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[192085_at] RNA binding protein

Description B0414.5 /REP_DB=WormBase Gene ID /WP=CE07735 /GEN=cpb-3 /TR=O01835 /GB=AAB57717.1 /SUBMIT=ST.LOUIS /CHR=1 /FEA=Sanger Annotation /DEF=RNA binding protein
Cluster 6grp_total > 97      4grp_total > 41      6grp_cgc > 69      6grp_cgc_sub > Da      6grp_total_sub > Increase      6grp_rule_based > S6      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 56
1 2 3 4 range
A 43
(3)
A 		30.3
(0.8)
A 		8.1
(-3)
A 		34.7
(1.6)
A 		35
B 37.8
(-1.9)
A 		57
(2)
A 		61.9
(3)
A 		32.1
(-3)
A 		30
C 32.1
(-3)
A 		46.4
(-0.3)
A 		64
(3)
A 		60.3
(2.3)
A 		32
avr 37.6
(-3) 		44.6
(2.9) 		44.7
(3) 		42.4
(1.1) 		7

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 313
1 2 3 4 5 6 range
A 6.6
(-3)
A 		28.7
(-2.6)
A 		39.1
(-2.4)
A 		83.5
(-1.5)
A 		168.8
(0.1)
P 		320
(3)
P 		313
B 26.5
(-3)
A 		54.5
(-2.1)
A 		27.1
(-3)
A 		71.5
(-1.5)
A 		167.7
(1.6)
P 		210
(3)
P 		184
C 30.9
(-2.7)
A 		59.1
(-1.9)
A 		20.8
(-3)
A 		74.8
(-1.4)
A 		188.2
(1.9)
P 		224.7
(3)
P 		204
avr 21.3
(-3) 		47.4
(-2.3) 		29
(-2.8) 		76.6
(-1.6) 		174.9
(1) 		251.6
(3) 		230
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 20
1 2 3 4 range
A 15.6
(3)
A 		6.6
(-1)
A 		2.1
(-3)
A 		5.1
(-1.7)
A 		14
B 12.1
(1.2)
A 		14.1
(2.8)
A 		14.3
(3)
A 		6.8
(-3)
A 		8
C 10.6
(-2.8)
A 		13.3
(-1.5)
A 		22.3
(3)
A 		10.2
(-3)
A 		12
avr 12.8
(2.9) 		11.3
(1.3) 		12.9
(3) 		7.4
(-3) 		6

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 77
1 2 3 4 5 6 range
A 1.2
(-3)
A 		10.2
(-2.3)
A 		8.5
(-2.4)
A 		21.2
(-1.4)
A 		51
(0.9)
P 		77.9
(3)
P 		77
B 9.2
(-2.8)
A 		18.1
(-2)
A 		6.6
(-3)
A 		18.9
(-2)
A 		68.1
(2.1)
P 		78.3
(3)
P 		72
C 11.5
(-2.5)
A 		18
(-1.9)
A 		5.3
(-3)
A 		15
(-2.2)
A 		60.9
(1.8)
P 		75.2
(3)
P 		70
avr 7.3
(-3) 		15.4
(-2.3) 		6.8
(-3) 		18.4
(-2) 		60
(1.5) 		77.1
(3) 		70
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 192085_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.1231
Sequence Type Exemplar sequence
Representative Public ID B0414.5 NCBI
Target Description B0414.5 /REP_DB=WormBase Gene ID /WP=CE07735 /GEN=cpb-3 /TR=O01835 /GB=AAB57717.1 /SUBMIT=ST.LOUIS /CHR=1 /FEA=Sanger Annotation /DEF=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_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
SNAP00000011712 ENSEMBL cdna:SNAP chromosome:CEL140:I:5797306:5799859:-1 11/11 None
GENEFINDER00000011724 ENSEMBL cdna:GeneFinder chromosome:CEL140:I:5797306:5800437:-1 11/11 None
B0414.5 ENSEMBL cdna:known chromosome:CEL140:I:5796797:5799888:-1 gene:B0414.5 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
chrI:5797305-5799859(-) 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
Pfam IPR000504 EMBL-EBI RNA-binding region RNP-1 (RNA recognition motif) 8.5E-7
Sequence
Target Sequence 
>C. ELEGANS:192085_AT
tccagtgattgtaccatcgtcggcttcgaaagcgtttccaggagcaactactcgtcgttc
gcaagtttcaagcagcttgtcgttgaaaaatggatctaacaattctcaagtcaataattc
gattcctcattttccttcggcaggtttccctatcatcgtcggcgcacctgcacaaacatt
gtcagctctctatggatatattcaaaatggtcaacaactgttgaaaccagccgtttttga
gccaccaatgacaccatcaccaagtgagatcaacaagaatagaagaagcttcacagagtt
ttcgactccgccaacagtcttcttcaattcaactcctgtcatatctccacaaaagagtgt
gtccgacggttctccattgccagcatactacaactcggctgcattcctaactccaccacc
aacatactacggttctccaaaccacccgacatctagcaacatttcgcaacctcagcaacc
atactatggc

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
TCCAGTGATTGTACCATCGTCGGCT 271 589 1701 Antisense
GCGTTTCCAGGAGCAACTACTCGTC 425 289 1732 Antisense
AATAATTCGATTCCTCATTTTCCTT 555 171 1813 Antisense
TGAAACCAGCCGTTTTTGAGCCACC 24 571 1922 Antisense
TTCACAGAGTTTTCGACTCCGCCAA 44 687 1990 Antisense
TCAATTCAACTCCTGTCATATCTCC 97 635 2024 Antisense
AAAGAGTGTGTCCGACGGTTCTCCA 246 121 2052 Antisense
GTTCTCCATTGCCAGCATACTACAA 63 441 2069 Antisense
CACCACCAACATACTACGGTTCTCC 46 203 2114 Antisense
TCTAGCAACATTTCGCAACCTCAGC 562 613 2152 Antisense
GCAACCTCAGCAACCATACTATGGC 171 319 2166 Antisense
Sequence Source Affymetrix Proprietary Database