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[174512_at] RNA binding protein

Description C51641_rc /REP_DB=TREMBL Accession /GB=C51641 /CHR=1 /FEA=Genomic Cluster /DEF=C.elegans cDNA clone yk220a12 : 3prime end, single read.
Cluster 4grp_high_8_8 > 15      6grp_total > 87      4grp_total > 16      6grp_cgc > 59      6grp_cgc_sub > Da      6grp_total_sub > Increase      6grp_rule_based > S6      4grp_rule_based > L4      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 219
1 2 3 4 range
A 55.1
(-2.7)
P 		50.7
(-3)
P 		106.7
(1)
P 		135.7
(3)
P 		85
B 58.3
(-3)
P 		63.6
(-2.7)
A 		88.8
(-1.2)
P 		160.6
(3)
P 		102
C 46.9
(-3)
P 		104.7
(-1.4)
P 		101.2
(-1.5)
P 		265.6
(3)
P 		219
avr 53.4
(-3) 		73
(-2.1) 		98.9
(-1) 		187.3
(3) 		134

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 1018
1 2 3 4 5 6 range
A 7
(-3)
A 		39.8
(-2.8)
A 		106.2
(-2.3)
P 		171.2
(-1.8)
P 		607.6
(1.2)
P 		862.7
(3)
P 		856
B 27
(-3)
A 		52.6
(-2.8)
A 		59.1
(-2.7)
M 		199.4
(-1.6)
P 		458.8
(0.4)
P 		779.4
(3)
P 		752
C 35.7
(-3)
A 		70.9
(-2.8)
P 		45.1
(-2.9)
A 		158.6
(-2.3)
P 		390.5
(-0.8)
P 		1024.8
(3)
P 		989
avr 23.2
(-3) 		54.4
(-2.8) 		70.1
(-2.7) 		176.4
(-1.9) 		485.6
(0.2) 		889
(3) 		866
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 34
1 2 3 4 range
A 20.1
(0.2)
P 		11
(-3)
P 		27.9
(3)
P 		19.9
(0.2)
P 		17
B 18.6
(-2.1)
P 		15.7
(-3)
A 		20.6
(-1.4)
P 		34.2
(3)
P 		19
C 15.5
(-3)
P 		30.1
(-0)
P 		35.3
(1.1)
P 		44.8
(3)
P 		29
avr 18.1
(-3) 		18.9
(-2.7) 		27.9
(0.9) 		33
(3) 		15

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 342
1 2 3 4 5 6 range
A 1.3
(-3)
A 		14.2
(-2.6)
A 		23.1
(-2.4)
P 		43.4
(-1.8)
P 		183.4
(2.2)
P 		210
(3)
P 		209
B 9.4
(-3)
A 		17.5
(-2.8)
A 		14.4
(-2.9)
M 		52.8
(-2.1)
P 		186.4
(0.8)
P 		290.6
(3)
P 		281
C 13.2
(-3)
A 		21.6
(-2.8)
P 		11.5
(-3)
A 		31.9
(-2.6)
P 		126.4
(-0.9)
P 		343.1
(3)
P 		332
avr 8
(-3) 		17.8
(-2.8) 		16.3
(-2.8) 		42.7
(-2.2) 		165.4
(0.5) 		281.2
(3) 		273
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 174512_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.20344
Sequence Type Exemplar sequence
Representative Public ID C51641 NCBI
Target Description C51641_rc /REP_DB=TREMBL Accession /GB=C51641 /CHR=1 /FEA=Genomic Cluster /DEF=C.elegans cDNA clone yk220a12 : 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_059279(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_059279 NCBI Caenorhabditis elegans CPEB polyA binding family member (cpb-3) (cpb-3) mRNA, complete cds. 11/11 None
B0414.5 ENSEMBL cdna:known chromosome:CEL140:I:5796797:5799888:-1 gene:B0414.5 11/11 A 
Annotation Notes
Cross Hybridizing mRNA Matched Probes Nature of Assignment Related Probesets by Grade
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrI:5796806-5797127(-) 100.0 100.0
Public Domain and Genome References
Gene Title RNA binding protein
Gene Symbol cpb-3
Ensembl B0414.5
Entrez Gene 172244 Entrez gene
SwissProt O01835 EMBL-EBI
WormBase CE07735 Wormbase
Functional Annotations
Protein Similarities
Method ID Description E-Value
blast AAB57717 Cpeb polya binding family protein 3 [Caenorhabditis elegans] ref|NP_491680.1| CPEB polyA binding family member (cpb-3) [Caenorhabditis elegans] sp|O01835|CPB3_CAEEL Cytoplasmic polyadenylation element binding protein 0.0
blast AAT72445 CPB-3 [Caenorhabditis sp. CB5161] gb|AAT72416.1| CPB-3 [Caenorhabditis sp. CB5161] 0.0
blast AAT72444 CPB-3 [Caenorhabditis remanei] gb|AAT72415.1| CPB-3 [Caenorhabditis remanei] sp|Q6E3D4|CPB3_CAERE Cytoplasmic polyadenylation element binding protein 0.0
Protein Domains
Database ID Description E-Value
Pfam IPR000504 EMBL-EBI RNA-binding region RNP-1 (RNA recognition motif) 8.5E-7
Sequence
Target Sequence 
>C. ELEGANS:174512_AT
tgtagcgtttagtttgggccttcttaattgtttgtttttttaatcaattttgttattttg
ttgtgtttctaatcatccatctcccaactcttatccgaatctgatgccatttttccttgt
cattcgcaatcaattcgtatgccattttcttggtcccatctgtagatttaaactctccgc
attgcgttttacctccctctcgtttaatgtatacaagaagaatcgaaggtaacgttttat
cttttttatcacttataaaattattcatcttaagtactctttcacatc

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
TGTAGCGTTTAGTTTGGGCCTTCTT 645 559 16 Antisense
GTTGTGTTTCTAATCATCCATCTCC 495 437 75 Antisense
CTCCCAACTCTTATCCGAATCTGAT 160 233 96 Antisense
GAATCTGATGCCATTTTTCCTTGTC 427 329 112 Antisense
CCATTTTTCCTTGTCATTCGCAATC 60 269 122 Antisense
ATTCGCAATCAATTCGTATGCCATT 450 9 137 Antisense
TTCGTATGCCATTTTCTTGGTCCCA 362 695 149 Antisense
TTTCTTGGTCCCATCTGTAGATTTA 63 673 161 Antisense
AAACTCTCCGCATTGCGTTTTACCT 376 127 185 Antisense
TTACCTCCCTCTCGTTTAATGTATA 297 683 204 Antisense
TTCATCTTAAGTACTCTTTCACATC 114 689 279 Antisense
Sequence Source Affymetrix Proprietary Database