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[190000_s_at] helicase

Description T12F5.3 /REP_DB=WormBase Gene ID /WP=CE13599 /GEN=glh-4 /TR=O44758 /GB=AAB96745.1 /SUBMIT=ST.LOUIS /CHR=1 /FEA=Sanger Annotation /DEF=helicase
Cluster 6grp_high1_10_10 > 88      6grp_total > 87      4grp_total > 0      6grp_cgc > 59      6grp_high1_sub > Da      6grp_cgc_sub > Da      6grp_total_sub > Increase      6grp_rule_based > S6      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 74
1 2 3 4 range
A 109.4
(-2)
P 		101.3
(-3)
A 		134.4
(1)
P 		150.9
(3)
A 		50
B 116.7
(2.2)
P 		77.3
(-3)
A 		96.2
(-0.5)
M 		122.9
(3)
A 		46
C 99.5
(-3)
P 		125.4
(3)
A 		109.1
(-0.8)
P 		106.1
(-1.5)
P 		26
avr 108.5
(-1.3) 		101.3
(-3) 		113.2
(-0.2) 		126.6
(3) 		25

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 477
1 2 3 4 5 6 range
A 110.7
(-2.7)
A 		97
(-2.9)
P 		85.8
(-3)
P 		193
(-1.6)
P 		294.8
(-0.3)
P 		552
(3)
P 		466
B 107.3
(-3)
P 		110.7
(-3)
P 		119.4
(-2.8)
P 		188
(-1.9)
P 		261.1
(-1)
P 		562.8
(3)
P 		456
C 108.2
(-3)
P 		120.5
(-2.7)
P 		145
(-2.2)
P 		123.8
(-2.7)
P 		351.9
(2.1)
P 		397.6
(3)
P 		289
avr 108.7
(-3) 		109.4
(-3) 		116.7
(-2.9) 		168.3
(-2.1) 		302.6
(-0.1) 		504.1
(3) 		395
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 22
1 2 3 4 range
A 39.8
(3)
P 		22
(-3)
A 		35.1
(1.4)
P 		22.1
(-3)
A 		18
B 37.2
(3)
P 		19.1
(-3)
A 		22.3
(-1.9)
M 		26.2
(-0.6)
A 		18
C 33
(1.5)
P 		36.1
(2.4)
A 		38
(3)
P 		17.9
(-3)
P 		20
avr 36.7
(3) 		25.7
(-1.5) 		31.8
(1) 		22.1
(-3) 		15

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 191
1 2 3 4 5 6 range
A 20.4
(-2.9)
A 		34.5
(-2.2)
P 		18.7
(-3)
P 		48.9
(-1.4)
P 		88.9
(0.6)
P 		134.4
(3)
P 		116
B 37.3
(-2.7)
P 		36.8
(-2.7)
P 		29
(-3)
P 		49.8
(-2.3)
P 		106.1
(-0.4)
P 		209.9
(3)
P 		181
C 40.1
(-2.2)
P 		36.8
(-2.3)
P 		36.9
(-2.3)
P 		24.9
(-3)
P 		113.9
(1.9)
P 		133.1
(3)
P 		108
avr 32.6
(-2.8) 		36
(-2.6) 		28.2
(-3) 		41.2
(-2.4) 		103
(0.4) 		159.1
(3) 		131
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 190000_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.137
Sequence Type Exemplar sequence
Representative Public ID T12F5.3 NCBI
Target Description T12F5.3 /REP_DB=WormBase Gene ID /WP=CE13599 /GEN=glh-4 /TR=O44758 /GB=AAB96745.1 /SUBMIT=ST.LOUIS /CHR=1 /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_058806(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_058806 NCBI Caenorhabditis elegans T12F5.3 (helicase) mRNA, complete cds. 11/11 None
SNAP00000015201 ENSEMBL cdna:SNAP chromosome:CEL140:I:3727063:3730939:1 10/11 None
GENEFINDER00000015211 ENSEMBL cdna:GeneFinder chromosome:CEL140:I:3727063:3730939:1 11/11 None
SNAP00000032586 ENSEMBL cdna:SNAP chromosome:CEL140:X:181284:198310:-1 10/11 None
GENEFINDER00000032588 ENSEMBL cdna:GeneFinder chromosome:CEL140:X:181284:191525:-1 10/11 None
T12F5.3 ENSEMBL cdna:known chromosome:CEL140:I:3726013:3731220:1 gene:T12F5.3 11/11 None
Annotation Notes
Cross Hybridizing mRNA Matched Probes Nature of Assignment Related Probesets by Grade
NM_075655 6/11 Cross Hyb Matching Probes None
T08D2.3 6/11 Cross Hyb Matching Probes None
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrI:3727062-3730939(+) 100.0 100.0
chrX:181283-185104(-) 96.53 97.02
Public Domain and Genome References
Gene Title helicase
Gene Symbol glh-4
Ensembl T12F5.3
Entrez Gene 171941 Entrez gene
SwissProt O76743 EMBL-EBI
WormBase CE29052 Wormbase
Functional Annotations
Gene Ontology
GO Biological Process (view graph)
ID Description Evidence Links
6810 transport 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
5488 binding 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
8289 lipid binding inferred from electronic annotation QuickGO AmiGO
3724 RNA helicase activity inferred from sequence similarity QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast AAB96745 Germ-line helicase protein 4 [Caenorhabditis elegans] ref|NP_491207.3| T12F5.3 [Caenorhabditis elegans] sp|O76743|GLH4_CAEEL ATP-dependent RNA helicase glh-4 (Germline helicase 4) 0.0
blast AAC28387 germline RNA helicase-4 [Caenorhabditis elegans] 0.0
blast CAB07418 Hypothetical protein T08D2.3 [Caenorhabditis elegans] ref|NP_508056.1| T08D2.3 [Caenorhabditis elegans] 0.0
Protein Domains
Database ID Description E-Value
Pfam IPR001878 EMBL-EBI Zn-finger, CCHC type 4.6E-7
Pfam IPR001878 EMBL-EBI Zn-finger, CCHC type 3.2E-5
Pfam IPR001878 EMBL-EBI Zn-finger, CCHC type 1.3E-5
Pfam IPR001878 EMBL-EBI Zn-finger, CCHC type 1.9E-7
Pfam IPR001650 EMBL-EBI Helicase, C-terminal 9.3E-26
Pfam IPR001410 EMBL-EBI DEAD/DEAH box helicase 1.8E-66
Pfam IPR001650 EMBL-EBI Helicase, C-terminal 3.5E-27
Pfam IPR001878 EMBL-EBI Zn-finger, CCHC type 4.6E-7
Pfam IPR001878 EMBL-EBI Zn-finger, CCHC type 3.2E-5
Pfam IPR001878 EMBL-EBI Zn-finger, CCHC type 1.3E-5
Pfam IPR001878 EMBL-EBI Zn-finger, CCHC type 1.9E-7
Pfam IPR001650 EMBL-EBI Helicase, C-terminal 3.5E-27
Pfam IPR001410 EMBL-EBI DEAD/DEAH box helicase 1.8E-66
Pfam IPR001878 EMBL-EBI Zn-finger, CCHC type 1.9E-7
Pfam IPR001650 EMBL-EBI Helicase, C-terminal 2.2E-17
Pfam IPR008164 EMBL-EBI Repeat of unknown function XGLTT 7.3E-7
Pfam IPR008164 EMBL-EBI Repeat of unknown function XGLTT 3.3E-9
Pfam IPR008164 EMBL-EBI Repeat of unknown function XGLTT 1.7E-9
Pfam IPR008164 EMBL-EBI Repeat of unknown function XGLTT 1.5E-8
Pfam IPR008164 EMBL-EBI Repeat of unknown function XGLTT 2.2E-7
Pfam IPR001410 EMBL-EBI DEAD/DEAH box helicase 2.0E-66
Trans Membrane
ID Number Of Domains Domain Boundaries
SNAP00000032586 5 118-140,155-177,198-220,235-257,264-286
Sequence
Target Sequence 
>C. ELEGANS:190000_S_AT
gagggttacactatgctgcaagtcgacaagttcggaacagctaatgaaaagatcgaccag
aagattcttcctgtgcctcgaaccgagaaacgagacgcgatttacaagcttctcggaatt
gatgaaaacactgtgactctcttgccggacgcacccatcgagaaacaaaagacgctgatc
ttcgtgaactcggtgaagttctgtgacactcttgcggctctcatctcgagcgctggcgtt
agcactatttcgatgcatagctaccaaaatcaagaacagcgtgatcgtacattggatgat
ttccgtcgtggtaaataccagtgtatggtagcttcaaatgtgtgtgctcgtggattgaat
attgccgggctcgatcatgtcgtcaactacgatatgccggataaaaatggctttgatgag
tatgtcaaccgtatcggacgtactggaagagctggattcaccggaacgtcgactgcattc
gttgacgtggagaacgacacggacattattccatgcctcg

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GAGGGTTACACTATGCTGCAAGTCG 694 401 2902 Antisense
GACCAGAAGATTCTTCCTGTGCCTC 528 381 2956 Antisense
ACGCGATTTACAAGCTTCTCGGAAT 183 91 2996 Antisense
TGAAAACACTGTGACTCTCTTGCCG 514 573 3024 Antisense
AGACGCTGATCTTCGTGAACTCGGT 144 71 3071 Antisense
TGAAGTTCTGTGACACTCTTGCGGC 166 575 3095 Antisense
TCATCTCGAGCGCTGGCGTTAGCAC 272 619 3122 Antisense
GTGGATTGAATATTGCCGGGCTCGA 161 489 3251 Antisense
GGCTCGATCATGTCGTCAACTACGA 621 537 3269 Antisense
TCACCGGAACGTCGACTGCATTCGT 82 623 3359 Antisense
GACACGGACATTATTCCATGCCTCG 564 367 3397 Antisense
Sequence Source Affymetrix Proprietary Database