
(-0.4)
P 		76.3
(1.4)
P 		25
(-3)
P 		70
B 145.9
(3)
P 		68
(-1.3)
P 		57.3
(-1.9)
P 		37.8
(-3)
P 		108
C 138.8
(3)
P 		80.6
(-0.2)
P 		84.4
(0.1)
P 		28.1
(-3)
P 		111
avr 126.4
(3) 		68.1
(-0.6) 		72.7
(-0.4) 		30.3
(-3) 		96

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 100
1 2 3 4 5 6 range
A 55
(-1.6)
P 		117.1
(3)
P 		36.6
(-3)
P 		59.7
(-1.3)
P 		71.4
(-0.4)
P 		86.2
(0.7)
P 		81
B 106.4
(3)
P 		97.4
(1.8)
P 		62.1
(-3)
P 		67.1
(-2.3)
P 		91.2
(0.9)
P 		95.9
(1.6)
P 		44
C 136.3
(3)
P 		86
(-0)
P 		65.7
(-1.2)
P 		36.3
(-3)
P 		77.8
(-0.5)
P 		81.6
(-0.3)
P 		100
avr 99.2
(2.9) 		100.2
(3) 		54.8
(-2.9) 		54.4
(-3) 		80.1
(0.4) 		87.9
(1.4) 		46
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 175076_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.28218
Sequence Type Exemplar sequence
Representative Public ID C58962 NCBI
Target Description C58962_rc /REP_DB=TREMBL Accession /GB=C58962 /CHR=2 /FEA=Genomic Cluster /REVCOMP /DEF=C.elegans cDNA clone yk384b11 : 3prime end, single read.
Cluster Evidence This cluster is supported by a Genomic Cluster.
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_063489(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_063489 NCBI Caenorhabditis elegans RNA HelicAse family member (rha-1) (rha-1) mRNA, complete cds. 11/11 A 
SNAP00000030619 ENSEMBL cdna:SNAP chromosome:CEL140:II:8878531:8882865:-1 11/11 None
GENEFINDER00000030624 ENSEMBL cdna:GeneFinder chromosome:CEL140:II:8878503:8883571:-1 11/11 None
T07D4.3 ENSEMBL cdna:known chromosome:CEL140:II:8878417:8884217:-1 gene:T07D4.3 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
Alignment(s)
Position Identity Coverage Cytoband
chrII:8880423-8880703(-) 100.0 100.0
Public Domain and Genome References
Gene Title ATP-dependent RNA helicase
Gene Symbol rha-1
Ensembl T07D4.3
Entrez Gene 174417 Entrez gene
SwissProt Q22307 EMBL-EBI
WormBase CE18218 Wormbase
Functional Annotations
Ortholog
ID Title Organism
CANINE:1597915_AT similar to ATP-dependent RNA helicase A (Nuclear DNA helicase II) (NDH II) (DEAH-box protein 9) cfa
CANINE:1591101_AT similar to ATP-dependent RNA helicase A (Nuclear DNA helicase II) (NDH II) (DEAH-box protein 9) cfa
CANINE:1588986_AT similar to ATP-dependent RNA helicase A (Nuclear DNA helicase II) (NDH II) (DEAH-box protein 9) cfa
CANINE_2:CFA.10855.1.S1_AT similar to ATP-dependent RNA helicase A (Nuclear DNA helicase II) (NDH II) (DEAH-box protein 9) cfa
CANINE_2:CFA.14207.1.A1_AT similar to ATP-dependent RNA helicase A (Nuclear DNA helicase II) (NDH II) (DEAH-box protein 9) cfa
CANINE_2:CFA.17358.3.S1_S_AT similar to ATP-dependent RNA helicase A (Nuclear DNA helicase II) (NDH II) (DEAH-box protein 9) cfa
CANINE_2:CFAAFFX.20455.1.S1_S_AT similar to ATP-dependent RNA helicase A (Nuclear DNA helicase II) (NDH II) (DEAH-box protein 9) cfa
DROSOPHILA_2:1629507_A_AT maleless dm
DROSGENOME1:143266_AT maleless dm
HG-U95AV2:662_AT DEAH (Asp-Glu-Ala-His) box polypeptide 9 hs
HC-G110:662_AT DEAH (Asp-Glu-Ala-His) box polypeptide 9 hs
HU35KSUBC:RC_N70377_AT DEAH (Asp-Glu-Ala-His) box polypeptide 9 hs
HUGENEFL:L13848_AT DEAH (Asp-Glu-Ala-His) box polypeptide 9 hs
HG-U133A:202420_S_AT DEAH (Asp-Glu-Ala-His) box polypeptide 9 hs
HG-U133_PLUS_2:202420_S_AT DEAH (Asp-Glu-Ala-His) box polypeptide 9 hs
HG-FOCUS:202420_S_AT DEAH (Asp-Glu-Ala-His) box polypeptide 9 hs
HG-U133A_2:202420_S_AT DEAH (Asp-Glu-Ala-His) box polypeptide 9 hs
U133_X3P:G13514819_3P_A_AT DEAH (Asp-Glu-Ala-His) box polypeptide 9 hs
U133_X3P:HS.74578.2.S2_3P_A_AT DEAH (Asp-Glu-Ala-His) box polypeptide 9 hs
U133_X3P:HS.74578.2.S1_3P_A_AT DEAH (Asp-Glu-Ala-His) box polypeptide 9 hs
HG-U133_PLUS_2:212107_S_AT DEAH (Asp-Glu-Ala-His) box polypeptide 9 hs
HG-U133A_2:212107_S_AT DEAH (Asp-Glu-Ala-His) box polypeptide 9 hs
HG-U133A:212107_S_AT DEAH (Asp-Glu-Ala-His) box polypeptide 9 hs
HG-U133A_2:212105_S_AT DEAH (Asp-Glu-Ala-His) box polypeptide 9 hs
HG-U133_PLUS_2:212105_S_AT DEAH (Asp-Glu-Ala-His) box polypeptide 9 hs
HG-U133A:212105_S_AT DEAH (Asp-Glu-Ala-His) box polypeptide 9 hs
HG-U95AV2:36153_AT DEAH (Asp-Glu-Ala-His) box polypeptide 9 hs
HG-U95D:67980_AT DEAH (Asp-Glu-Ala-His) box polypeptide 9 hs
HG-U95D:67983_G_AT DEAH (Asp-Glu-Ala-His) box polypeptide 9 hs
U133_X3P:HS.140402.0.S1_3P_X_AT DEAH (Asp-Glu-Ala-His) box polypeptide 9 hs
U133_X3P:215467_3P_X_AT DEAH (Asp-Glu-Ala-His) box polypeptide 9 hs
HG-U133A_2:215467_X_AT DEAH (Asp-Glu-Ala-His) box polypeptide 9 hs
HG-U133_PLUS_2:215467_X_AT DEAH (Asp-Glu-Ala-His) box polypeptide 9 hs
HG-U133A:215467_X_AT DEAH (Asp-Glu-Ala-His) box polypeptide 9 hs
HG-U133_PLUS_2:215468_AT DEAH (Asp-Glu-Ala-His) box polypeptide 9 hs
HG-U133A_2:215468_AT DEAH (Asp-Glu-Ala-His) box polypeptide 9 hs
HG-U133A:215468_AT DEAH (Asp-Glu-Ala-His) box polypeptide 9 hs
HG-U95D:67954_AT DEAH (Asp-Glu-Ala-His) box polypeptide 9 hs
HG-U95E:79227_AT DEAH (Asp-Glu-Ala-His) box polypeptide 9 hs
MOUSE430_2:1425617_AT DEAH (Asp-Glu-Ala-His) box polypeptide 9 mm
MOE430A:1425617_AT DEAH (Asp-Glu-Ala-His) box polypeptide 9 mm
MOUSE430A_2:1425617_AT DEAH (Asp-Glu-Ala-His) box polypeptide 9 mm
MU11KSUBB:MSA.10110.0_S_AT DEAH (Asp-Glu-Ala-His) box polypeptide 9 mm
MG-U74AV2:103598_AT DEAH (Asp-Glu-Ala-His) box polypeptide 9 mm
MOE430A:1425618_AT DEAH (Asp-Glu-Ala-His) box polypeptide 9 mm
MOUSE430A_2:1425618_AT DEAH (Asp-Glu-Ala-His) box polypeptide 9 mm
MOUSE430_2:1425618_AT DEAH (Asp-Glu-Ala-His) box polypeptide 9 mm
MOE430A:1451770_S_AT DEAH (Asp-Glu-Ala-His) box polypeptide 9 mm
MOUSE430A_2:1451770_S_AT DEAH (Asp-Glu-Ala-His) box polypeptide 9 mm
MOUSE430_2:1451770_S_AT DEAH (Asp-Glu-Ala-His) box polypeptide 9 mm
MU19KSUBB:TC31843_AT DEAH (Asp-Glu-Ala-His) box polypeptide 9 (Dhx9), mRNA mm
RAE230A:1374299_AT DEAH (Asp-Glu-Ala-His) box polypeptide 9 (predicted) rn
RAT230_2:1374299_AT DEAH (Asp-Glu-Ala-His) box polypeptide 9 (predicted) rn
RG-U34A:RC_AI639188_AT DEAH (Asp-Glu-Ala-His) box polypeptide 9 (predicted) rn
Gene Ontology
GO Cellular Component (view graph)
ID Description Evidence Links
5622 intracellular inferred from electronic annotation QuickGO AmiGO
5634 nucleus inferred from direct assay QuickGO AmiGO
5737 cytoplasm inferred from direct assay QuickGO AmiGO
GO Molecular Function (view graph)
ID Description Evidence Links
3676 nucleic acid 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
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 NP_495890 RNA HelicAse family member (rha-1) [Caenorhabditis elegans] pir||T24664 hypothetical protein T07D4.3 - Caenorhabditis elegans 0.0
blast CAA90409 Hypothetical protein T07D4.3 [Caenorhabditis elegans] sp|Q22307|DHX9_CAEEL Probable ATP-dependent RNA helicase A (Nuclear DNA helicase II) (NDH II) 0.0
blast CAE59755 Hypothetical protein CBG03202 [Caenorhabditis briggsae] 0.0
Protein Domains
Database ID Description E-Value
Pfam IPR007502 EMBL-EBI Helicase-associated region 1.3E-26
Pfam IPR001650 EMBL-EBI Helicase, C-terminal 9.9E-19
Pfam IPR001159 EMBL-EBI Double-stranded RNA binding (DsRBD) domain 2.0E-16
Pfam IPR001159 EMBL-EBI Double-stranded RNA binding (DsRBD) domain 2.1E-14
Pfam IPR007502 EMBL-EBI Helicase-associated region 1.3E-26
Pfam IPR001650 EMBL-EBI Helicase, C-terminal 9.9E-19
Pfam IPR001159 EMBL-EBI Double-stranded RNA binding (DsRBD) domain 8.2E-6
Pfam IPR007502 EMBL-EBI Helicase-associated region 1.3E-26
Pfam IPR001650 EMBL-EBI Helicase, C-terminal 9.9E-19
Pfam IPR001159 EMBL-EBI Double-stranded RNA binding (DsRBD) domain 2.0E-16
Pfam IPR001159 EMBL-EBI Double-stranded RNA binding (DsRBD) domain 2.1E-14
Sequence
Target Sequence 
>C. ELEGANS:175076_S_AT
ttgacaatcaaacttctccgtctcggatccgtcggtgaattccttggaaaggctcttcaa
cctccaccgtatgatatggtcgtcgaaagtgaagcagtgttacaagcgatgggagctctt
gatcgtaatttagaattgacaagtctcggaaaaatgctcgctcgtatgccaattgagcct
gtcattgccaaagtgcttattcttggaactgctcttggtgcaggatctgtgatgtgtgac
gtggca

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
TTGACAATCAAACTTCTCCGTCTCG 618 703 17 Antisense
GTCTCGGATCCGTCGGTGAATTCCT 229 471 36 Antisense
CTTGGAAAGGCTCTTCAACCTCCAC 548 201 59 Antisense
ACCTCCACCGTATGATATGGTCGTC 324 87 76 Antisense
ATGGGAGCTCTTGATCGTAATTTAG 66 51 125 Antisense
GGAAAAATGCTCGCTCGTATGCCAA 634 527 164 Antisense
CTCGTATGCCAATTGAGCCTGTCAT 483 231 177 Antisense
GAGCCTGTCATTGCCAAAGTGCTTA 564 385 191 Antisense
AGTGCTTATTCTTGGAACTGCTCTT 624 59 208 Antisense
GAACTGCTCTTGGTGCAGGATCTGT 398 349 222 Antisense
AGGATCTGTGATGTGTGACGTGGCA 202 57 238 Antisense
Sequence Source Affymetrix Proprietary Database