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[188994_at] RNA helicase

Description C55B7.1 /REP_DB=WormBase Gene ID /WP=CE09012 /GEN=glh-2 /GB=AAK68269.1 /SUBMIT=ST.LOUIS /CHR=1 /FEA=Sanger Annotation /DEF=RNA helicase
Cluster 6grp_high1_10_10 > 87      4grp_high_8_8 > 22      6grp_total > 87      4grp_total > 16      6grp_cgc > 58      6grp_high1_sub > In      6grp_cgc_sub > In      6grp_total_sub > Increase      6grp_rule_based > S6      4grp_rule_based > L4      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 84
1 2 3 4 range
A 84.8
(-3)
M 		109.3
(-0.5)
P 		122.8
(0.8)
P 		144.6
(3)
P 		60
B 90.7
(-3)
P 		120.2
(-0.7)
P 		107.4
(-1.7)
P 		168.7
(3)
P 		78
C 117.6
(0.9)
P 		96.4
(-3)
M 		117.3
(0.9)
P 		128.7
(3)
P 		32
avr 97.7
(-3) 		108.6
(-1.7) 		115.8
(-0.8) 		147.3
(3) 		50

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 645
1 2 3 4 5 6 range
A 82.3
(-2.7)
A 		83.9
(-2.7)
P 		51.4
(-3)
P 		195.6
(-1.6)
P 		334.5
(-0.3)
P 		688.4
(3)
P 		637
B 74
(-3)
P 		128
(-2.4)
P 		108.9
(-2.6)
A 		113.2
(-2.6)
P 		284.1
(-0.7)
P 		614.6
(3)
P 		541
C 43.9
(-3)
A 		126
(-2)
M 		122.5
(-2)
P 		177.4
(-1.3)
P 		332.1
(0.6)
P 		519.1
(3)
P 		475
avr 66.7
(-3) 		112.6
(-2.5) 		94.3
(-2.7) 		162.1
(-1.9) 		316.9
(-0.2) 		607.4
(3) 		541
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 20
1 2 3 4 range
A 30.9
(2.3)
M 		23.7
(-1.6)
P 		32.1
(3)
P 		21.2
(-3)
P 		11
B 28.9
(-0.8)
P 		29.7
(-0.4)
P 		24.9
(-3)
P 		35.9
(3)
P 		11
C 38.9
(2.4)
P 		27.7
(-1.1)
M 		40.9
(3)
P 		21.7
(-3)
P 		19
avr 32.9
(3) 		27
(-2.4) 		32.6
(2.7) 		26.3
(-3) 		7

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 218
1 2 3 4 5 6 range
A 15.2
(-2.8)
A 		29.9
(-2.3)
P 		11.2
(-3)
P 		49.6
(-1.5)
P 		100.9
(0.4)
P 		167.6
(3)
P 		156
B 25.7
(-3)
P 		42.6
(-2.5)
P 		26.4
(-3)
A 		30
(-2.9)
P 		115.4
(-0.4)
P 		229.2
(3)
P 		204
C 16.3
(-3)
A 		38.5
(-2.2)
M 		31.2
(-2.4)
P 		35.7
(-2.3)
P 		107.5
(0.5)
P 		173.8
(3)
P 		158
avr 19.1
(-3) 		37
(-2.4) 		22.9
(-2.9) 		38.4
(-2.3) 		107.9
(0.1) 		190.2
(3) 		171
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 188994_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.1190
Sequence Type Exemplar sequence
Representative Public ID C55B7.1 NCBI
Target Description C55B7.1 /REP_DB=WormBase Gene ID /WP=CE09012 /GEN=glh-2 /GB=AAK68269.1 /SUBMIT=ST.LOUIS /CHR=1 /FEA=Sanger Annotation /DEF=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_059475(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_059475 NCBI Caenorhabditis elegans Germ-Line Helicase family member (glh-2) (glh-2) mRNA, complete cds. 11/11 None
SNAP00000038303 ENSEMBL cdna:SNAP chromosome:CEL140:I:6516042:6525441:1 11/11 None
GENEFINDER00000038311 ENSEMBL cdna:GeneFinder chromosome:CEL140:I:6522155:6525441:1 11/11 None
C55B7.1 ENSEMBL cdna:known chromosome:CEL140:I:6522155:6525638:1 gene:C55B7.1 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
chrI:6522083-6525370(+) 100.0 100.0
Public Domain and Genome References
Gene Title RNA helicase
Gene Symbol glh-2
Ensembl C55B7.1
Entrez Gene 172361 Entrez gene
SwissProt Q966L9 EMBL-EBI
WormBase CE09012 Wormbase
Functional Annotations
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 AAB03510 GLH-2 [Caenorhabditis elegans] gb|AAB03337.1| RNA helicase GLH-2 [Caenorhabditis elegans] 0.0
blast NP_491876 Germ-Line Helicase family member (glh-2) [Caenorhabditis elegans] gb|AAK68269.1| Germ-line helicase protein 2 [Caenorhabditis elegans] sp|Q966L9|GLH2_CAEEL ATP-dependent RNA helicase glh-2 (Germline helicase 2) 0.0
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 NP_491874 GLYcosylation related family member (gly-2) [Caenorhabditis elegans] gb|AAF74523.1| N-acetylglucosaminyltransferase V [Caenorhabditis elegans] gb|AAK94767.1| GLY-2 [Caenorhabditis elegans] gb|AAK68273.1| Glycosylation related protein 2 [Caenorhabditis elegans] 0.0
blast AAK94765 GLY-2 [Caenorhabditis elegans] 0.0
Protein Domains
Database ID Description E-Value
Pfam IPR001878 EMBL-EBI Zn-finger, CCHC type 1.3E-7
Pfam IPR001878 EMBL-EBI Zn-finger, CCHC type 2.1E-8
Pfam IPR001878 EMBL-EBI Zn-finger, CCHC type 1.3E-7
Pfam IPR001878 EMBL-EBI Zn-finger, CCHC type 2.1E-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 1.0E-69
Pfam IPR001878 EMBL-EBI Zn-finger, CCHC type 7.2E-7
Pfam IPR001878 EMBL-EBI Zn-finger, CCHC type 1.3E-7
Pfam IPR001878 EMBL-EBI Zn-finger, CCHC type 2.1E-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 1.0E-69
Trans Membrane
ID Number Of Domains Domain Boundaries
SNAP00000038303 1 7-29
Sequence
Target Sequence 
>C. ELEGANS:188994_AT
aaattggggccgccaacaagtgcgtccttcaggagtttgaaaagtgcgatagaagcgaaa
agaaggacaaacttctggaaattctaggaattgatatcgacagttacacgacagaaaaaa
attctgaagtgtacactaagaagactatcgtttttgtctcgcaaagagcaatggctgata
cgttggcctccattttatcatcggctcaagtaccagcaatcacgatccacggtgcccgtg
agcagagagagcgttcagaggctttgagacaattccgaaatggatcgaaacctgttctta
ttgctactgcggttgccgaacgtggacttgatatcaaaggagtggatcatgtcatcaact
atgacatgccagacaacattgatgactacattcatcgtattggaagaacgggtcgagttg
gaaacgctggaagagccaccagtttcatctctgaagattgtaatcttctgtccgaacttg
ttcgcgttctctctgacgcggatcaactggttcc

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
AAATTGGGGCCGCCAACAAGTGCGT 684 113 2327 Antisense
ACAAGTGCGTCCTTCAGGAGTTTGA 464 111 2342 Antisense
GAAGACTATCGTTTTTGTCTCGCAA 32 341 2466 Antisense
GCAATGGCTGATACGTTGGCCTCCA 691 321 2494 Antisense
TTGGCCTCCATTTTATCATCGGCTC 639 707 2509 Antisense
ATCATCGGCTCAAGTACCAGCAATC 250 29 2523 Antisense
TACCAGCAATCACGATCCACGGTGC 96 649 2537 Antisense
GCTACTGCGGTTGCCGAACGTGGAC 641 301 2629 Antisense
AAGAGCCACCAGTTTCATCTCTGAA 154 155 2757 Antisense
TGTCCGAACTTGTTCGCGTTCTCTC 673 557 2795 Antisense
TCTCTGACGCGGATCAACTGGTTCC 6 611 2816 Antisense
Sequence Source Affymetrix Proprietary Database