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[174682_at] helicase

Description CEK024D6R_rc /REP_DB=TREMBL Accession /GB=D32982 /CHR=3 /FEA=Genomic Cluster /DEF=C.elegans cDNA clone yk24d6 : 3prime end, single read.
Cluster 6grp_highest_10_10 > 71      6grp_high1_10_10 > 28      4grp_highest_8_8 > 58      4grp_high_8_8 > 33      6grp_highest_nonorm > 60      6grp_total > 17      4grp_total > 47      6grp_highest_sub > De      6grp_high1_sub > De      6grp_total_sub > Decrease      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 258
1 2 3 4 range
A 293.6
(3)
P 		199.7
(-1.6)
P 		171.2
(-3)
P 		269.9
(1.8)
P 		122
B 295.8
(3)
P 		184.4
(-3)
P 		205.7
(-1.9)
P 		220.5
(-1.1)
P 		111
C 429.6
(3)
P 		314.5
(0)
P 		267.8
(-1.2)
P 		197.6
(-3)
P 		232
avr 339.7
(3) 		232.9
(-2.1) 		214.9
(-3) 		229.3
(-2.3) 		125

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 342
1 2 3 4 5 6 range
A 411.1
(3)
P 		381.6
(1.9)
P 		399.3
(2.6)
P 		250.5
(-3)
P 		376.5
(1.7)
P 		278.1
(-2)
P 		161
B 592.6
(3)
P 		328.9
(-1.7)
P 		322.3
(-1.8)
P 		256.8
(-3)
P 		275.4
(-2.7)
P 		389.2
(-0.6)
P 		336
C 536.8
(3)
P 		329.7
(-2)
P 		314.6
(-2.3)
P 		328.6
(-2)
P 		286.1
(-3)
P 		350.5
(-1.5)
P 		251
avr 513.5
(3) 		346.7
(-1.3) 		345.4
(-1.3) 		278.6
(-3) 		312.7
(-2.1) 		339.3
(-1.4) 		235
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 109
1 2 3 4 range
A 106.9
(3)
P 		43.3
(-2.7)
P 		44.8
(-2.5)
P 		39.5
(-3)
P 		67
B 94.3
(3)
P 		45.5
(-3)
P 		47.7
(-2.7)
P 		47
(-2.8)
P 		49
C 142.2
(3)
P 		90.4
(0.1)
P 		93.3
(0.3)
P 		33.3
(-3)
P 		109
avr 114.5
(3) 		59.7
(-1.4) 		61.9
(-1.2) 		39.9
(-3) 		75

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 143
1 2 3 4 5 6 range
A 75.8
(-2)
P 		135.7
(3)
P 		86.9
(-1.1)
P 		63.5
(-3)
P 		113.6
(1.2)
P 		67.7
(-2.7)
P 		72
B 206.2
(3)
P 		109.5
(-1.2)
P 		78.3
(-2.6)
P 		68
(-3)
P 		111.9
(-1.1)
P 		145.1
(0.3)
P 		138
C 199
(3)
P 		100.6
(-1.4)
P 		80.1
(-2.4)
P 		66.1
(-3)
P 		92.6
(-1.8)
P 		117.3
(-0.7)
P 		133
avr 160.3
(3) 		115.3
(0.1) 		81.8
(-2) 		65.9
(-3) 		106
(-0.5) 		110
(-0.2) 		94
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 174682_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.21092
Sequence Type Exemplar sequence
Representative Public ID CEK024D6R NCBI
Target Description CEK024D6R_rc /REP_DB=TREMBL Accession /GB=D32982 /CHR=3 /FEA=Genomic Cluster /DEF=C.elegans cDNA clone yk24d6 : 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_066900(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_066900 NCBI Caenorhabditis elegans M03C11.8 (helicase) mRNA, complete cds. 11/11 None
M03C11.8 ENSEMBL cdna:known chromosome:CEL140:III:10428238:10435865:-1 gene:M03C11.8 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
chrIII:10428243-10428574(-) 82.18 100.0
Public Domain and Genome References
Gene Title helicase
Ensembl M03C11.8
Entrez Gene 176462 Entrez gene
SwissProt O45609 EMBL-EBI
WormBase CE34059 Wormbase
Functional Annotations
Ortholog
ID Title Organism
ATGENOME1:17818_AT SNF2 domain-containing protein / helicase domain-containing protein at
ATH1-121501:266122_AT SNF2 domain-containing protein / helicase domain-containing protein at
CANINE:1606025_AT similar to SWI/SNF-related, matrix-associated actin-dependent regulator of chromatin, subfamily a, containing DEAD/H box 1 cfa
CANINE:1602463_AT similar to SWI/SNF-related, matrix-associated actin-dependent regulator of chromatin, subfamily a, containing DEAD/H box 1 cfa
CANINE_2:CFA.1741.1.S1_S_AT similar to SWI/SNF-related, matrix-associated actin-dependent regulator of chromatin, subfamily a, containing DEAD/H box 1 cfa
CANINE_2:CFA.9945.1.A1_AT similar to SWI/SNF-related, matrix-associated actin-dependent regulator of chromatin, subfamily a, containing DEAD/H box 1 cfa
CANINE_2:CFAAFFX.15733.1.S1_AT similar to SWI/SNF-related, matrix-associated actin-dependent regulator of chromatin, subfamily a, containing DEAD/H box 1 cfa
DROSOPHILA_2:1624673_AT dm
DROSGENOME1:151787_AT dm
CHICKEN:GGAAFFX.23225.1.S1_S_AT similar to hypothetical protein DKFZp762K2015 gga
HU35KSUBB:RC_W74507_AT SWI/SNF-related, matrix-associated actin-dependent regulator of chromatin, subfamily a, containing DEAD/H box 1 hs
HU35KSUBD:RC_R59694_S_AT SWI/SNF-related, matrix-associated actin-dependent regulator of chromatin, subfamily a, containing DEAD/H box 1 hs
HU35KSUBD:RC_AA446100_AT SWI/SNF-related, matrix-associated actin-dependent regulator of chromatin, subfamily a, containing DEAD/H box 1 hs
U133_X3P:HS.21356.0.S1_3P_A_AT SWI/SNF-related, matrix-associated actin-dependent regulator of chromatin, subfamily a, containing DEAD/H box 1 hs
HG-U133_PLUS_2:223197_S_AT SWI/SNF-related, matrix-associated actin-dependent regulator of chromatin, subfamily a, containing DEAD/H box 1 hs
HG-U133B:223197_S_AT SWI/SNF-related, matrix-associated actin-dependent regulator of chromatin, subfamily a, containing DEAD/H box 1 hs
HG-U95B:49457_AT SWI/SNF-related, matrix-associated actin-dependent regulator of chromatin, subfamily a, containing DEAD/H box 1 hs
HG-U95B:56209_AT SWI/SNF-related, matrix-associated actin-dependent regulator of chromatin, subfamily a, containing DEAD/H box 1 hs
HG-U95C:56522_R_AT SWI/SNF-related, matrix-associated actin-dependent regulator of chromatin, subfamily a, containing DEAD/H box 1 hs
HG-U95D:76202_AT SWI/SNF-related, matrix-associated actin-dependent regulator of chromatin, subfamily a, containing DEAD/H box 1 hs
HG-U95D:78837_R_AT SWI/SNF-related, matrix-associated actin-dependent regulator of chromatin, subfamily a, containing DEAD/H box 1 hs
MU11KSUBB:X69942_S_AT SWI/SNF-related, matrix-associated actin-dependent regulator of chromatin, subfamily a, containing DEAD/H box 1` mm
MG-U74AV2:98991_AT SWI/SNF-related, matrix-associated actin-dependent regulator of chromatin, subfamily a, containing DEAD/H box 1` mm
MG-U74AV2:161920_R_AT SWI/SNF-related, matrix-associated actin-dependent regulator of chromatin, subfamily a, containing DEAD/H box 1` mm
MOE430A:1435651_A_AT SWI/SNF-related, matrix-associated actin-dependent regulator of chromatin, subfamily a, containing DEAD/H box 1` mm
MOUSE430A_2:1435651_A_AT SWI/SNF-related, matrix-associated actin-dependent regulator of chromatin, subfamily a, containing DEAD/H box 1` mm
MOUSE430_2:1435651_A_AT SWI/SNF-related, matrix-associated actin-dependent regulator of chromatin, subfamily a, containing DEAD/H box 1` mm
MOE430A:1452276_AT SWI/SNF-related, matrix-associated actin-dependent regulator of chromatin, subfamily a, containing DEAD/H box 1` mm
MOUSE430A_2:1452276_AT SWI/SNF-related, matrix-associated actin-dependent regulator of chromatin, subfamily a, containing DEAD/H box 1` mm
MOUSE430_2:1452276_AT SWI/SNF-related, matrix-associated actin-dependent regulator of chromatin, subfamily a, containing DEAD/H box 1` mm
MG-U74CV2:165645_AT SWI/SNF-related, matrix-associated actin-dependent regulator of chromatin, subfamily a, containing DEAD/H box 1` mm
MU19KSUBC:TC38281_S_AT SWI/SNF-related, matrix-associated actin-dependent regulator of chromatin, subfamily a, containing DEAD/H box 1` mm
MOE430B:1440066_AT MRNA of enhancer-trap-locus 1 mm
MOUSE430_2:1440066_AT MRNA of enhancer-trap-locus 1 mm
MU19KSUBA:TC18070_S_AT MRNA of enhancer-trap-locus 1 mm
RAE230B:1384851_AT SWI/SNF-related, matrix-associated actin-dependent regulator of chromatin, subfamily a, containing DEAD/H box 1` (predicted) rn
RAT230_2:1384851_AT SWI/SNF-related, matrix-associated actin-dependent regulator of chromatin, subfamily a, containing DEAD/H box 1` (predicted) rn
RAE230A:1377012_AT SWI/SNF-related, matrix-associated actin-dependent regulator of chromatin, subfamily a, containing DEAD/H box 1` (predicted) rn
RAT230_2:1377012_AT SWI/SNF-related, matrix-associated actin-dependent regulator of chromatin, subfamily a, containing DEAD/H box 1` (predicted) rn
RAE230A:1390629_AT SWI/SNF-related, matrix-associated actin-dependent regulator of chromatin, subfamily a, containing DEAD/H box 1` (predicted) rn
RAT230_2:1390629_AT SWI/SNF-related, matrix-associated actin-dependent regulator of chromatin, subfamily a, containing DEAD/H box 1` (predicted) rn
RAE230B:1397253_AT SWI/SNF-related, matrix-associated actin-dependent regulator of chromatin, subfamily a, containing DEAD/H box 1` (predicted) rn
RAT230_2:1397253_AT SWI/SNF-related, matrix-associated actin-dependent regulator of chromatin, subfamily a, containing DEAD/H box 1` (predicted) rn
RG-U34C:RC_AI236127_AT SWI/SNF-related, matrix-associated actin-dependent regulator of chromatin, subfamily a, containing DEAD/H box 1` (predicted) rn
RG-U34B:RC_AA965085_AT SWI/SNF-related, matrix-associated actin-dependent regulator of chromatin, subfamily a, containing DEAD/H box 1` (predicted) rn
YEAST_2:1779662_AT Protein whose overexpression affects chromosome stability, potential Cdc28p substrate; homolog of Snf2p Sc
Gene Ontology
GO Molecular Function (view graph)
ID Description Evidence Links
3676 nucleic acid binding inferred from electronic annotation QuickGO AmiGO
3677 DNA binding inferred from electronic annotation QuickGO AmiGO
4386 helicase activity inferred from electronic annotation QuickGO AmiGO
5509 calcium ion binding 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 CAA88960 Hypothetical protein M03C11.8 [Caenorhabditis elegans] emb|CAA15960.2| Hypothetical protein M03C11.8 [Caenorhabditis elegans] ref|NP_499301.2| M03C11.8 [Caenorhabditis elegans] 0.0
blast CAE71470 Hypothetical protein CBG18388 [Caenorhabditis briggsae] 0.0
blast NP_001015697 MGC108253 protein [Xenopus tropicalis] gb|AAH89242.1| MGC108253 protein [Xenopus tropicalis] 1.0E-139
Protein Domains
Database ID Description E-Value
Pfam IPR000330 EMBL-EBI SNF2 related domain 1.9E-84
Pfam IPR001650 EMBL-EBI Helicase, C-terminal 4.5E-26
Sequence
Target Sequence 
>C. ELEGANS:174682_AT
ttcaattactagtgatctccatccatcatcccatctgcaaaacactttaaacgttggttc
tcaattgtttcttttttcaaaatttcaatttttatatatttattttcatccatatatatt
tttttctgtaattcctacatttcaaaaaaaatctcatcatttttatcccaaaatattctt
tgtaaaacaattgttttctgtccagtattgcatattccgtttttttttgtgaaaaattat
tggcaccttaat

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
TTCAATTACTAGTGATCTCCATCCA 45 685 47 Antisense
TTACTAGTGATCTCCATCCATCATC 494 681 52 Antisense
ATCATCCCATCTGCAAAACACTTTA 682 29 71 Antisense
CCCATCTGCAAAACACTTTAAACGT 503 257 76 Antisense
TAAACGTTGGTTCTCAATTGTTTCT 615 135 94 Antisense
TTTTTCTGTAATTCCTACATTTCAA 390 675 167 Antisense
TCTCATCATTTTTATCCCAAAATAT 390 613 198 Antisense
AAACAATTGTTTTCTGTCCAGTATT 162 129 231 Antisense
TTCTGTCCAGTATTGCATATTCCGT 155 693 242 Antisense
CAGTATTGCATATTCCGTTTTTTTT 703 205 249 Antisense
TGTGAAAAATTATTGGCACCTTAAT 549 555 274 Antisense
Sequence Source Affymetrix Proprietary Database