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[187802_at] ATP-dependent RNA helicase

Description C07H6.5 /REP_DB=WormBase Gene ID /WP=CE00839 /SUBMIT=ST.LOUIS /CHR=3 /FEA=Sanger Annotation /DEF=ATP-dependent RNA helicase
Cluster 6grp_highest_10_10 > 97      6grp_high1_10_10 > 79      4grp_highest_8_8 > 10      4grp_high_8_8 > 55      6grp_highest_nonorm > 68      6grp_total > 69      4grp_total > 48      6grp_highest_sub > Cu      6grp_cgc > 29      6grp_high1_sub > Cu      6grp_cgc_sub > Cu      6grp_total_sub > Cup      4grp_rule_based > L3      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 708
1 2 3 4 range
A 1348.7
(-2)
P 		1860
(2.6)
P 		1902.5
(3)
P 		1240.1
(-3)
P 		662
B 1194.1
(-3)
P 		1384.3
(-0.9)
P 		1733.4
(3)
P 		1493.3
(0.3)
P 		539
C 1382
(-1.3)
P 		1693.2
(3)
P 		1582.8
(1.5)
P 		1254.4
(-3)
P 		439
avr 1308.3
(-3) 		1645.8
(1.7) 		1739.6
(3) 		1329.3
(-2.7) 		431

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 1564
1 2 3 4 5 6 range
A 1708.3
(-2)
P 		1562
(-2.6)
P 		1450.7
(-3)
P 		1497
(-2.8)
P 		2295.4
(0.2)
P 		3014.4
(3)
P 		1564
B 1827.9
(-0.6)
P 		1762
(-1.1)
P 		1529.1
(-3)
P 		1756
(-1.2)
P 		1927
(0.2)
P 		2267.5
(3)
P 		738
C 2066.1
(3)
P 		1752.4
(-0.1)
P 		1542.3
(-2.2)
P 		1458.4
(-3)
P 		1861.4
(1)
P 		2013.2
(2.5)
P 		608
avr 1867.4
(-0.7) 		1692.1
(-1.8) 		1507.4
(-3) 		1570.5
(-2.6) 		2027.9
(0.4) 		2431.7
(3) 		924
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 370
1 2 3 4 range
A 491
(2.9)
P 		403.8
(1.2)
P 		497.3
(3)
P 		181.5
(-3)
P 		316
B 380.8
(1.5)
P 		341.9
(-1.3)
P 		401.7
(3)
P 		318.2
(-3)
P 		84
C 457.5
(1.3)
P 		486.8
(1.9)
P 		551.6
(3)
P 		211.5
(-3)
P 		340
avr 443.1
(2) 		410.8
(1.2) 		483.5
(3) 		237.1
(-3) 		246

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 552
1 2 3 4 5 6 range
A 314.9
(-3)
P 		555.5
(0.4)
P 		315.9
(-3)
P 		379.7
(-2.1)
P 		692.6
(2.4)
P 		733.9
(3)
P 		419
B 636
(0.3)
P 		586.5
(-0.3)
P 		371.3
(-3)
P 		465.1
(-1.8)
P 		782.9
(2.2)
P 		845.5
(3)
P 		474
C 765.8
(3)
P 		534.7
(0.1)
P 		392.5
(-1.7)
P 		293.3
(-3)
P 		602.3
(0.9)
P 		674
(1.8)
P 		473
avr 572.2
(0.3) 		558.9
(0.1) 		359.9
(-3) 		379.4
(-2.7) 		692.6
(2.1) 		751.1
(3) 		391
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 187802_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.7280
Sequence Type Exemplar sequence
Representative Public ID C07H6.5 NCBI
Target Description C07H6.5 /REP_DB=WormBase Gene ID /WP=CE00839 /SUBMIT=ST.LOUIS /CHR=3 /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_066245(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_066245 NCBI Caenorhabditis elegans Conserved Germline Helicase family member (cgh-1) (cgh-1) mRNA, complete cds. 11/11 None
SNAP00000039488 ENSEMBL cdna:SNAP chromosome:CEL140:III:7496181:7497713:-1 11/11 None
GENEFINDER00000039503 ENSEMBL cdna:GeneFinder chromosome:CEL140:III:7496181:7499147:-1 11/11 None
C07H6.5.2 ENSEMBL cdna:known chromosome:CEL140:III:7495089:7497753:-1 gene:C07H6.5 11/11 None
C07H6.5.1 ENSEMBL cdna:known chromosome:CEL140:III:7495089:7497751:-1 gene:C07H6.5 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
chrIII:7496178-7497711(-) 100.0 100.0
Public Domain and Genome References
Gene Title ATP-dependent RNA helicase
Gene Symbol cgh-1
Ensembl C07H6.5
Entrez Gene 176061 Entrez gene
SwissProt Q95YF3 EMBL-EBI
WormBase CE00839 Wormbase
Functional Annotations
Ortholog
ID Title Organism
ATGENOME1:18547_S_AT DEAD/DEAH box helicase, putative at
ATH1-121501:255688_AT DEAD/DEAH box helicase, putative at
CANINE:1597113_AT similar to Probable ATP-dependent RNA helicase DDX6 (DEAD-box protein 6) (ATP-dependent RNA helicase p54) (Oncogene RCK) cfa
CANINE_2:CFA.14787.1.S1_AT similar to Probable ATP-dependent RNA helicase DDX6 (DEAD-box protein 6) (ATP-dependent RNA helicase p54) (Oncogene RCK) cfa
CANINE_2:CFAAFFX.19292.1.S1_S_AT similar to Probable ATP-dependent RNA helicase DDX6 (DEAD-box protein 6) (ATP-dependent RNA helicase p54) (Oncogene RCK) cfa
DROSOPHILA_2:1628017_A_AT maternal expression at 31B dm
DROSGENOME1:153996_AT maternal expression at 31B dm
CHICKEN:GGA.2331.1.S1_AT DEAD (Asp-Glu-Ala-Asp) box polypeptide 6 gga
CHICKEN:GGAAFFX.12268.1.S1_AT DEAD (Asp-Glu-Ala-Asp) box polypeptide 6 gga
HG-U133_PLUS_2:204909_AT DEAD (Asp-Glu-Ala-Asp) box polypeptide 6 hs
HG-U133A_2:204909_AT DEAD (Asp-Glu-Ala-Asp) box polypeptide 6 hs
HG-U133A:204909_AT DEAD (Asp-Glu-Ala-Asp) box polypeptide 6 hs
HG-FOCUS:204909_AT DEAD (Asp-Glu-Ala-Asp) box polypeptide 6 hs
HUGENEFL:Z11685_S_AT DEAD (Asp-Glu-Ala-Asp) box polypeptide 6 hs
HUGENEFL:D17532_AT DEAD (Asp-Glu-Ala-Asp) box polypeptide 6 hs
U133_X3P:G13514828_3P_AT DEAD (Asp-Glu-Ala-Asp) box polypeptide 6 hs
HG-U95AV2:36283_AT DEAD (Asp-Glu-Ala-Asp) box polypeptide 6 hs
HU35KSUBB:RC_AA046007_AT DEAD (Asp-Glu-Ala-Asp) box polypeptide 6 hs
U133_X3P:HS.271541.0.S1_3P_AT DEAD (Asp-Glu-Ala-Asp) box polypeptide 6 hs
HG-U133_PLUS_2:225549_AT DEAD (Asp-Glu-Ala-Asp) box polypeptide 6 hs
HG-U133B:225549_AT DEAD (Asp-Glu-Ala-Asp) box polypeptide 6 hs
HG-U95B:52993_AT DEAD (Asp-Glu-Ala-Asp) box polypeptide 6 hs
HG-U95E:70792_AT DEAD (Asp-Glu-Ala-Asp) box polypeptide 6 hs
HG-U133_PLUS_2:1562836_AT DEAD (Asp-Glu-Ala-Asp) box polypeptide 6 hs
HG-U95D:79233_AT DEAD (Asp-Glu-Ala-Asp) box polypeptide 6 hs
MOE430A:1424598_AT DEAD (Asp-Glu-Ala-Asp) box polypeptide 6 mm
MOUSE430A_2:1424598_AT DEAD (Asp-Glu-Ala-Asp) box polypeptide 6 mm
MOUSE430_2:1424598_AT DEAD (Asp-Glu-Ala-Asp) box polypeptide 6 mm
MG-U74AV2:93965_R_AT DEAD (Asp-Glu-Ala-Asp) box polypeptide 6 mm
MG-U74AV2:93964_S_AT DEAD (Asp-Glu-Ala-Asp) box polypeptide 6 mm
MOE430B:1447789_X_AT DEAD (Asp-Glu-Ala-Asp) box polypeptide 6, mRNA (cDNA clone MGC:29113 IMAGE:5043599) mm
MOUSE430_2:1447789_X_AT DEAD (Asp-Glu-Ala-Asp) box polypeptide 6, mRNA (cDNA clone MGC:29113 IMAGE:5043599) mm
MOE430B:1457618_AT DEAD (Asp-Glu-Ala-Asp) box polypeptide 6, mRNA (cDNA clone MGC:29113 IMAGE:5043599) mm
MOUSE430_2:1457618_AT DEAD (Asp-Glu-Ala-Asp) box polypeptide 6, mRNA (cDNA clone MGC:29113 IMAGE:5043599) mm
RG-U34B:RC_AA850780_AT similar to RCK rn
RAE230A:1389868_AT similar to RCK rn
RAT230_2:1389868_AT similar to RCK rn
RAE230B:1392854_AT similar to RCK rn
RAT230_2:1392854_AT similar to RCK rn
RAE230A:1398945_AT DEAD (Asp-Glu-Ala-Asp) box polypeptide 6 rn
RAT230_2:1398945_AT DEAD (Asp-Glu-Ala-Asp) box polypeptide 6 rn
RG-U34B:RC_AA851439_AT DEAD (Asp-Glu-Ala-Asp) box polypeptide 6 rn
RG-U34C:RC_AI235046_AT DEAD (Asp-Glu-Ala-Asp) box polypeptide 6 rn
RG-U34B:RC_AA925853_AT Similar to RCK rn
YEAST_2:1774663_AT Cytoplasmic DExD/H-box helicase, stimulates mRNA decapping, coordinates distinct steps in mRNA function and decay, interacts with both the decapping and deadenylase complexes, may have a role in mRNA export and translation Sc
Gene Ontology
GO Cellular Component (view graph)
ID Description Evidence Links
5737 cytoplasm inferred from direct assay 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
3724 RNA helicase activity inferred from sequence similarity QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast AAK85443 Conserved germline helicase protein 1 [Caenorhabditis elegans] ref|NP_498646.1| Conserved Germline Helicase family member (cgh-1) [Caenorhabditis elegans] 0.0
blast CAE64461 Hypothetical protein CBG09177 [Caenorhabditis briggsae] 0.0
blast XP_624586 PREDICTED: similar to CG4916-PA, isoform A [Apis mellifera] 0.0
Protein Domains
Database ID Description E-Value
Pfam IPR001650 EMBL-EBI Helicase, C-terminal 3.3E-32
Pfam IPR001410 EMBL-EBI DEAD/DEAH box helicase 5.4E-72
Pfam IPR001650 EMBL-EBI Helicase, C-terminal 3.3E-32
Pfam IPR001410 EMBL-EBI DEAD/DEAH box helicase 5.4E-72
Trans Membrane
ID Number Of Domains Domain Boundaries
GENEFINDER00000039503 1 7-29
Sequence
Target Sequence 
>C. ELEGANS:187802_AT
tggaggagcttactcttcttggtgtcacccaatactatgcctttgttcaagagaagcaaa
aggtccactgtttgaatacgttgttccgaaaacttcaaatcaaccagtcgatcatcttct
gtaactctactcaacgtgttgagcttctcgctaagaaaatcacggaaatcggttactcgt
gctactacattcattccaagatggctcagaatcacagaaaccgtgtcttccatgacttcc
gtcaaggaaactgcagaaacttggtttgctccgatcttctcacccgtggtatcgatatcc
aggctgtcaatgttgtcatcaactttgacttcccaagaaacgccgagacttaccttcaca
gaatcggtcgctctggacgtttcggtcacctcggagttgcaatcaaccttatcacctacg
aagaccgtcacacccttcgccgtatcgagcaggagcttcgtactcgcattgagcccatcc
cgaaaacggttgacccgaagctgtatgtcgct

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
TGGAGGAGCTTACTCTTCTTGGTGT 398 549 752 Antisense
GTCACCCAATACTATGCCTTTGTTC 327 463 775 Antisense
GTCGATCATCTTCTGTAACTCTACT 201 473 858 Antisense
TACTCGTGCTACTACATTCATTCCA 307 647 925 Antisense
CAGAAACCGTGTCTTCCATGACTTC 306 205 966 Antisense
ATCTTCTCACCCGTGGTATCGATAT 161 31 1025 Antisense
ATATCCAGGCTGTCAATGTTGTCAT 446 21 1046 Antisense
ACAGAATCGGTCGCTCTGGACGTTT 181 109 1109 Antisense
TTTCGGTCACCTCGGAGTTGCAATC 478 669 1131 Antisense
TGCAATCAACCTTATCACCTACGAA 77 577 1149 Antisense
GGTTGACCCGAAGCTGTATGTCGCT 9 507 1239 Antisense
Sequence Source Affymetrix Proprietary Database