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[191193_at] ATP-dependent RNA helicase

Description C08F8.2 /REP_DB=WormBase Gene ID /WP=CE19689 /TR=Q17828 /GB=CAA97429.1 /SUBMIT=HINXTON /CHR=4 /FEA=Sanger Annotation /DEF=ATP-dependent RNA helicase
Cluster 6grp_highest_10_10 > 65      6grp_high1_10_10 > 56      4grp_highest_8_8 > 26      4grp_high_8_8 > 57      6grp_highest_nonorm > 83      6grp_total > 57      4grp_total > 61      6grp_high1_sub > Cu      6grp_total_sub > Cup      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 150
1 2 3 4 range
A 469.4
(2.7)
P 		414
(0.4)
P 		475.4
(3)
P 		331.8
(-3)
P 		144
B 481.7
(3)
P 		427
(-2.7)
P 		456.8
(0.4)
P 		424
(-3)
P 		58
C 444.9
(-0.4)
P 		436
(-1.3)
P 		479.7
(3)
P 		418.5
(-3)
P 		61
avr 465.3
(2.6) 		425.7
(-0.4) 		470.6
(3) 		391.4
(-3) 		79

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 254
1 2 3 4 5 6 range
A 466.4
(-0.5)
P 		507.3
(0.5)
P 		360.5
(-3)
P 		506.6
(0.5)
P 		470.9
(-0.4)
P 		614
(3)
P 		254
B 457.9
(-0)
P 		506.5
(2.8)
P 		477.3
(1.1)
P 		406.9
(-3)
P 		425.8
(-1.9)
P 		510.5
(3)
P 		104
C 547.1
(3)
P 		486.7
(0.6)
P 		504.5
(1.3)
P 		526.9
(2.2)
P 		393.9
(-3)
P 		537.6
(2.6)
P 		153
avr 490.5
(-0.1) 		500.2
(0.4) 		447.4
(-2.2) 		480.1
(-0.6) 		430.2
(-3) 		554
(3) 		124
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 122
1 2 3 4 range
A 170.9
(3)
P 		89.9
(-1)
P 		124.3
(0.7)
P 		48.6
(-3)
P 		122
B 153.6
(3)
P 		105.4
(-1.6)
P 		105.9
(-1.5)
P 		90.4
(-3)
P 		63
C 147.3
(1.8)
P 		125.3
(0.4)
P 		167.2
(3)
P 		70.6
(-3)
P 		97
avr 157.3
(3) 		106.9
(-0.5) 		132.5
(1.3) 		69.9
(-3) 		87

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 124
1 2 3 4 5 6 range
A 86
(-2.6)
P 		180.4
(3)
P 		78.5
(-3)
P 		128.5
(-0.1)
P 		142.1
(0.7)
P 		149.5
(1.2)
P 		102
B 159.3
(0.7)
P 		168.6
(1.4)
P 		115.9
(-2.4)
P 		107.8
(-3)
P 		173
(1.7)
P 		190.4
(3)
P 		83
C 202.8
(3)
P 		148.5
(-0.4)
P 		128.4
(-1.6)
P 		106
(-3)
P 		127.5
(-1.7)
P 		180
(1.6)
P 		97
avr 149.4
(0.8) 		165.8
(2.3) 		107.6
(-3) 		114.1
(-2.4) 		147.5
(0.6) 		173.3
(3) 		66
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 191193_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.8716
Sequence Type Exemplar sequence
Representative Public ID C08F8.2 NCBI
Target Description C08F8.2 /REP_DB=WormBase Gene ID /WP=CE19689 /TR=Q17828 /GB=CAA97429.1 /SUBMIT=HINXTON /CHR=4 /FEA=Sanger Annotation /DEF=ATP-dependent RNA 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_069687(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_069687 NCBI Caenorhabditis elegans C08F8.2 (C08F8.2) mRNA, complete cds. 11/11 None
SNAP00000012974 ENSEMBL cdna:SNAP chromosome:CEL140:IV:11151062:11154074:1 11/11 None
GENEFINDER00000012984 ENSEMBL cdna:GeneFinder chromosome:CEL140:IV:11150969:11154197:1 11/11 None
C08F8.2 ENSEMBL cdna:known chromosome:CEL140:IV:11149161:11154306:1 gene:C08F8.2 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:11150971-11154080(+) 99.86 99.86
Public Domain and Genome References
Gene Title ATP-dependent RNA helicase
Ensembl C08F8.2
Entrez Gene 178022 Entrez gene
SwissProt Q17828 EMBL-EBI
WormBase CE19689 Wormbase
Functional Annotations
Ortholog
ID Title Organism
ATH1-121501:249426_AT ATP-dependent RNA helicase, mitochondrial, putative at
CANINE_2:CFAAFFX.21373.1.S1_AT similar to suppressor of var1, 3-like 1 cfa
DROSOPHILA_2:1637793_AT dm
DROSGENOME1:154162_AT dm
CHICKEN:GGAAFFX.12457.1.S1_S_AT suppressor of var1, 3-like 1 (S. cerevisiae) gga
CHICKEN:GGAAFFX.2596.2.S1_AT suppressor of var1, 3-like 1 (S. cerevisiae) gga
CHICKEN:GGAAFFX.2596.2.S1_S_AT suppressor of var1, 3-like 1 (S. cerevisiae) gga
CHICKEN:GGAAFFX.2596.3.S1_AT suppressor of var1, 3-like 1 (S. cerevisiae) gga
CHICKEN:GGAAFFX.2596.3.S1_S_AT suppressor of var1, 3-like 1 (S. cerevisiae) gga
HU35KSUBC:RC_AA046407_AT suppressor of var1, 3-like 1 (S. cerevisiae) hs
U133_X3P:HS.106469.0.S1_3P_AT suppressor of var1, 3-like 1 (S. cerevisiae) hs
HG-U133A_2:212894_AT suppressor of var1, 3-like 1 (S. cerevisiae) hs
HG-FOCUS:212894_AT suppressor of var1, 3-like 1 (S. cerevisiae) hs
HG-U133_PLUS_2:212894_AT suppressor of var1, 3-like 1 (S. cerevisiae) hs
HG-U133A:212894_AT suppressor of var1, 3-like 1 (S. cerevisiae) hs
HG-U95AV2:41408_AT suppressor of var1, 3-like 1 (S. cerevisiae) hs
MOUSE430A_2:1432623_AT suppressor of var1, 3-like 1 (S. cerevisiae) mm
MOE430A:1432623_AT suppressor of var1, 3-like 1 (S. cerevisiae) mm
MOUSE430_2:1432623_AT suppressor of var1, 3-like 1 (S. cerevisiae) mm
MU11KSUBB:W91752_RC_S_AT suppressor of var1, 3-like 1 (S. cerevisiae) mm
MG-U74AV2:94368_AT suppressor of var1, 3-like 1 (S. cerevisiae) mm
MG-U74CV2:135436_AT suppressor of var1, 3-like 1 (S. cerevisiae) mm
MOE430A:1460557_AT suppressor of var1, 3-like 1 (S. cerevisiae) mm
MOUSE430A_2:1460557_AT suppressor of var1, 3-like 1 (S. cerevisiae) mm
MOUSE430_2:1460557_AT suppressor of var1, 3-like 1 (S. cerevisiae) mm
RG-U34A:RC_AA799741_AT suppressor of var1, 3-like 1 (S. cerevisiae) (predicted) rn
RAE230A:1372350_AT suppressor of var1, 3-like 1 (S. cerevisiae) (predicted) rn
RAT230_2:1372350_AT suppressor of var1, 3-like 1 (S. cerevisiae) (predicted) rn
YEAST_2:1776319_AT ATP-dependent RNA helicase, component of the mitochondrial degradosome along with the RNase Msu1p; the degradosome associates with the ribosome and mediates turnover of aberrant or unprocessed RNAs Sc
Gene Ontology
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 CAA97429 Hypothetical protein C08F8.2 [Caenorhabditis elegans] ref|NP_502088.1| C08F8.2 [Caenorhabditis elegans] 0.0
blast CAE62014 Hypothetical protein CBG06022 [Caenorhabditis briggsae] 0.0
blast XP_699468 PREDICTED: similar to suppressor of var1, 3-like 1 [Danio rerio] 1.0E-177
Protein Domains
Database ID Description E-Value
Pfam IPR001650 EMBL-EBI Helicase, C-terminal 1.4E-18
Pfam IPR001650 EMBL-EBI Helicase, C-terminal 1.4E-18
Pfam IPR001650 EMBL-EBI Helicase, C-terminal 1.4E-18
Sequence
Target Sequence 
>C. ELEGANS:191193_AT
tgatcatttcttcatctgcactgtctatgatatgcgtgaactcgctgtactcattgatca
gattccattaccattgaaagttcgatacacattctgtacatctccattgaatactgagga
taagagaacatcggcagtatttgtgaaaatggccagaaggttctccactggtcaagctct
tacctacgaatggctgatcgatatgcttgaatggccgcctaaacctgctacaactcttaa
cgaactgagtcttttggaacagaactatgaaattcttgatcagtatatgtggctgtcaat
gcgtttcccagatatgcttccagatgaaccgcgtgtccgtgaagcttccaaacatctgga
tagcatgattcaagaaggagtcgaaagttttatgagccttctctctgttggagcaactg

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
TGATCATTTCTTCATCTGCACTGTC 255 565 1581 Antisense
TATGCGTGAACTCGCTGTACTCATT 529 657 1611 Antisense
TACACATTCTGTACATCTCCATTGA 298 643 1666 Antisense
ATGGCCAGAAGGTTCTCCACTGGTC 277 51 1729 Antisense
CACTGGTCAAGCTCTTACCTACGAA 308 195 1746 Antisense
TTGAATGGCCGCCTAAACCTGCTAC 411 701 1787 Antisense
AACCTGCTACAACTCTTAACGAACT 577 145 1802 Antisense
ATATGTGGCTGTCAATGCGTTTCCC 484 21 1865 Antisense
AATGCGTTTCCCAGATATGCTTCCA 267 167 1878 Antisense
GTGTCCGTGAAGCTTCCAAACATCT 282 487 1913 Antisense
AGCCTTCTCTCTGTTGGAGCAACTG 331 83 1975 Antisense
Sequence Source Affymetrix Proprietary Database