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[192895_s_at] Helicases conserved C-terminal domain

Description Y54E2A.6 /REP_DB=WormBase Gene ID /WP=CE20305 /TR=Q9XWI5 /GB=CAA21682.1 /SUBMIT=HINXTON /CHR=2 /FEA=Sanger Annotation /DEF=Helicases conserved C-terminal domain
Cluster 6grp_high1_10_10 > 28      4grp_high_8_8 > 48      6grp_total > 27      4grp_total > 54      6grp_high1_sub > De      6grp_total_sub > Decrease      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 190
1 2 3 4 range
A 230.2
(3)
P 		135.4
(-1.2)
P 		116.1
(-2.1)
P 		96.2
(-3)
P 		134
B 173.2
(3)
P 		113.1
(-2)
P 		156.4
(1.6)
P 		100.8
(-3)
P 		72
C 244.5
(3)
P 		117.3
(-1)
P 		154.9
(0.2)
P 		54.2
(-3)
A 		190
avr 216
(3) 		121.9
(-1.3) 		142.5
(-0.3) 		83.7
(-3) 		132

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 172
1 2 3 4 5 6 range
A 101.4
(-0.3)
A 		123.8
(1.4)
P 		98.7
(-0.5)
P 		81.3
(-1.7)
M 		63.6
(-3)
A 		146.3
(3)
P 		83
B 168.7
(3)
P 		148.7
(1.3)
P 		119.5
(-1.1)
P 		106.4
(-2.2)
P 		97.4
(-3)
P 		125.3
(-0.7)
P 		71
C 230.7
(3)
P 		89.6
(-1.9)
P 		101.4
(-1.5)
P 		58.5
(-3)
A 		100.4
(-1.5)
P 		81.2
(-2.2)
P 		172
avr 166.9
(3) 		120.7
(-0.3) 		106.5
(-1.3) 		82.1
(-3) 		87.1
(-2.6) 		117.6
(-0.5) 		85
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 75
1 2 3 4 range
A 83.8
(3)
P 		29.4
(-1.7)
P 		30.4
(-1.6)
P 		14.1
(-3)
P 		70
B 55.2
(3)
P 		27.9
(-1.9)
P 		36.2
(-0.4)
P 		21.5
(-3)
P 		34
C 80.9
(3)
P 		33.7
(-0.9)
P 		54
(0.8)
P 		9.1
(-3)
A 		72
avr 73.3
(3) 		30.3
(-1.4) 		40.2
(-0.4) 		14.9
(-3) 		58

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 74
1 2 3 4 5 6 range
A 18.7
(-3)
A 		44
(3)
P 		21.5
(-2.3)
P 		20.6
(-2.5)
M 		19.2
(-2.9)
A 		35.6
(1)
P 		25
B 58.7
(3)
P 		49.5
(1.2)
P 		29
(-2.8)
P 		28.2
(-3)
P 		39.6
(-0.8)
P 		46.7
(0.6)
P 		31
C 85.5
(3)
P 		27.3
(-1.7)
P 		25.8
(-1.9)
P 		11.8
(-3)
A 		32.5
(-1.3)
P 		27.2
(-1.7)
P 		74
avr 54.3
(3) 		40.3
(0.5) 		25.4
(-2.1) 		20.2
(-3) 		30.4
(-1.2) 		36.5
(-0.1) 		34
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 192895_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.3354
Sequence Type Exemplar sequence
Representative Public ID Y54E2A.6 NCBI
Target Description Y54E2A.6 /REP_DB=WormBase Gene ID /WP=CE20305 /TR=Q9XWI5 /GB=CAA21682.1 /SUBMIT=HINXTON /CHR=2 /FEA=Sanger Annotation /DEF=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_064661(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_064661 NCBI Caenorhabditis elegans Y54E2A.6 (Y54E2A.6) mRNA, complete cds. 11/11 None
SNAP00000025433 ENSEMBL cdna:SNAP chromosome:CEL140:II:14773309:14777627:1 11/11 None
GENEFINDER00000025441 ENSEMBL cdna:GeneFinder chromosome:CEL140:II:14773654:14777627:1 11/11 None
Y54E2A.6 ENSEMBL cdna:known chromosome:CEL140:II:14758009:14778027:1 gene:Y54E2A.6 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:14758005-14777624(+) 100.0 100.0
Public Domain and Genome References
Gene Title Helicases conserved C-terminal domain
Ensembl Y54E2A.6
Entrez Gene 175136 Entrez gene
SwissProt Q9XWI5 EMBL-EBI
WormBase CE20305 Wormbase
Functional Annotations
Ortholog
ID Title Organism
ATH1-121501:247564_AT DEAD box RNA helicase, putative at
CANINE:1604586_AT similar to Activating signal cointegrator 1 complex subunit 3 (ASC-1 complex subunit p200) (Trip4 complex subunit p200) (Helicase, ATP binding 1) cfa
CANINE_2:CFA.2025.1.A1_AT similar to Activating signal cointegrator 1 complex subunit 3 (ASC-1 complex subunit p200) (Trip4 complex subunit p200) (Helicase, ATP binding 1) cfa
CANINE_2:CFA.20474.1.S1_AT similar to Activating signal cointegrator 1 complex subunit 3 (ASC-1 complex subunit p200) (Trip4 complex subunit p200) (Helicase, ATP binding 1) cfa
CANINE_2:CFAAFFX.6265.1.S1_AT similar to Activating signal cointegrator 1 complex subunit 3 (ASC-1 complex subunit p200) (Trip4 complex subunit p200) (Helicase, ATP binding 1) cfa
CANINE_2:CFAAFFX.6271.1.S1_AT similar to Activating signal cointegrator 1 complex subunit 3 (ASC-1 complex subunit p200) (Trip4 complex subunit p200) (Helicase, ATP binding 1) cfa
CANINE_2:CFAAFFX.6271.1.S1_S_AT similar to Activating signal cointegrator 1 complex subunit 3 (ASC-1 complex subunit p200) (Trip4 complex subunit p200) (Helicase, ATP binding 1) cfa
CANINE_2:CFAAFFX.6273.1.S1_S_AT similar to Activating signal cointegrator 1 complex subunit 3 (ASC-1 complex subunit p200) (Trip4 complex subunit p200) (Helicase, ATP binding 1) cfa
DROSOPHILA_2:1641576_A_AT dm
DROSOPHILA_2:1628807_AT dm
DROSGENOME1:152730_AT dm
CHICKEN:GGA.13012.1.S1_S_AT similar to helicase, ATP binding 1; RNA helicase family; ASC-1 complex subunit P200; B630009I04Rik gga
CHICKEN:GGAAFFX.24685.1.S1_AT similar to helicase, ATP binding 1; RNA helicase family; ASC-1 complex subunit P200; B630009I04Rik gga
CHICKEN:GGAAFFX.24685.1.S1_S_AT similar to helicase, ATP binding 1; RNA helicase family; ASC-1 complex subunit P200; B630009I04Rik gga
CHICKEN:GGAAFFX.9843.1.S1_S_AT similar to helicase, ATP binding 1; RNA helicase family; ASC-1 complex subunit P200; B630009I04Rik gga
HU35KSUBC:RC_AA405505_AT activating signal cointegrator 1 complex subunit 3 hs
U133_X3P:HS.48295.0.S1_3P_AT activating signal cointegrator 1 complex subunit 3 hs
U133_X3P:HS.143917.0.S2_3P_AT activating signal cointegrator 1 complex subunit 3 hs
HG-U133A_2:212815_AT activating signal cointegrator 1 complex subunit 3 hs
HG-U133_PLUS_2:212815_AT activating signal cointegrator 1 complex subunit 3 hs
HG-U133A:212815_AT activating signal cointegrator 1 complex subunit 3 hs
HG-U133_PLUS_2:231269_AT activating signal cointegrator 1 complex subunit 3 hs
HG-U133B:231269_AT activating signal cointegrator 1 complex subunit 3 hs
HG-U95AV2:36045_AT activating signal cointegrator 1 complex subunit 3 hs
HG-U95E:75511_AT activating signal cointegrator 1 complex subunit 3 hs
HG-U95C:64524_I_AT Activating signal cointegrator 1 complex subunit 3 hs
HG-U95D:72053_AT Activating signal cointegrator 1 complex subunit 3 hs
HG-U95E:72634_R_AT Activating signal cointegrator 1 complex subunit 3 hs
HG-U95D:89160_AT Activating signal cointegrator 1 complex subunit 3 hs
HU35KSUBB:RC_AA232372_AT Activating signal cointegrator 1 complex subunit 3 hs
HU35KSUBB:RC_R49099_AT Activating signal cointegrator 1 complex subunit 3 hs
MOUSE430_2:1457069_AT activating signal cointegrator 1 complex subunit 3 mm
MOE430B:1457069_AT activating signal cointegrator 1 complex subunit 3 mm
MOE430B:1457900_AT activating signal cointegrator 1 complex subunit 3 mm
MOUSE430_2:1457900_AT activating signal cointegrator 1 complex subunit 3 mm
MG-U74BV2:116037_AT activating signal cointegrator 1 complex subunit 3 mm
MG-U74CV2:133355_R_AT Activating signal cointegrator 1 complex subunit 3, mRNA (cDNA clone IMAGE:5321369) mm
MOE430B:1443370_AT Activating signal cointegrator 1 complex subunit 3, mRNA (cDNA clone IMAGE:5321369) mm
MOUSE430_2:1443370_AT Activating signal cointegrator 1 complex subunit 3, mRNA (cDNA clone IMAGE:5321369) mm
MOUSE430_2:1459239_AT Activating signal cointegrator 1 complex subunit 3, mRNA (cDNA clone IMAGE:5321369) mm
MOE430B:1459239_AT Activating signal cointegrator 1 complex subunit 3, mRNA (cDNA clone IMAGE:5321369) mm
MU19KSUBC:TC38732_AT Activating signal cointegrator 1 complex subunit 3, mRNA (cDNA clone IMAGE:5321369) mm
RAE230B:1395981_AT helicase, ATP binding 1 (predicted) rn
RAT230_2:1395981_AT helicase, ATP binding 1 (predicted) rn
RAE230B:1377755_AT helicase, ATP binding 1 (predicted) rn
RAT230_2:1377755_AT helicase, ATP binding 1 (predicted) rn
RG-U34C:RC_AI179403_AT Helicase, ATP binding 1 (predicted) rn
YEAST_2:1773984_AT Putative RNA helicase related to Ski2p, involved in translation inhibition of non-poly(A) mRNAs; required for repressing propagation of dsRNA viruses Sc
Gene Ontology
GO Biological Process (view graph)
ID Description Evidence Links
9307 DNA restriction-modification system inferred from electronic annotation QuickGO AmiGO
GO Cellular Component (view graph)
ID Description Evidence Links
5634 nucleus inferred from electronic annotation QuickGO AmiGO
GO Molecular Function (view graph)
ID Description Evidence Links
166 nucleotide binding inferred from electronic annotation QuickGO AmiGO
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
15668 type III site-specific deoxyribonuclease activity inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast CAA21682 Hypothetical protein Y54E2A.6 [Caenorhabditis elegans] ref|NP_497062.1| Y54E2A.6 [Caenorhabditis elegans] 0.0
blast CAE60612 Hypothetical protein CBG04253 [Caenorhabditis briggsae] 0.0
blast CAI19454 RP1-121G13.4 [Homo sapiens] emb|CAH73862.1| RP1-121G13.4 [Homo sapiens] emb|CAI16190.1| RP1-121G13.4 [Homo sapiens] emb|CAI19627.1| RP1-121G13.4 [Homo sapiens] emb|CAI21439.1| RP1-121G13.4 [Homo sapiens] 0.0
Protein Domains
Database ID Description E-Value
Pfam IPR001650 EMBL-EBI Helicase, C-terminal 1.9E-11
Pfam IPR001410 EMBL-EBI DEAD/DEAH box helicase 6.3E-48
Pfam IPR001410 EMBL-EBI DEAD/DEAH box helicase 1.8E-42
Pfam IPR004179 EMBL-EBI Sec63 domain 1.0E-126
Pfam IPR004179 EMBL-EBI Sec63 domain 1.0E-126
Pfam IPR004179 EMBL-EBI Sec63 domain 1.0E-126
Pfam IPR004179 EMBL-EBI Sec63 domain 1.0E-126
Sequence
Target Sequence 
>C. ELEGANS:192895_S_AT
gaggatgctcgttcaatcggcgatggaatgacaattccacagcttcaaaaccatctggaa
atcgagaaatccacgtcattagacgacgcgaaacttgctcgacgagcccagaaactcttc
agagagtgcaccaagttagatgaagctcaaagccgggaagtgctgaaagctctgtgcaat
tggccaattatcaacatgaaaatcatgcaattagtggattcccgcggtaattgtgtagat
attgatgagacgaagaaaccggtgaaagtgacggctggcgaggtgtacaaattgagaatt
gtcatggaacgagtcggaccgggaaagaacaactcatcaatgcatcttccacaatggcca
aaaccaaaacaggctggatggataattgttgtgggaaacgtgtcggccgacatgattctt
aacacgactaccgtaaccggctcacattcgactcggtcgaccgccaaattggatattcgt
gcgccggcgacgaaaggaaaccacgagctcgccgtcctaattctcagcgattgc

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GAGGATGCTCGTTCAATCGGCGATG 709 403 4828 Antisense
AGACGACGCGAAACTTGCTCGACGA 44 71 4908 Antisense
CTCGACGAGCCCAGAAACTCTTCAG 529 231 4925 Antisense
GAAAGCTCTGTGCAATTGGCCAATT 703 359 4992 Antisense
GGATTCCCGCGGTAATTGTGTAGAT 109 509 5043 Antisense
GTGACGGCTGGCGAGGTGTACAAAT 147 483 5095 Antisense
AACTCATCAATGCATCTTCCACAAT 371 141 5158 Antisense
GTCGGCCGACATGATTCTTAACACG 59 473 5229 Antisense
TAACACGACTACCGTAACCGGCTCA 703 633 5247 Antisense
GCCAAATTGGATATTCGTGCGCCGG 177 279 5290 Antisense
CGCCGTCCTAATTCTCAGCGATTGC 262 257 5337 Antisense
Sequence Source Affymetrix Proprietary Database