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[189916_at] helicase

Description T04A11.6 /REP_DB=WormBase Gene ID /WP=CE13130 /GEN=him-6 /TR=O18017 /GB=CAB05609.1 /SUBMIT=HINXTON /CHR=4 /FEA=Sanger Annotation /DEF=helicase
Cluster 6grp_highest_10_10 > 87      6grp_high1_10_10 > 87      4grp_highest_8_8 > 45      4grp_high_8_8 > 09      6grp_highest_nonorm > 92      6grp_total > 78      4grp_total > 23      6grp_highest_sub > Da      6grp_cgc > 49      6grp_high1_sub > In      6grp_cgc_sub > Da      6grp_total_sub > Increase      6grp_rule_based > S6      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 90
1 2 3 4 range
A 176.9
(3)
P 		100.7
(-2.9)
P 		99.1
(-3)
P 		177.5
(3)
P 		78
B 161.1
(3)
P 		117.3
(-1.3)
P 		100.3
(-3)
P 		133.8
(0.3)
P 		61
C 172.6
(3)
P 		87.8
(-3)
P 		104.3
(-1.8)
P 		147
(1.2)
P 		85
avr 170.2
(3) 		101.9
(-2.9) 		101.2
(-3) 		152.8
(1.5) 		69

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 367
1 2 3 4 5 6 range
A 208.7
(-1.1)
P 		162.3
(-2.3)
P 		133.8
(-3)
P 		208.6
(-1.1)
P 		253.4
(0)
P 		372.6
(3)
P 		239
B 194.8
(-2.6)
P 		181.1
(-2.8)
P 		173.3
(-3)
P 		239.1
(-1.7)
P 		255.7
(-1.3)
P 		470.3
(3)
P 		297
C 188.3
(-2.2)
P 		193.4
(-2.1)
P 		137
(-3)
P 		231.5
(-1.4)
P 		279.1
(-0.7)
P 		500.5
(3)
P 		364
avr 197.3
(-2) 		178.9
(-2.4) 		148
(-3) 		226.4
(-1.4) 		262.7
(-0.7) 		447.8
(3) 		300
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 43
1 2 3 4 range
A 64.4
(3)
P 		21.9
(-3)
P 		25.9
(-2.4)
P 		26
(-2.4)
P 		43
B 51.4
(3)
P 		29
(-1.8)
P 		23.2
(-3)
P 		28.5
(-1.9)
P 		28
C 57.1
(3)
P 		25.2
(-2.9)
P 		36.3
(-0.9)
P 		24.8
(-3)
P 		32
avr 57.6
(3) 		25.4
(-3) 		28.5
(-2.4) 		26.4
(-2.8) 		32

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 146
1 2 3 4 5 6 range
A 38.5
(-2.1)
P 		57.7
(-0.2)
P 		29.1
(-3)
P 		52.9
(-0.7)
P 		76.5
(1.6)
P 		90.7
(3)
P 		62
B 67.8
(-1.8)
P 		60.3
(-2.2)
P 		42.1
(-3)
P 		63.3
(-2)
P 		103.9
(-0.2)
P 		175.4
(3)
P 		133
C 69.8
(-1.4)
P 		59
(-1.9)
P 		34.9
(-3)
P 		46.5
(-2.5)
P 		90.3
(-0.5)
P 		167.5
(3)
P 		133
avr 58.7
(-1.7) 		59
(-1.7) 		35.4
(-3) 		54.2
(-2) 		90.2
(0) 		144.5
(3) 		109
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 189916_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.8427
Sequence Type Exemplar sequence
Representative Public ID T04A11.6 NCBI
Target Description T04A11.6 /REP_DB=WormBase Gene ID /WP=CE13130 /GEN=him-6 /TR=O18017 /GB=CAB05609.1 /SUBMIT=HINXTON /CHR=4 /FEA=Sanger Annotation /DEF=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_069989(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_069989 NCBI Caenorhabditis elegans T04A11.6 (helicase) mRNA, complete cds. 11/11 None
SNAP00000015162 ENSEMBL cdna:SNAP chromosome:CEL140:IV:12490769:12497815:1 11/11 None
GENEFINDER00000015168 ENSEMBL cdna:GeneFinder chromosome:CEL140:IV:12490769:12495111:1 11/11 None
T04A11.6 ENSEMBL cdna:known chromosome:CEL140:IV:12490762:12495260:1 gene:T04A11.6 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
chrIV:12487555-12495117(+) 99.46 100.0
Public Domain and Genome References
Gene Title helicase
Gene Symbol him-6
Ensembl T04A11.6
Entrez Gene 178201 Entrez gene
SwissProt O18017 EMBL-EBI
WormBase CE31724 Wormbase
Functional Annotations
Ortholog
ID Title Organism
DROSOPHILA_2:1637039_AT mutagen-sensitive 309 dm
DROSGENOME1:143846_AT mutagen-sensitive 309 dm
CHICKEN:GGA.1914.1.S1_S_AT Bloom syndrome gga
HG-U95AV2:1544_AT Bloom syndrome hs
HC-G110:1544_AT Bloom syndrome hs
HG-U133_PLUS_2:205733_AT Bloom syndrome hs
HG-U133A:205733_AT Bloom syndrome hs
HG-FOCUS:205733_AT Bloom syndrome hs
HG-U133A_2:205733_AT Bloom syndrome hs
HUGENEFL:U39817_AT Bloom syndrome hs
U133_X3P:G4557364_3P_AT Bloom syndrome hs
HU35KSUBB:RC_T99721_AT Bloom syndrome hs
HG-U95B:48165_AT Bloom syndrome hs
HG-U95D:71974_R_AT Bloom syndrome hs
HU35KSUBB:RC_T99033_AT Bloom syndrome hs
HU35KSUBD:RC_T95850_AT Bloom syndrome hs
MG-U74AV2:102631_AT Bloom syndrome homolog (human) mm
MOE430A:1448953_AT Bloom syndrome homolog (human) mm
MOUSE430A_2:1448953_AT Bloom syndrome homolog (human) mm
MOUSE430_2:1448953_AT Bloom syndrome homolog (human) mm
RAE230B:1382783_AT Bloom syndrome (predicted) rn
RAT230_2:1382783_AT Bloom syndrome (predicted) rn
Gene Ontology
GO Biological Process (view graph)
ID Description Evidence Links
6259 DNA metabolism inferred from electronic annotation QuickGO AmiGO
GO Cellular Component (view graph)
ID Description Evidence Links
5622 intracellular 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
Protein Similarities
Method ID Description E-Value
blast CAB05609 Hypothetical protein T04A11.6 [Caenorhabditis elegans] gb|AAM26298.1| RecQ helicase [Caenorhabditis elegans] ref|NP_502390.2| T04A11.6 [Caenorhabditis elegans] sp|O18017|BLM_CAEEL Bloom's syndrome protein homolog (RecQ helicase homolog) 0.0
blast T24415 hypothetical protein T04A11.6 - Caenorhabditis elegans 0.0
blast CAE74027 Hypothetical protein CBG21676 [Caenorhabditis briggsae] 0.0
Protein Domains
Database ID Description E-Value
Pfam IPR002121 EMBL-EBI HRDC domain 2.6E-24
Pfam IPR001650 EMBL-EBI Helicase, C-terminal 1.0E-26
Pfam IPR001410 EMBL-EBI DEAD/DEAH box helicase 4.5E-47
Pfam IPR003839 EMBL-EBI Protein of unknown function DUF215 1.5E-34
Pfam IPR002121 EMBL-EBI HRDC domain 2.6E-24
Pfam IPR001650 EMBL-EBI Helicase, C-terminal 1.0E-26
Pfam IPR001410 EMBL-EBI DEAD/DEAH box helicase 4.5E-47
Trans Membrane
ID Number Of Domains Domain Boundaries
SNAP00000015162 3 1015-1037,1057-1079,1099-1121
Sequence
Target Sequence 
>C. ELEGANS:189916_AT
atgctggcctcatcgaattatccaatatgaatatcgtctcagaagcccaggcactaaaag
aacgtcatatggttaaacatggagatgtttttacgagatgtcttcaagatttgactcatc
ttattactgcagttgccgagagttctggattatccggtccttattcaattgtgtcccgag
aaggaatcgaacaaatcgctgctcttcttccacggacgaattcggatcttttgagaattg
attccatgacccagattaaagttacaaagtatggccgtctaatcatggagcttctagcaa
cttactggaaacaggttgatgaacgagaggaagaagaaatgcgaaaccagcttgacaaat
tgaaaagcggagaaattgtgatgggtggtttcgccacattacaatcggatccaggttttc
catctgtaccctacatgaagccacttggaggaggaggaggatgcaggggaagaggaaaga
agagggcattttctggcttttcctccggtcgagcaacgaagaagccacgcgcaactgctc
catcggcacgtggcaagacaagcggacgaggcggggcaaaaccagctac

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
ATGCTGGCCTCATCGAATTATCCAA 593 39 3080 Antisense
GACTCATCTTATTACTGCAGTTGCC 696 373 3192 Antisense
TCCGGTCCTTATTCAATTGTGTCCC 273 595 3232 Antisense
GGAATCGAACAAATCGCTGCTCTTC 62 533 3262 Antisense
TGGCCGTCTAATCATGGAGCTTCTA 590 543 3351 Antisense
GTTTCGCCACATTACAATCGGATCC 195 449 3467 Antisense
TCGGATCCAGGTTTTCCATCTGTAC 652 605 3484 Antisense
TGTACCCTACATGAAGCCACTTGGA 352 559 3504 Antisense
GAAGAGGGCATTTTCTGGCTTTTCC 178 339 3558 Antisense
TTTTCCTCCGGTCGAGCAACGAAGA 98 675 3577 Antisense
GACGAGGCGGGGCAAAACCAGCTAC 564 377 3644 Antisense
Sequence Source Affymetrix Proprietary Database