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[175430_s_at] RNA helicase

Description AV200263_rc /REP_DB=TREMBL Accession /GB=AV200263 /CHR=1 /FEA=Genomic Cluster /DEF=Caenorhabditis elegans cDNA clone:yk559e9 : 3prime end, single read.
Cluster 6grp_highest_10_10 > 79      6grp_high1_10_10 > 97      4grp_highest_8_8 > 11      4grp_high_8_8 > 47      6grp_highest_nonorm > 99      6grp_total > 97      4grp_total > 48      6grp_highest_sub > In      6grp_cgc > 68      6grp_high1_sub > In      6grp_cgc_sub > In      6grp_total_sub > Increase      6grp_rule_based > S6      4grp_rule_based > L3      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 861
1 2 3 4 range
A 295.4
(-3)
P 		722
(0)
P 		1140.1
(3)
P 		483.9
(-1.7)
P 		845
B 278.7
(-3)
P 		718.2
(0.2)
P 		1106.1
(3)
P 		505.6
(-1.4)
P 		827
C 303.5
(-3)
P 		657.7
(-0.4)
P 		1126.8
(3)
P 		463.7
(-1.8)
P 		823
avr 292.5
(-3) 		699.3
(-0.1) 		1124.3
(3) 		484.4
(-1.6) 		832

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 2004
1 2 3 4 5 6 range
A 193.5
(-3)
P 		331.3
(-2.6)
P 		511.1
(-2)
P 		982.4
(-0.6)
P 		1297.7
(0.3)
P 		2196.7
(3)
P 		2003
B 218.2
(-3)
P 		332.2
(-2.6)
P 		510.1
(-2)
P 		800.8
(-1.1)
P 		1473.5
(1.2)
P 		2031.3
(3)
P 		1813
C 192.3
(-3)
P 		329.5
(-2.5)
P 		607
(-1.5)
P 		664.6
(-1.3)
P 		1463.7
(1.6)
P 		1867.8
(3)
P 		1676
avr 201.3
(-3) 		331
(-2.6) 		542.7
(-1.9) 		815.9
(-1) 		1411.6
(1) 		2031.9
(3) 		1831
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 322
1 2 3 4 range
A 107.6
(-2)
P 		156.7
(-0.7)
P 		298
(3)
P 		70.8
(-3)
P 		227
B 88.9
(-3)
P 		177.4
(0.2)
P 		256.3
(3)
P 		107.7
(-2.3)
P 		167
C 100.5
(-2.6)
P 		189.1
(-0.9)
P 		392.7
(3)
P 		78.2
(-3)
P 		315
avr 99
(-2.7) 		174.4
(-0.7) 		315.7
(3) 		85.6
(-3) 		230

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 722
1 2 3 4 5 6 range
A 35.7
(-3)
P 		117.8
(-2)
P 		111.3
(-2.1)
P 		249.2
(-0.4)
P 		391.6
(1.3)
P 		534.8
(3)
P 		499
B 75.9
(-3)
P 		110.6
(-2.7)
P 		123.9
(-2.6)
P 		212.1
(-1.8)
P 		598.7
(1.6)
P 		757.5
(3)
P 		682
C 71.3
(-3)
P 		100.5
(-2.7)
P 		154.5
(-2.1)
P 		133.6
(-2.3)
P 		473.6
(1.4)
P 		625.3
(3)
P 		554
avr 61
(-3) 		109.6
(-2.5) 		129.9
(-2.3) 		198.3
(-1.6) 		488
(1.4) 		639.2
(3) 		578
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 175430_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.20179
Sequence Type Exemplar sequence
Representative Public ID AV200263 NCBI
Target Description AV200263_rc /REP_DB=TREMBL Accession /GB=AV200263 /CHR=1 /FEA=Genomic Cluster /DEF=Caenorhabditis elegans cDNA clone:yk559e9 : 3prime end, single read.
Cluster Evidence This cluster is supported by a Genomic Cluster.
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_059562(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_059562 NCBI Caenorhabditis elegans Germ-Line Helicase family member (glh-1) (glh-1) mRNA, complete cds. 11/11 A 
SNAP00000016509 ENSEMBL cdna:SNAP chromosome:CEL140:I:6862944:6865525:1 11/11 None
GENEFINDER00000016520 ENSEMBL cdna:GeneFinder chromosome:CEL140:I:6862944:6865525:1 11/11 None
T21G5.3 ENSEMBL cdna:known chromosome:CEL140:I:6862820:6865665:1 gene:T21G5.3 11/11 A 
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:6865183-6865527(+) 100.0 100.0
Public Domain and Genome References
Gene Title RNA helicase
Gene Symbol glh-1
Ensembl T21G5.3
Entrez Gene 172414 Entrez gene
SwissProt P34689 EMBL-EBI
WormBase CE25121 Wormbase
Functional Annotations
Ortholog
ID Title Organism
CANINE_2:CFAAFFX.11231.1.S1_S_AT similar to DEAD (Asp-Glu-Ala-Asp) box polypeptide 4 cfa
DROSOPHILA_2:1631511_AT vasa dm
DROSGENOME1:143402_AT vasa dm
CHICKEN:GGA.241.1.S1_AT DEAD (Asp-Glu-Ala-Asp) box polypeptide 4 gga
HG-U133_PLUS_2:221630_S_AT DEAD (Asp-Glu-Ala-Asp) box polypeptide 4 hs
HG-FOCUS:221630_S_AT DEAD (Asp-Glu-Ala-Asp) box polypeptide 4 hs
HG-U133A:221630_S_AT DEAD (Asp-Glu-Ala-Asp) box polypeptide 4 hs
HG-U133A_2:221630_S_AT DEAD (Asp-Glu-Ala-Asp) box polypeptide 4 hs
HU35KSUBD:RC_AA608877_AT DEAD (Asp-Glu-Ala-Asp) box polypeptide 4 hs
U133_X3P:G9438226_3P_A_AT DEAD (Asp-Glu-Ala-Asp) box polypeptide 4 hs
HG-U95C:58335_AT DEAD (Asp-Glu-Ala-Asp) box polypeptide 4 hs
MOUSE430A_2:1427242_AT DEAD (Asp-Glu-Ala-Asp) box polypeptide 4 mm
MOE430A:1427242_AT DEAD (Asp-Glu-Ala-Asp) box polypeptide 4 mm
MOUSE430_2:1427242_AT DEAD (Asp-Glu-Ala-Asp) box polypeptide 4 mm
MU11KSUBB:MSA.3001.0_AT DEAD (Asp-Glu-Ala-Asp) box polypeptide 4 mm
MG-U74AV2:94162_AT DEAD (Asp-Glu-Ala-Asp) box polypeptide 4 mm
MG-U74CV2:165513_I_AT DEAD (Asp-Glu-Ala-Asp) box polypeptide 4 mm
RG-U34A:S75275_AT DEAD (Asp-Glu-Ala-Asp) box polypeptide 4 (predicted) rn
Gene Ontology
GO Biological Process (view graph)
ID Description Evidence Links
16070 RNA metabolism inferred from sequence similarity QuickGO AmiGO
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 direct assay QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast AAB52901 Germ-line helicase protein 1 [Caenorhabditis elegans] ref|NP_491963.1| Germ-Line Helicase family member (glh-1) [Caenorhabditis elegans] sp|P34689|GLH1_CAEEL ATP-dependent RNA helicase glh-1 (Germline helicase 1) 0.0
blast AAB04136 RNA helicase [Caenorhabditis elegans] 0.0
blast AAC27384 RNA helicase [Caenorhabditis elegans] 0.0
Protein Domains
Database ID Description E-Value
Pfam IPR001878 EMBL-EBI Zn-finger, CCHC type 8.6E-8
Pfam IPR001878 EMBL-EBI Zn-finger, CCHC type 2.9E-8
Pfam IPR001878 EMBL-EBI Zn-finger, CCHC type 5.3E-7
Pfam IPR001878 EMBL-EBI Zn-finger, CCHC type 2.3E-7
Pfam IPR001650 EMBL-EBI Helicase, C-terminal 5.9E-36
Pfam IPR001410 EMBL-EBI DEAD/DEAH box helicase 2.4E-71
Sequence
Target Sequence 
>C. ELEGANS:175430_S_AT
agctacaagcttcatctcggaggattgcagtcttctgtccgaacttgttggtgttctcgc
cgacgcacaacagattgttccagactggatgcaaggtgctgctggaggcaattacggagc
tagtggatttgggtccagtgtaccaactcaagtccctcaagatga

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
AGCTACAAGCTTCATCTCGGAGGAT 638 63 49 Antisense
TCTCGGAGGATTGCAGTCTTCTGTC 412 611 63 Antisense
GTCCGAACTTGTTGGTGTTCTCGCC 603 475 85 Antisense
CTCGCCGACGCACAACAGATTGTTC 698 233 104 Antisense
GACGCACAACAGATTGTTCCAGACT 59 381 110 Antisense
GTTCCAGACTGGATGCAAGGTGCTG 424 439 125 Antisense
GCAAGGTGCTGCTGGAGGCAATTAC 668 321 139 Antisense
GGAGGCAATTACGGAGCTAGTGGAT 567 515 152 Antisense
GGAGCTAGTGGATTTGGGTCCAGTG 148 521 164 Antisense
TGGGTCCAGTGTACCAACTCAAGTC 378 553 178 Antisense
TACCAACTCAAGTCCCTCAAGATGA 390 643 189 Antisense
Sequence Source Affymetrix Proprietary Database