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[194082_s_at] Pumilio-family RNA binding domains (aka PUM-HD, Pumilio homology domain) (6 domains)

Description F54C9.8 /REP_DB=WormBase Gene ID /WP=CE02258 /GEN=puf-5 /TR=Q20757 /GB=CAA90254.1 /SUBMIT=HINXTON /CHR=2 /FEA=Sanger Annotation /DEF=Pumilio-family RNA binding domains (aka PUM-HD, Pumilio homology domain) (6 domains)
Cluster 6grp_total > 88      4grp_total > 0      6grp_cgc > 59      6grp_cgc_sub > Da      6grp_total_sub > Increase      6grp_rule_based > S6      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 91
1 2 3 4 range
A 113
(2)
A 		38
(-3)
A 		67.5
(-1)
A 		128.7
(3)
P 		91
B 63
(-3)
A 		75
(-1.5)
A 		105.5
(2.5)
M 		109.5
(3)
P 		47
C 90.7
(-2.5)
P 		89.2
(-3)
A 		101.2
(0.8)
A 		108
(3)
A 		19
avr 88.9
(-0.3) 		67.4
(-3) 		91.4
(0) 		115.4
(3) 		48

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 4271
1 2 3 4 5 6 range
A 45.5
(-3)
A 		56.8
(-3)
A 		54.6
(-3)
A 		238.7
(-2.7)
P 		2340.2
(0.2)
P 		4311.2
(3)
P 		4266
B 94.9
(-2.9)
A 		40.4
(-3)
A 		101.1
(-2.9)
M 		209.2
(-2.8)
P 		2236.1
(0.2)
P 		4190.4
(3)
P 		4150
C 68.8
(-3)
A 		86.3
(-3)
A 		68.8
(-3)
A 		161.1
(-2.9)
P 		2344.4
(0.5)
P 		3991.1
(3)
P 		3922
avr 69.7
(-3) 		61.2
(-3) 		74.8
(-3) 		203
(-2.8) 		2306.9
(0.3) 		4164.2
(3) 		4103
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 33
1 2 3 4 range
A 41.2
(3)
A 		8.2
(-3)
A 		17.7
(-1.3)
A 		18.8
(-1.1)
P 		33
B 20.1
(-1.4)
A 		18.5
(-3)
A 		24.4
(3)
M 		23.3
(1.9)
P 		6
C 30
(1.1)
P 		25.7
(-0.4)
A 		35.3
(3)
A 		18.2
(-3)
A 		17
avr 30.4
(3) 		17.5
(-3) 		25.8
(0.9) 		20.1
(-1.8) 		13

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 1554
1 2 3 4 5 6 range
A 8.4
(-3)
A 		20.2
(-2.9)
A 		11.9
(-3)
A 		60.5
(-2.7)
P 		706.2
(1)
P 		1049.6
(3)
P 		1041
B 33
(-2.9)
A 		13.5
(-3)
A 		24.5
(-3)
M 		55.4
(-2.8)
P 		908.5
(0.5)
P 		1562.6
(3)
P 		1549
C 25.5
(-3)
A 		26.3
(-3)
A 		17.5
(-3)
A 		32.4
(-2.9)
P 		758.6
(0.4)
P 		1336.1
(3)
P 		1319
avr 22.3
(-3) 		20
(-3) 		18
(-3) 		49.4
(-2.9) 		791.1
(0.6) 		1316.1
(3) 		1298
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 194082_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.4008
Sequence Type Exemplar sequence
Representative Public ID F54C9.8 NCBI
Target Description F54C9.8 /REP_DB=WormBase Gene ID /WP=CE02258 /GEN=puf-5 /TR=Q20757 /GB=CAA90254.1 /SUBMIT=HINXTON /CHR=2 /FEA=Sanger Annotation /DEF=Pumilio-family RNA binding domains (aka PUM-HD, Pumilio homology domain) (6 domains)
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_063413(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_063413 NCBI Caenorhabditis elegans PUF (Pumilio/FBF) domain-containing family member (puf-5) (puf-5) mRNA, complete cds. 11/11 None
SNAP00000013424 ENSEMBL cdna:SNAP chromosome:CEL140:II:8575499:8577338:1 11/11 None
GENEFINDER00000013443 ENSEMBL cdna:GeneFinder chromosome:CEL140:II:8575499:8577338:1 11/11 None
F54C9.8 ENSEMBL cdna:known chromosome:CEL140:II:8575463:8577644:1 gene:F54C9.8 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
chrII:8575495-8577335(+) 100.0 100.0
Public Domain and Genome References
Gene Title Pumilio-family RNA binding domains (aka PUM-HD, Pumilio homology domain) (6 domains)
Gene Symbol puf-5
Ensembl F54C9.8
Entrez Gene 174373 Entrez gene
SwissProt Q20757 EMBL-EBI
WormBase CE02258 Wormbase
Functional Annotations
Gene Ontology
GO Molecular Function (view graph)
ID Description Evidence Links
3723 RNA binding inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast CAA90254 Hypothetical protein F54C9.8 [Caenorhabditis elegans] ref|NP_495814.1| PUF (Pumilio/FBF) domain-containing family member (puf-5) [Caenorhabditis elegans] 0.0
blast CAE57668 Hypothetical protein CBG00661 [Caenorhabditis briggsae] 0.0
blast AAB88353 Puf (pumilio/fbf) domain-containing protein 7 [Caenorhabditis elegans] ref|NP_500820.1| PUF (Pumilio/FBF) domain-containing family member (puf-7) [Caenorhabditis elegans] 1.0E-144
Sequence
Target Sequence 
>C. ELEGANS:194082_S_AT
acatcagtggcacgcaactgcttccgactttcatcgaacgagttcgctaactacgtcgtt
caatacgtcatcaagtcctctggagtcatggaaatgtaccgtgatacaatcatcgaaaaa
tgtcttctccgtaacattctatcgatgtcgcaagacaagtatgcttcccatgttgtggaa
ggagcttttctctttgctccacctctcttgctctcagagatgatggacgaaatcttcgat
ggatatgtgaaggatcaggagacgaaccgtgatgctctggacatcttgttgttccatcaa
tacgggaactatgtcgtccaacagatgatttccatctgcatttctgcacttctcggaaaa
gaggaacgtaagatggtggcatcggaaatgcgcctctatgccaaatggttcgatcggatc
aagaatcgtgtcaaccgtcattccggccgccttgagcgtttttcctctggaaagaaaata
atcgagtcgctccagaagctcaatgtgccaatgacgatgacgaatgagccaatgccatac
tgggctatgccaactccactcatggacatcagtgcccatttcatgaac

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
ACATCAGTGGCACGCAACTGCTTCC 92 105 1048 Antisense
CTGCTTCCGACTTTCATCGAACGAG 702 237 1065 Antisense
ATACGTCATCAAGTCCTCTGGAGTC 659 21 1110 Antisense
GTCTTCTCCGTAACATTCTATCGAT 152 469 1169 Antisense
GATGATTTCCATCTGCATTTCTGCA 617 409 1371 Antisense
AATGCGCCTCTATGCCAAATGGTTC 484 165 1434 Antisense
AAGAATCGTGTCAACCGTCATTCCG 38 153 1468 Antisense
GTCGCTCCAGAAGCTCAATGTGCCA 404 475 1533 Antisense
GCCAATGCCATACTGGGCTATGCCA 507 277 1575 Antisense
TATGCCAACTCCACTCATGGACATC 537 657 1593 Antisense
GGACATCAGTGCCCATTTCATGAAC 41 527 1611 Antisense
Sequence Source Affymetrix Proprietary Database