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[192240_s_at] Eukaryotic initiation factor 4A

Description F57B9.3 /REP_DB=WormBase Gene ID /WP=CE01338 /TR=Q20935 /GB=AAA21169.1 /SUBMIT=ST.LOUIS /CHR=3 /FEA=Sanger Annotation /DEF=Eukaryotic initiation factor 4A
Cluster 6grp_highest_10_10 > 51      6grp_high1_10_10 > 26      4grp_highest_8_8 > 16      4grp_high_8_8 > 60      6grp_highest_nonorm > 03      6grp_total > 25      4grp_total > 59      6grp_highest_sub > De      6grp_high1_sub > De      6grp_total_sub > Decrease      6grp_rule_based > S1      4grp_rule_based > L3      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 4235
1 2 3 4 range
A 5415.8
(1.8)
P 		5434.5
(1.8)
P 		6238.2
(3)
P 		2233.9
(-3)
P 		4004
B 5090.5
(0.9)
P 		5966.8
(2.3)
P 		6422.5
(3)
P 		2671.7
(-3)
P 		3751
C 4818.7
(0.9)
P 		5998.7
(2.7)
P 		6228.5
(3)
P 		2187.7
(-3)
P 		4041
avr 5108.3
(1.2) 		5800
(2.2) 		6296.4
(3) 		2364.4
(-3) 		3932

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 1914
1 2 3 4 5 6 range
A 3389.5
(1.3)
P 		3839.8
(3)
P 		3136.8
(0.3)
P 		2735.6
(-1.3)
P 		2282.1
(-3)
P 		2759.2
(-1.2)
P 		1558
B 4021.6
(3)
P 		3612.4
(1.7)
P 		2475.2
(-2.1)
P 		2616.7
(-1.6)
P 		2194.5
(-3)
P 		2405.7
(-2.3)
P 		1827
C 4085.1
(3)
P 		3254
(0.4)
P 		3085.3
(-0.1)
P 		2171.3
(-3)
P 		2913.5
(-0.7)
P 		2477
(-2)
P 		1914
avr 3832.1
(3) 		3568.7
(1.8) 		2899.1
(-1.1) 		2507.9
(-2.8) 		2463.4
(-3) 		2547.3
(-2.6) 		1369
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 1844
1 2 3 4 range
A 1971.9
(3)
P 		1179.7
(0.1)
P 		1630.8
(1.8)
P 		327
(-3)
P 		1645
B 1623.3
(3)
P 		1473.7
(2.1)
P 		1488.2
(2.2)
P 		569.3
(-3)
P 		1054
C 1595.1
(1.1)
P 		1724.7
(1.5)
P 		2170.8
(3)
P 		368.9
(-3)
P 		1802
avr 1730.1
(2.9) 		1459.4
(1.6) 		1763.3
(3) 		421.7
(-3) 		1342

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 1078
1 2 3 4 5 6 range
A 624.8
(-3)
P 		1365.6
(3)
P 		683.1
(-2.5)
P 		693.8
(-2.4)
P 		688.6
(-2.5)
P 		671.8
(-2.6)
P 		741
B 1399.3
(3)
P 		1202.4
(1.5)
P 		601
(-3)
P 		693.1
(-2.3)
P 		891.6
(-0.8)
P 		897.1
(-0.8)
P 		798
C 1514.2
(3)
P 		992.9
(0.1)
P 		785.3
(-1.1)
P 		436.6
(-3)
P 		942.8
(-0.2)
P 		829.2
(-0.8)
P 		1078
avr 1179.4
(2.9) 		1187
(3) 		689.8
(-2.2) 		607.8
(-3) 		841
(-0.6) 		799.4
(-1) 		579
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 192240_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.7804
Sequence Type Exemplar sequence
Representative Public ID F57B9.3 NCBI
Target Description F57B9.3 /REP_DB=WormBase Gene ID /WP=CE01338 /TR=Q20935 /GB=AAA21169.1 /SUBMIT=ST.LOUIS /CHR=3 /FEA=Sanger Annotation /DEF=Eukaryotic initiation factor 4A
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_001027452(11), NM_001027453(11), NM_066113(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_001027452 NCBI Caenorhabditis elegans INitiation Factor family member (inf-1) (inf-1) mRNA, complete cds. 11/11 None
NM_001027453 NCBI Caenorhabditis elegans INitiation Factor family member (inf-1) (inf-1) mRNA, complete cds. 11/11 None
NM_066113 NCBI Caenorhabditis elegans F57B9.3 (F57B9.3) mRNA, complete cds. 11/11 A 
SNAP00000019896 ENSEMBL cdna:SNAP chromosome:CEL140:III:6930068:6931516:1 11/11 None
GENEFINDER00000019912 ENSEMBL cdna:GeneFinder chromosome:CEL140:III:6930068:6931516:1 11/11 None
SNAP00000019900 ENSEMBL cdna:SNAP chromosome:CEL140:III:6939819:6941667:1 11/11 None
GENEFINDER00000019916 ENSEMBL cdna:GeneFinder chromosome:CEL140:III:6939819:6941667:1 11/11 None
F57B9.6.1 ENSEMBL cdna:known chromosome:CEL140:III:6929970:6931884:1 gene:F57B9.6 11/11 None
F57B9.6.2 ENSEMBL cdna:known chromosome:CEL140:III:6930016:6931884:1 gene:F57B9.6 11/11 None
F57B9.3 ENSEMBL cdna:known chromosome:CEL140:III:6940108:6941667:1 gene:F57B9.3 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
chrIII:6940106-6941666(+) 100.0 100.0
Public Domain and Genome References
Gene Title Eukaryotic initiation factor 4A
Ensembl F57B9.6
F57B9.3
Entrez Gene 186440 Entrez gene
SwissProt Q20935 EMBL-EBI
WormBase CE01338 Wormbase
Functional Annotations
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 CAA78102 unnamed protein product [Caenorhabditis elegans] gb|AAA21170.1| Initiation factor protein 1, isoform a [Caenorhabditis elegans] ref|NP_001022623.1| INitiation Factor family member (inf-1) [Caenorhabditis elegans] sp|P27639|IF4A_CAEEL Eukaryotic initiation factor 4A (eIF4A) (eIF-4A) 0.0
blast CAE70046 Hypothetical protein CBG16478 [Caenorhabditis briggsae] 0.0
blast AAA21169 Hypothetical protein F57B9.3 [Caenorhabditis elegans] ref|NP_498514.1| F57B9.3 [Caenorhabditis elegans] 0.0
Protein Domains
Database ID Description E-Value
Pfam IPR001650 EMBL-EBI Helicase, C-terminal 1.3E-18
Pfam IPR001410 EMBL-EBI DEAD/DEAH box helicase 1.4E-53
Pfam IPR001650 EMBL-EBI Helicase, C-terminal 1.8E-37
Pfam IPR001410 EMBL-EBI DEAD/DEAH box helicase 4.3E-83
Pfam IPR001650 EMBL-EBI Helicase, C-terminal 2.1E-35
Pfam IPR001650 EMBL-EBI Helicase, C-terminal 1.3E-18
Pfam IPR001410 EMBL-EBI DEAD/DEAH box helicase 1.4E-53
Sequence
Target Sequence 
>C. ELEGANS:192240_S_AT
gttccatgccacaagacgttcaagtagtccttctttcggctactatgccatctgaagttc
ttgatgtcactaatcgtttcatgcgtgatccaatccgtattcttgtcaagaaggacgagc
tcacccttgaaggtatcagacagttctacatcaacgttcaaaagg

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GTTCCATGCCACAAGACGTTCAAGT 397 441 479 Antisense
GACGTTCAAGTAGTCCTTCTTTCGG 589 377 493 Antisense
AAGTAGTCCTTCTTTCGGCTACTAT 532 157 500 Antisense
TCCTTCTTTCGGCTACTATGCCATC 511 591 506 Antisense
TCTTTCGGCTACTATGCCATCTGAA 313 615 510 Antisense
GGCTACTATGCCATCTGAAGTTCTT 102 539 516 Antisense
GAAGTTCTTGATGTCACTAATCGTT 242 337 532 Antisense
TTGATGTCACTAATCGTTTCATGCG 560 701 539 Antisense
GACGAGCTCACCCTTGAAGGTATCA 191 379 592 Antisense
TGAAGGTATCAGACAGTTCTACATC 529 575 606 Antisense
CAGTTCTACATCAACGTTCAAAAGG 36 205 619 Antisense
Sequence Source Affymetrix Proprietary Database