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[194007_at] DEAD/DEAH box helicase ; Helicases conserved C-terminal domain

Description Y54G11A.3 /REP_DB=WormBase Gene ID /WP=CE22474 /TR=Q9XVZ6 /GB=CAA22456.1 /SUBMIT=HINXTON /CHR=2 /FEA=Sanger Annotation /DEF=DEAD-DEAH box helicase ; Helicases conserved C-terminal domain
Cluster 6grp_total > 96      4grp_total > 32      6grp_total_sub > Increase      6grp_rule_based > S6      4grp_rule_based > L3      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 114
1 2 3 4 range
A 7.1
(-3)
A 		14.1
(-2.2)
A 		37.2
(0.3)
A 		61.7
(3)
A 		55
B 4.2
(-3)
A 		12.4
(-2.5)
A 		111
(3)
A 		86.4
(1.6)
A 		107
C 6.4
(-3)
A 		20.2
(-2.3)
A 		117.9
(3)
A 		57.5
(-0.3)
A 		112
avr 5.9
(-3) 		15.6
(-2.3) 		88.7
(3) 		68.5
(1.5) 		83

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 413
1 2 3 4 5 6 range
A 4.4
(-3)
A 		8.6
(-2.9)
A 		2.8
(-3)
A 		112.7
(-1.2)
A 		287.7
(1.7)
P 		369.2
(3)
P 		366
B 4.1
(-3)
A 		5.2
(-3)
A 		19.9
(-2.7)
A 		100.6
(-1.4)
A 		308.9
(2)
P 		369.8
(3)
P 		366
C 9.3
(-3)
A 		8.3
(-3)
A 		13.2
(-2.9)
A 		111.1
(-1.5)
A 		246.6
(0.5)
P 		415.8
(3)
P 		408
avr 5.9
(-3) 		7.4
(-3) 		12
(-2.9) 		108.1
(-1.4) 		281.1
(1.4) 		384.9
(3) 		379
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 40
1 2 3 4 range
A 2.6
(-3)
A 		3.1
(-2.6)
A 		9.7
(3)
A 		9
(2.4)
A 		7
B 1.3
(-3)
A 		3.1
(-2.6)
A 		25.7
(3)
A 		18.4
(1.2)
A 		24
C 2.1
(-3)
A 		5.8
(-2.4)
A 		41.1
(3)
A 		9.7
(-1.8)
A 		39
avr 2
(-3) 		4
(-2.5) 		25.5
(3) 		12.4
(-0.3) 		24

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 139
1 2 3 4 5 6 range
A 0.8
(-3)
A 		3
(-2.8)
A 		0.6
(-3)
A 		28.6
(-1.1)
A 		86.8
(2.8)
P 		89.9
(3)
P 		89
B 1.4
(-3)
A 		1.7
(-3)
A 		4.8
(-2.9)
A 		26.7
(-1.9)
A 		125.5
(2.5)
P 		137.9
(3)
P 		137
C 3.4
(-3)
A 		2.5
(-3)
A 		3.4
(-3)
A 		22.3
(-2.1)
A 		79.8
(0.4)
P 		139.2
(3)
P 		137
avr 1.9
(-3) 		2.4
(-3) 		2.9
(-3) 		25.9
(-1.8) 		97.4
(1.8) 		122.3
(3) 		120
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 194007_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.3876
Sequence Type Exemplar sequence
Representative Public ID Y54G11A.3 NCBI
Target Description Y54G11A.3 /REP_DB=WormBase Gene ID /WP=CE22474 /TR=Q9XVZ6 /GB=CAA22456.1 /SUBMIT=HINXTON /CHR=2 /FEA=Sanger Annotation /DEF=DEAD-DEAH box helicase ; Helicases conserved C-terminal domain
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_064572(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_064572 NCBI Caenorhabditis elegans Y54G11A.3 (Y54G11A.3) mRNA, complete cds. 11/11 None
SNAP00000023646 ENSEMBL cdna:SNAP chromosome:CEL140:II:14278305:14283742:1 11/11 None
GENEFINDER00000023682 ENSEMBL cdna:GeneFinder chromosome:CEL140:II:14279336:14283742:1 9/11 None
Y54G11A.3.1 ENSEMBL cdna:known chromosome:CEL140:II:14276569:14283849:1 gene:Y54G11A.3 11/11 None
Y54G11A.3.2 ENSEMBL cdna:known chromosome:CEL140:II:14276598:14283888:1 gene:Y54G11A.3 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
chrII:14276600-14283739(+) 100.0 100.0
Public Domain and Genome References
Gene Title DEAD/DEAH box helicase ; Helicases conserved C-terminal domain
Ensembl Y54G11A.3
Entrez Gene 175083 Entrez gene
SwissProt Q9XVZ6 EMBL-EBI
WormBase CE22474 Wormbase
Functional Annotations
Ortholog
ID Title Organism
CANINE_2:CFAAFFX.4842.1.S1_AT similar to DEAD (Asp-Glu-Ala-Asp) box polypeptide 43 cfa
DROSOPHILA_2:1639665_AT dm
DROSGENOME1:154657_AT dm
CHICKEN:GGAAFFX.10149.1.S1_AT similar to DEAD (Asp-Glu-Ala-Asp) box polypeptide 43; DEAD-box protein 43 gga
CHICKEN:GGAAFFX.10149.2.S1_AT similar to DEAD (Asp-Glu-Ala-Asp) box polypeptide 43; DEAD-box protein 43 gga
CHICKEN:GGAAFFX.10149.2.S1_S_AT similar to DEAD (Asp-Glu-Ala-Asp) box polypeptide 43; DEAD-box protein 43 gga
HG-U133_PLUS_2:220004_AT DEAD (Asp-Glu-Ala-Asp) box polypeptide 43 hs
HG-U133A:220004_AT DEAD (Asp-Glu-Ala-Asp) box polypeptide 43 hs
HG-FOCUS:220004_AT DEAD (Asp-Glu-Ala-Asp) box polypeptide 43 hs
HG-U133A_2:220004_AT DEAD (Asp-Glu-Ala-Asp) box polypeptide 43 hs
U133_X3P:G10346128_3P_AT DEAD (Asp-Glu-Ala-Asp) box polypeptide 43 hs
HG-U95E:73899_AT DEAD (Asp-Glu-Ala-Asp) box polypeptide 43 hs
MG-U74CV2:140645_AT similar to DEAD (Asp-Glu-Ala-Asp) box polypeptide 43 mm
MOE430B:1441045_AT similar to DEAD (Asp-Glu-Ala-Asp) box polypeptide 43 mm
MOUSE430_2:1441045_AT similar to DEAD (Asp-Glu-Ala-Asp) box polypeptide 43 mm
Gene Ontology
GO Biological Process (view graph)
ID Description Evidence Links
8152 metabolism inferred from electronic annotation QuickGO AmiGO
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
16491 oxidoreductase activity inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast CAA22456 Hypothetical protein Y54G11A.3 [Caenorhabditis elegans] ref|NP_496973.1| Y54G11A.3 [Caenorhabditis elegans] 0.0
blast CAE73250 Hypothetical protein CBG20666 [Caenorhabditis briggsae] 0.0
blast XP_394925 PREDICTED: similar to GA20653-PA [Apis mellifera] 1.0E-123
Protein Domains
Database ID Description E-Value
Pfam IPR001650 EMBL-EBI Helicase, C-terminal 5.0E-33
Pfam IPR001410 EMBL-EBI DEAD/DEAH box helicase 9.3E-72
Pfam IPR001650 EMBL-EBI Helicase, C-terminal 5.0E-33
Pfam IPR001410 EMBL-EBI DEAD/DEAH box helicase 1.4E-70
Pfam IPR001410 EMBL-EBI DEAD/DEAH box helicase 1.4E-23
Pfam IPR001650 EMBL-EBI Helicase, C-terminal 1.6E-15
Pfam IPR001650 EMBL-EBI Helicase, C-terminal 1.4E-10
Sequence
Target Sequence 
>C. ELEGANS:194007_AT
aaagtgtcacccaattcttcgaattcgtgccacacgacagccgattcctccgtgtctgcg
aaatcgtcaatttcttgacagcagctcacggtcaaaactacaaaatgatcatctttgtga
aatcaaaggtgatggcagatcatttatcgtcggatttctgcatgaaaggaatcaattcgc
aaggacttcacggtggaagatctcaatctgatcgcgaaatgtcgctgaatatgctgcgat
ctggagaagttcaaattctggttgccaccgatttggccagcagaggaatcgatgtgccgg
acattactcacgttctcaactacgatttcccaatggatatcgaggaatatgtgcatcgtg
tcggccgaaccggacgagctggccgcaagggagaagccatgagcttcctttggtggaatg
atcgctcaaacttcgagggattgatccagattttggaaaaatctgaacaagaggtgccgg
atcagctgagacgggacgccgagaaatatcgtctgaagtgtcaaagcggccgtgatggc

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
AAAGTGTCACCCAATTCTTCGAATT 376 121 929 Antisense
AATTCGTGCCACACGACAGCCGATT 530 177 950 Antisense
ACAGCAGCTCACGGTCAAAACTACA 134 109 1006 Antisense
TTCTGGTTGCCACCGATTTGGCCAG 406 691 1184 Antisense
GGAATCGATGTGCCGGACATTACTC 362 533 1213 Antisense
GACATTACTCACGTTCTCAACTACG 579 369 1228 Antisense
AATATGTGCATCGTGTCGGCCGAAC 129 171 1274 Antisense
CGGCCGAACCGGACGAGCTGGCCGC 626 241 1290 Antisense
AAGCCATGAGCTTCCTTTGGTGGAA 312 149 1322 Antisense
GGTGCCGGATCAGCTGAGACGGGAC 627 501 1401 Antisense
GAAGTGTCAAAGCGGCCGTGATGGC 525 321 1443 Antisense
Sequence Source Affymetrix Proprietary Database