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[192236_at] possible RNA binding protein

Description C06G4.1 /REP_DB=WormBase Gene ID /WP=CE28203 /TR=SW:P34307 /GB=AAA27939.2 /SUBMIT=ST.LOUIS /CHR=3 /FEA=Sanger Annotation /DEF=possible RNA binding protein
Cluster 6grp_highest_10_10 > 78      6grp_high1_10_10 > 97      4grp_high_8_8 > 04      6grp_highest_nonorm > 91      6grp_total > 87      4grp_total > 05      6grp_highest_sub > In      6grp_high1_sub > In      6grp_total_sub > Increase      6grp_rule_based > S6      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 147
1 2 3 4 range
A 91.8
(-2)
P 		70.7
(-3)
P 		95.5
(-1.8)
M 		193.3
(3)
P 		123
B 114.6
(-0.5)
P 		92.3
(-3)
P 		114
(-0.6)
P 		146.2
(3)
P 		54
C 154.7
(0.2)
P 		92.3
(-2.5)
P 		80.5
(-3)
P 		217.5
(3)
P 		137
avr 120.4
(-0.9) 		85.1
(-3) 		96.7
(-2.3) 		185.7
(3) 		101

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 293
1 2 3 4 5 6 range
A 89
(-3)
P 		116
(-2.4)
P 		88.4
(-3)
P 		157.9
(-1.6)
P 		238.2
(0.1)
P 		380.9
(3)
P 		293
B 97.4
(-3)
P 		118.9
(-2.5)
P 		140.9
(-1.9)
P 		161
(-1.4)
P 		253.5
(1)
P 		334.1
(3)
P 		237
C 92.7
(-3)
P 		140.6
(-1.9)
P 		146.3
(-1.8)
P 		148.8
(-1.8)
P 		201.9
(-0.6)
P 		362.8
(3)
P 		270
avr 93
(-3) 		125.2
(-2.3) 		125.2
(-2.3) 		155.9
(-1.6) 		231.2
(0.1) 		359.3
(3) 		266
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 36
1 2 3 4 range
A 33.4
(3)
P 		15.4
(-3)
P 		25
(0.2)
M 		28.3
(1.3)
P 		18
B 36.5
(3)
P 		22.8
(-3)
P 		26.4
(-1.4)
P 		31.2
(0.7)
P 		14
C 51.2
(3)
P 		26.5
(-3)
P 		28.1
(-2.6)
P 		36.7
(-0.5)
P 		25
avr 40.4
(3) 		21.6
(-3) 		26.5
(-1.4) 		32.1
(0.4) 		19

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 108
1 2 3 4 5 6 range
A 16.4
(-3)
P 		41.2
(-1)
P 		19.3
(-2.8)
P 		40.1
(-1.1)
P 		71.9
(1.4)
P 		92.7
(3)
P 		76
B 33.9
(-3)
P 		39.6
(-2.6)
P 		34.2
(-3)
P 		42.6
(-2.4)
P 		103
(1.6)
P 		124.6
(3)
P 		91
C 34.3
(-2.7)
P 		42.9
(-2.1)
P 		37.2
(-2.5)
P 		29.9
(-3)
P 		65.3
(-0.7)
P 		121.4
(3)
P 		92
avr 28.2
(-3) 		41.2
(-2.1) 		30.2
(-2.9) 		37.5
(-2.3) 		80.1
(0.7) 		112.9
(3) 		85
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 192236_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.7727
Sequence Type Exemplar sequence
Representative Public ID C06G4.1 NCBI
Target Description C06G4.1 /REP_DB=WormBase Gene ID /WP=CE28203 /TR=SW:P34307 /GB=AAA27939.2 /SUBMIT=ST.LOUIS /CHR=3 /FEA=Sanger Annotation /DEF=possible RNA binding protein
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_066341(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_066341 NCBI Caenorhabditis elegans C06G4.1 (C06G4.1) mRNA, complete cds. 11/11 None
SNAP00000040330 ENSEMBL cdna:SNAP chromosome:CEL140:III:7987053:7990374:1 11/11 None
GENEFINDER00000040333 ENSEMBL cdna:GeneFinder chromosome:CEL140:III:7987053:7990374:1 11/11 None
C06G4.1 ENSEMBL cdna:known chromosome:CEL140:III:7987053:7990473:1 gene:C06G4.1 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
chrIII:7986881-7990304(+) 100.0 100.0
Public Domain and Genome References
Gene Title possible RNA binding protein
Ensembl C06G4.1
Entrez Gene 176123 Entrez gene
SwissProt P34307 EMBL-EBI
WormBase CE28203 Wormbase
Functional Annotations
Gene Ontology
GO Molecular Function (view graph)
ID Description Evidence Links
3676 nucleic acid binding inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast AAA27939 Hypothetical protein C06G4.1 [Caenorhabditis elegans] ref|NP_498742.1| C06G4.1 [Caenorhabditis elegans] sp|P34307|YKR1_CAEEL Hypothetical protein C06G4.1 in chromosome III 0.0
Protein Domains
Database ID Description E-Value
Pfam IPR004087 EMBL-EBI KH 5.7E-7
Pfam IPR004087 EMBL-EBI KH 7.5E-8
Pfam IPR004087 EMBL-EBI KH 5.7E-7
Pfam IPR004087 EMBL-EBI KH 7.5E-8
Sequence
Target Sequence 
>C. ELEGANS:192236_AT
tcaaccgcaccactgaaacttactggaagtgttaattccattcacatggctagagaaacg
atgcaatcgaaaacaaagcgtttcctcgatgaagagaagttcaaggagactgtagaacat
tgtacgccaataagtttctaccgaaaaatcattggacgttgtggagagaacttgaaaact
atcgagaaagtgactcgtactgccatcgttttcaaacgctcatttgataataatgaggcg
tgcttttcaattcgtggaagaactgataacatcaagcaggctatcgagaaaattgaggag
atcacgcacgagaatcagccagcggatgatgatccgggtatcttccaagttcgtgttcca
gaaaacatggttgcccggcttattggaaggcatggcgt

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
TCAACCGCACCACTGAAACTTACTG 458 631 2134 Antisense
AACAAAGCGTTTCCTCGATGAAGAG 389 135 2205 Antisense
TGTACGCCAATAAGTTTCTACCGAA 32 561 2254 Antisense
AGAAAGTGACTCGTACTGCCATCGT 260 73 2318 Antisense
ACTGCCATCGTTTTCAAACGCTCAT 413 99 2332 Antisense
TGAGGCGTGCTTTTCAATTCGTGGA 388 567 2367 Antisense
AGATCACGCACGAGAATCAGCCAGC 176 67 2432 Antisense
GGATGATGATCCGGGTATCTTCCAA 663 513 2457 Antisense
GTATCTTCCAAGTTCGTGTTCCAGA 147 455 2471 Antisense
AGAAAACATGGTTGCCCGGCTTATT 413 71 2493 Antisense
CCCGGCTTATTGGAAGGCATGGCGT 134 195 2507 Antisense
Sequence Source Affymetrix Proprietary Database