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[193491_at] SNF2 and others N-terminal domain

Description W06D4.6 /REP_DB=WormBase Gene ID /WP=CE25143 /GEN=rad-54 /TR=Q9XW40 /GB=CAB63308.1 /SUBMIT=HINXTON /CHR=1 /FEA=Sanger Annotation /DEF=SNF2 and others N-terminal domain
Cluster 6grp_highest_10_10 > 86      6grp_high1_10_10 > 76      4grp_highest_8_8 > 12      4grp_high_8_8 > 31      6grp_highest_nonorm > 90      6grp_total > 78      4grp_total > 32      6grp_highest_sub > Da      6grp_cgc > 48      6grp_high1_sub > Da      6grp_cgc_sub > Da      6grp_total_sub > Increase      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 100
1 2 3 4 range
A 105.6
(-1.2)
P 		85.1
(-3)
P 		144.9
(2.3)
P 		152.4
(3)
P 		67
B 117.4
(-0.1)
P 		168.2
(3)
P 		112.2
(-0.4)
P 		68.7
(-3)
P 		100
C 98.6
(-3)
P 		100.6
(-2.8)
P 		109.3
(-1.8)
P 		154
(3)
P 		55
avr 107.2
(-3) 		118
(0.6) 		122.1
(2) 		125
(3) 		18

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 122
1 2 3 4 5 6 range
A 147.8
(-0.4)
P 		114.8
(-2.7)
P 		117.1
(-2.5)
P 		110.2
(-3)
P 		135
(-1.3)
P 		196.1
(3)
P 		86
B 93.7
(-3)
P 		129.8
(-0.7)
P 		112
(-1.8)
P 		105.1
(-2.3)
P 		147.7
(0.4)
P 		189
(3)
P 		95
C 81.6
(-2.6)
P 		164
(2.3)
P 		121.2
(-0.2)
P 		74.5
(-3)
P 		98.7
(-1.6)
P 		176.3
(3)
P 		102
avr 107.7
(-2.3) 		136.2
(-0.4) 		116.8
(-1.7) 		96.6
(-3) 		127.1
(-1) 		187.1
(3) 		91
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 27
1 2 3 4 range
A 38.4
(3)
P 		18.5
(-3)
P 		37.9
(2.8)
P 		22.3
(-1.9)
P 		20
B 37.4
(2.1)
P 		41.5
(3)
P 		26
(-0.5)
P 		14.6
(-3)
P 		27
C 32.7
(0.3)
P 		28.9
(-1.6)
P 		38.1
(3)
P 		26
(-3)
P 		12
avr 36.2
(3) 		29.6
(0.4) 		34
(2.1) 		21
(-3) 		15

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 56
1 2 3 4 5 6 range
A 27.2
(-2.5)
P 		40.8
(1.1)
P 		25.5
(-3)
P 		28
(-2.3)
P 		40.7
(1.1)
P 		47.7
(3)
P 		22
B 32.6
(-2.3)
P 		43.2
(-0.8)
P 		27.2
(-3)
P 		27.8
(-2.9)
P 		60
(1.5)
P 		70.5
(3)
P 		43
C 30.3
(-0.9)
P 		50
(1.8)
P 		30.8
(-0.8)
P 		15
(-3)
P 		31.9
(-0.7)
P 		59
(3)
P 		44
avr 30
(-1.9) 		44.7
(0.6) 		27.8
(-2.3) 		23.6
(-3) 		44.2
(0.5) 		59.1
(3) 		36
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 193491_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.674
Sequence Type Exemplar sequence
Representative Public ID W06D4.6 NCBI
Target Description W06D4.6 /REP_DB=WormBase Gene ID /WP=CE25143 /GEN=rad-54 /TR=Q9XW40 /GB=CAB63308.1 /SUBMIT=HINXTON /CHR=1 /FEA=Sanger Annotation /DEF=SNF2 and others N-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_060037(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_060037 NCBI Caenorhabditis elegans RADiation sensitivity abnormal/yeast RAD-related family member (rad-54) (rad-54) mRNA, complete cds. 11/11 None
SNAP00000013469 ENSEMBL cdna:SNAP chromosome:CEL140:I:9076032:9078181:1 11/11 None
GENEFINDER00000013472 ENSEMBL cdna:GeneFinder chromosome:CEL140:I:9076097:9078181:1 11/11 None
W06D4.6 ENSEMBL cdna:known chromosome:CEL140:I:9073211:9078371:1 gene:W06D4.6 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
chrI:9073141-9078112(+) 100.0 100.0
Public Domain and Genome References
Gene Title SNF2 and others N-terminal domain
Gene Symbol rad-54
Ensembl W06D4.6
Entrez Gene 172728 Entrez gene
SwissProt Q9XW40 EMBL-EBI
WormBase CE25143 Wormbase
Functional Annotations
Ortholog
ID Title Organism
ATH1-121501:257027_AT DNA repair protein RAD54, putative at
CANINE:1606076_AT similar to DNA repair and recombination protein RAD54-like (RAD54 homolog) (hRAD54) (hHR54) cfa
CANINE_2:CFAAFFX.7339.1.S1_AT similar to DNA repair and recombination protein RAD54-like (RAD54 homolog) (hRAD54) (hHR54) cfa
DROSOPHILA_2:1628198_AT okra dm
DROSGENOME1:154714_AT okra dm
HG-U133A_2:204558_AT RAD54-like (S. cerevisiae) hs
HG-U133_PLUS_2:204558_AT RAD54-like (S. cerevisiae) hs
HG-FOCUS:204558_AT RAD54-like (S. cerevisiae) hs
HG-U133A:204558_AT RAD54-like (S. cerevisiae) hs
HG-U95AV2:966_AT RAD54-like (S. cerevisiae) hs
HC-G110:966_AT RAD54-like (S. cerevisiae) hs
HG-U95AV2:967_G_AT RAD54-like (S. cerevisiae) hs
HC-G110:967_G_AT RAD54-like (S. cerevisiae) hs
HU35KSUBB:RC_AA227900_S_AT RAD54-like (S. cerevisiae) hs
HUGENEFL:X97795_AT RAD54-like (S. cerevisiae) hs
U133_X3P:G4506396_3P_AT RAD54-like (S. cerevisiae) hs
HG-U95B:42148_AT RAD54-like (S. cerevisiae) hs
HU35KSUBD:RC_AA416874_AT RAD54-like (S. cerevisiae) hs
MOE430B:1453926_AT RAD54 like (S. cerevisiae) mm
MOUSE430_2:1453926_AT RAD54 like (S. cerevisiae) mm
MU11KSUBB:X97796_S_AT RAD54 like (S. cerevisiae) mm
MG-U74AV2:98971_AT RAD54 like (S. cerevisiae) mm
MOE430A:1423124_X_AT RAD54 like (S. cerevisiae) mm
MOUSE430A_2:1423124_X_AT RAD54 like (S. cerevisiae) mm
MOUSE430_2:1423124_X_AT RAD54 like (S. cerevisiae) mm
MOE430A:1423123_AT RAD54 like (S. cerevisiae) mm
MOUSE430A_2:1423123_AT RAD54 like (S. cerevisiae) mm
MOUSE430_2:1423123_AT RAD54 like (S. cerevisiae) mm
MOE430A:1450862_AT RAD54 like (S. cerevisiae) mm
MOUSE430A_2:1450862_AT RAD54 like (S. cerevisiae) mm
MOUSE430_2:1450862_AT RAD54 like (S. cerevisiae) mm
MOE430B:1459446_AT RAD54 like (S. cerevisiae), mRNA (cDNA clone MGC:13963 IMAGE:3987790) mm
MOUSE430_2:1459446_AT RAD54 like (S. cerevisiae), mRNA (cDNA clone MGC:13963 IMAGE:3987790) mm
RAE230B:1393655_AT RAD54 like (S. cerevisiae) (predicted) rn
RAT230_2:1393655_AT RAD54 like (S. cerevisiae) (predicted) rn
YEAST_2:1773281_AT DNA-dependent ATPase, stimulates strand exchange by modifying the topology of double-stranded DNA; involved in the recombinational repair of double-strand breaks in DNA during vegetative growth and meiosis; member of the SWI/SNF family 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
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 CAB63308 Hypothetical protein W06D4.6 [Caenorhabditis elegans] emb|CAA22254.2| Hypothetical protein W06D4.6 [Caenorhabditis elegans] ref|NP_492438.1| RADiation sensitivity abnormal/yeast RAD-related family member (rad-54) [Caenorhabditis elegans] 0.0
blast CAE67033 Hypothetical protein CBG12435 [Caenorhabditis briggsae] 0.0
blast AAH67986 RAD54-like [Xenopus tropicalis] ref|NP_001001241.1| RAD54-like [Xenopus tropicalis] 0.0
blast CAB63308 Hypothetical protein W06D4.6 [Caenorhabditis elegans] emb|CAA22254.2| Hypothetical protein W06D4.6 [Caenorhabditis elegans] ref|NP_492438.1| RADiation sensitivity abnormal/yeast RAD-related family member (rad-54) [Caenorhabditis elegans] 1.0E-157
blast CAE67033 Hypothetical protein CBG12435 [Caenorhabditis briggsae] 1.0E-149
blast CAB63308 Hypothetical protein W06D4.6 [Caenorhabditis elegans] emb|CAA22254.2| Hypothetical protein W06D4.6 [Caenorhabditis elegans] ref|NP_492438.1| RADiation sensitivity abnormal/yeast RAD-related family member (rad-54) [Caenorhabditis elegans] 1.0E-144
blast CAE67033 Hypothetical protein CBG12435 [Caenorhabditis briggsae] 1.0E-136
Protein Domains
Database ID Description E-Value
Pfam IPR000330 EMBL-EBI SNF2 related domain 1.2E-104
Pfam IPR001650 EMBL-EBI Helicase, C-terminal 7.0E-26
Pfam IPR001650 EMBL-EBI Helicase, C-terminal 7.0E-26
Pfam IPR001650 EMBL-EBI Helicase, C-terminal 7.0E-26
Sequence
Target Sequence 
>C. ELEGANS:193491_AT
tcaatgatccagccagcactatcttctgtttccttctttcttcgaaagctggtggatgtg
gtctaaatcttattggagccaatcgattagttatgtttgatccggattggaatccagcga
atgacgatcaagcaatggcgagagtttggagagatggacagaagaaaatgtgtttcatct
atagacttttagcaactggatcaattgaagagaaaatgtttcaacgtcagacacataaaa
aagcattgtcatcgtgtgtggttgatgcgggtgaagacgtagctcgtcattttagttccg
agcaacttcgagaactcttcaagttggaatcaacagtggcatcggatacacatgaaaaat
taaaatgtaaaagatgtattcaaggagttgaaagtgttgatccaccaaccaatgcggact
gtgcaagtgatttatcgaattggtttcattctcagaaatcagctagaaaagtggctgata
atgtgctccgagccgtcttcgaatgtggatcgatctcctttgtttttcatca

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
TCAATGATCCAGCCAGCACTATCTT 555 631 1841 Antisense
CTGTTTCCTTCTTTCTTCGAAAGCT 580 237 1866 Antisense
GGAATCCAGCGAATGACGATCAAGC 109 533 1949 Antisense
AAAGCATTGTCATCGTGTGTGGTTG 163 125 2080 Antisense
GATGCGGGTGAAGACGTAGCTCGTC 196 415 2104 Antisense
GACGTAGCTCGTCATTTTAGTTCCG 118 379 2116 Antisense
GAGCAACTTCGAGAACTCTTCAAGT 102 391 2140 Antisense
GTGTTGATCCACCAACCAATGCGGA 679 481 2234 Antisense
TGATAATGTGCTCCGAGCCGTCTTC 399 565 2316 Antisense
CCGAGCCGTCTTCGAATGTGGATCG 517 263 2328 Antisense
GATCGATCTCCTTTGTTTTTCATCA 12 419 2348 Antisense
Sequence Source Affymetrix Proprietary Database