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[189004_at] DNA helicase

Description F26F12.7 /REP_DB=WormBase Gene ID /WP=CE17716 /TR=Q19815 /GB=AAC25894.1 /SUBMIT=ST.LOUIS /CHR=5 /FEA=Sanger Annotation /DEF=DNA helicase
Cluster 6grp_highest_10_10 > 63      6grp_high1_10_10 > 46      4grp_highest_8_8 > 41      4grp_high_8_8 > 42      6grp_highest_nonorm > 77      6grp_total > 36      4grp_total > 53      6grp_highest_sub > Cu      6grp_cgc > 25      6grp_high1_sub > Cu      6grp_total_sub > Cup      4grp_rule_based > L1      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 984
1 2 3 4 range
A 1365.1
(3)
P 		1064.1
(0.3)
P 		909
(-1.1)
P 		696.6
(-3)
P 		669
B 1352.7
(3)
P 		1102
(0.7)
P 		996.1
(-0.2)
P 		685.2
(-3)
P 		668
C 1463.8
(3)
P 		1075.8
(0.6)
P 		1047.3
(0.5)
P 		480.1
(-3)
P 		984
avr 1393.9
(3) 		1080.6
(0.6) 		984.1
(-0.2) 		620.6
(-3) 		773

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 1056
1 2 3 4 5 6 range
A 1460.3
(2.2)
P 		1509.4
(2.7)
P 		1169.7
(-0.6)
P 		930
(-3)
P 		962.2
(-2.7)
P 		1540.5
(3)
P 		611
B 1765.3
(3)
P 		1379.6
(0.8)
P 		1187.1
(-0.3)
P 		1411.3
(1)
P 		709.5
(-3)
P 		1252.2
(0.1)
P 		1056
C 1465.9
(3)
P 		1445.2
(2.8)
P 		1295.4
(1.5)
P 		1214.7
(0.8)
P 		771
(-3)
P 		1325.8
(1.8)
P 		695
avr 1563.8
(3) 		1444.7
(2) 		1217.4
(0.2) 		1185.3
(-0) 		814.2
(-3) 		1372.8
(1.5) 		750
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 416
1 2 3 4 range
A 497
(3)
P 		231
(-1)
P 		237.6
(-0.9)
P 		102
(-3)
P 		395
B 431.4
(3)
P 		272.2
(-0.3)
P 		230.8
(-1.2)
P 		146
(-3)
P 		285
C 484.6
(3)
P 		309.3
(0.4)
P 		365
(1.2)
P 		81
(-3)
P 		404
avr 471
(3) 		270.8
(-0.3) 		277.8
(-0.2) 		109.7
(-3) 		361

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 378
1 2 3 4 5 6 range
A 269.2
(-2.3)
P 		536.8
(3)
P 		254.7
(-2.6)
P 		235.9
(-3)
P 		290.4
(-1.9)
P 		375.1
(-0.2)
P 		301
B 614.2
(3)
P 		459.2
(0.1)
P 		288.3
(-3)
P 		373.8
(-1.4)
P 		288.3
(-3)
P 		466.9
(0.3)
P 		326
C 543.4
(3)
P 		441
(0.9)
P 		329.7
(-1.3)
P 		244.3
(-3)
P 		249.5
(-2.9)
P 		443.8
(1)
P 		299
avr 475.6
(2.9) 		479
(3) 		290.9
(-2.6) 		284.7
(-2.7) 		276.1
(-3) 		428.6
(1.5) 		203
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 189004_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.11746
Sequence Type Exemplar sequence
Representative Public ID F26F12.7 NCBI
Target Description F26F12.7 /REP_DB=WormBase Gene ID /WP=CE17716 /TR=Q19815 /GB=AAC25894.1 /SUBMIT=ST.LOUIS /CHR=5 /FEA=Sanger Annotation /DEF=DNA helicase
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_072122(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_072122 NCBI Caenorhabditis elegans LEThal family member (let-418) (let-418) mRNA, complete cds. 11/11 None
SNAP00000007005 ENSEMBL cdna:SNAP chromosome:CEL140:V:5829427:5835288:1 11/11 None
GENEFINDER00000007012 ENSEMBL cdna:GeneFinder chromosome:CEL140:V:5829455:5835288:1 11/11 None
F26F12.7 ENSEMBL cdna:known chromosome:CEL140:V:5829427:5835455:1 gene:F26F12.7 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
chrV:5829454-5835288(+) 98.91 100.0
Public Domain and Genome References
Gene Title DNA helicase
Gene Symbol let-418
Ensembl F26F12.7
Entrez Gene 178970 Entrez gene
SwissProt Q19815 EMBL-EBI
WormBase CE17716 Wormbase
Functional Annotations
Ortholog
ID Title Organism
ATGENOME1:16394_AT chromatin remodeling factor CHD3 (PICKLE) at
ATH1-121501:264384_AT chromatin remodeling factor CHD3 (PICKLE) at
CANINE:1583997_X_AT similar to chromodomain helicase DNA binding protein 4 cfa
CANINE:1583996_S_AT similar to chromodomain helicase DNA binding protein 4 cfa
CANINE:1605027_AT similar to chromodomain helicase DNA binding protein 4 cfa
CANINE:1588724_AT similar to chromodomain helicase DNA binding protein 4 cfa
CANINE:1585917_AT similar to chromodomain helicase DNA binding protein 4 cfa
CANINE_2:CFA.16737.1.S1_AT similar to chromodomain helicase DNA binding protein 4 cfa
CANINE_2:CFA.19479.1.S1_S_AT similar to chromodomain helicase DNA binding protein 4 cfa
CANINE_2:CFA.7305.1.A1_S_AT similar to chromodomain helicase DNA binding protein 4 cfa
CANINE_2:CFAAFFX.23023.1.S1_S_AT similar to chromodomain helicase DNA binding protein 4 cfa
CANINE_2:CFAAFFX.23079.1.S1_S_AT similar to chromodomain helicase DNA binding protein 4 cfa
DROSOPHILA_2:1640441_AT armadillo promoter construct of Kehle dm
DROSGENOME1:143982_AT armadillo promoter construct of Kehle dm
CHICKEN:GGAAFFX.9174.1.S1_AT similar to Chromodomain helicase DNA binding protein 4 gga
CHICKEN:GGAAFFX.9174.2.S1_S_AT similar to Chromodomain helicase DNA binding protein 4 gga
HG-U133A:201184_S_AT chromodomain helicase DNA binding protein 4 hs
HG-U133A_2:201184_S_AT chromodomain helicase DNA binding protein 4 hs
HG-U133_PLUS_2:201184_S_AT chromodomain helicase DNA binding protein 4 hs
HUGENEFL:X86691_AT chromodomain helicase DNA binding protein 4 hs
U133_X3P:G4557452_3P_A_AT chromodomain helicase DNA binding protein 4 hs
U133_X3P:HS.74441.0.S2_3P_A_AT chromodomain helicase DNA binding protein 4 hs
U133_X3P:HS.74441.0.S1_3P_A_AT chromodomain helicase DNA binding protein 4 hs
HG-U133A_2:201182_S_AT chromodomain helicase DNA binding protein 4 hs
HG-U133_PLUS_2:201182_S_AT chromodomain helicase DNA binding protein 4 hs
HG-U133A:201182_S_AT chromodomain helicase DNA binding protein 4 hs
HG-U133A_2:201183_S_AT chromodomain helicase DNA binding protein 4 hs
HG-FOCUS:201183_S_AT chromodomain helicase DNA binding protein 4 hs
HG-U133_PLUS_2:201183_S_AT chromodomain helicase DNA binding protein 4 hs
HG-U133A:201183_S_AT chromodomain helicase DNA binding protein 4 hs
HG-U95AV2:36137_AT chromodomain helicase DNA binding protein 4 hs
U133_X3P:HS2.369370.1.A1_3P_X_AT Chromodomain helicase DNA binding protein 4 hs
U133_X3P:HS2.369370.1.A1_3P_AT Chromodomain helicase DNA binding protein 4 hs
HG-U133_PLUS_2:1560419_AT Chromodomain helicase DNA binding protein 4 hs
HG-U95D:68965_AT Chromodomain helicase DNA binding protein 4 hs
HG-U95D:84279_AT Chromodomain helicase DNA binding protein 4 hs
MG-U74AV2:99120_F_AT chromodomain helicase DNA binding protein 4 mm
MOE430A:1438476_A_AT chromodomain helicase DNA binding protein 4 mm
MOUSE430A_2:1438476_A_AT chromodomain helicase DNA binding protein 4 mm
MOUSE430_2:1438476_A_AT chromodomain helicase DNA binding protein 4 mm
MU11KSUBA:AA617397_RC_S_AT chromodomain helicase DNA binding protein 4 mm
MU11KSUBA:R75450_RC_S_AT chromodomain helicase DNA binding protein 4 mm
MU11KSUBB:MSA.8530.0_F_AT chromodomain helicase DNA binding protein 4 mm
MG-U74BV2:110040_AT chromodomain helicase DNA binding protein 4 mm
MG-U74BV2:108356_AT chromodomain helicase DNA binding protein 4 mm
MOE430A:1451295_A_AT chromodomain helicase DNA binding protein 4 mm
MOUSE430A_2:1451295_A_AT chromodomain helicase DNA binding protein 4 mm
MOUSE430_2:1451295_A_AT chromodomain helicase DNA binding protein 4 mm
MOE430A:1436343_AT chromodomain helicase DNA binding protein 4 mm
MOUSE430A_2:1436343_AT chromodomain helicase DNA binding protein 4 mm
MOUSE430_2:1436343_AT chromodomain helicase DNA binding protein 4 mm
MU19KSUBA:TC19748_AT Chromodomain helicase DNA binding protein 4, mRNA (cDNA clone IMAGE:3492938) mm
MU19KSUBA:TC25237_AT Chromodomain helicase DNA binding protein 4, mRNA (cDNA clone IMAGE:3492938) mm
MU19KSUBB:TC34929_AT Chromodomain helicase DNA binding protein 4, mRNA (cDNA clone IMAGE:3492938) mm
MU19KSUBC:TC37290_AT Chromodomain helicase DNA binding protein 4, mRNA (cDNA clone IMAGE:3492938) mm
MU19KSUBC:TC37480_AT Chromodomain helicase DNA binding protein 4, mRNA (cDNA clone IMAGE:3492938) mm
RG-U34B:RC_AA956746_AT chromodomain helicase DNA binding protein 4 rn
RAE230A:1372441_AT chromodomain helicase DNA binding protein 4 rn
RAT230_2:1372441_AT chromodomain helicase DNA binding protein 4 rn
RAE230B:1397200_AT chromodomain helicase DNA binding protein 4 rn
RAT230_2:1397200_AT chromodomain helicase DNA binding protein 4 rn
RAE230B:1385779_AT chromodomain helicase DNA binding protein 4 rn
RAT230_2:1385779_AT chromodomain helicase DNA binding protein 4 rn
Gene Ontology
GO Biological Process (view graph)
ID Description Evidence Links
6333 chromatin assembly or disassembly inferred from electronic annotation QuickGO AmiGO
6355 regulation of transcription, DNA-dependent inferred from electronic annotation QuickGO AmiGO
9307 DNA restriction-modification system inferred from electronic annotation QuickGO AmiGO
GO Cellular Component (view graph)
ID Description Evidence Links
785 chromatin inferred from electronic annotation QuickGO AmiGO
5634 nucleus 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
3677 DNA binding inferred from electronic annotation QuickGO AmiGO
3682 chromatin 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 NP_504523 LEThal family member (let-418) [Caenorhabditis elegans] gb|AAC25894.1| Lethal protein 418 [Caenorhabditis elegans] gb|AAG29838.1| LET-418 [Caenorhabditis elegans] 0.0
blast CAE64562 Hypothetical protein CBG09312 [Caenorhabditis briggsae] 0.0
blast CAA91810 Hypothetical protein T14G8.1 [Caenorhabditis elegans] emb|CAA91798.1| Hypothetical protein T14G8.1 [Caenorhabditis elegans] ref|NP_510140.1| CHromoDomain protein family member (chd-3) [Caenorhabditis elegans] gb|AAG29837.1| CHD-3 [Caenorhabditis elegans] sp|Q22516|CHD3_CAEEL Chromodomain helicase-DNA-binding protein 3 homolog (CHD-3) 0.0
Protein Domains
Database ID Description E-Value
Pfam IPR009463 EMBL-EBI Protein of unknown function DUF1087 1.6E-29
Pfam IPR000330 EMBL-EBI SNF2 related domain 1.9E-98
Pfam IPR001965 EMBL-EBI Zn-finger-like, PHD finger 1.7E-19
Pfam IPR001965 EMBL-EBI Zn-finger-like, PHD finger 2.4E-17
Pfam IPR000953 EMBL-EBI Chromo 9.7E-6
Pfam IPR001650 EMBL-EBI Helicase, C-terminal 2.1E-25
Pfam IPR009462 EMBL-EBI Protein of unknown function DUF1086 4.3E-100
Pfam IPR009463 EMBL-EBI Protein of unknown function DUF1087 1.6E-29
Pfam IPR000330 EMBL-EBI SNF2 related domain 1.9E-98
Pfam IPR001965 EMBL-EBI Zn-finger-like, PHD finger 1.7E-19
Pfam IPR001965 EMBL-EBI Zn-finger-like, PHD finger 2.4E-17
Pfam IPR000953 EMBL-EBI Chromo 9.7E-6
Pfam IPR001650 EMBL-EBI Helicase, C-terminal 2.1E-25
Pfam IPR009462 EMBL-EBI Protein of unknown function DUF1086 4.3E-100
Sequence
Target Sequence 
>C. ELEGANS:189004_AT
gtaatgcgaatgccgttctacacaaaacattggttcagctcgacgaaatactttccgata
tgaaggccgacgtgtctagacttccatctacttttacacagttagcgactgtcaccgaac
gtctcaacatgaccgagagacaaattctttcgcgactgaccacaaaagacgaggacgcga
tagccaaccgtagcgtacttccaccaccaggaccatttgtaactccaatacttcgccagc
agatggatggcattcaaccaaagtttgcagctctttacagtaaattcatgtctgaaaatg
gagaaaggatggaagaggatgaaccagtagaggcagaagaggaagaaggtgtaaaacaag
aaccagatgatgagactcaagatagcgccgaagctccgccagttcttagtgcagaagt

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GTAATGCGAATGCCGTTCTACACAA 200 463 4949 Antisense
GGTTCAGCTCGACGAAATACTTTCC 381 505 4980 Antisense
TCCGATATGAAGGCCGACGTGTCTA 622 595 5002 Antisense
GTGTCTAGACTTCCATCTACTTTTA 288 485 5020 Antisense
CAGTTAGCGACTGTCACCGAACGTC 473 205 5047 Antisense
CACCGAACGTCTCAACATGACCGAG 244 199 5061 Antisense
AGAGACAAATTCTTTCGCGACTGAC 90 67 5084 Antisense
AGACGAGGACGCGATAGCCAACCGT 325 71 5115 Antisense
TTTGTAACTCCAATACTTCGCCAGC 594 665 5164 Antisense
GACTCAAGATAGCGCCGAAGCTCCG 501 373 5322 Antisense
CTCCGCCAGTTCTTAGTGCAGAAGT 202 235 5342 Antisense
Sequence Source Affymetrix Proprietary Database