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[194076_s_at] Pumilio-family RNA binding domains (aka PUM-HD, Pumilio homology domain)

Description Y45F10A.2 /REP_DB=WormBase Gene ID /WP=CE18393 /GEN=puf-3 /TR=Q9U2G4 /GB=CAB63369.1 /SUBMIT=HINXTON /CHR=4 /FEA=Sanger Annotation /DEF=Pumilio-family RNA binding domains (aka PUM-HD, Pumilio homology domain)
Cluster 6grp_total > 88      4grp_total > 33      6grp_cgc > 69      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.
4 125
1 2 3 4 range
A 33.8
(-3)
A 		76.7
(-0.3)
A 		95.8
(0.9)
A 		128.4
(3)
A 		95
B 11.1
(-3)
A 		70.3
(2.6)
A 		74
(3)
A 		60.2
(1.7)
A 		63
C 20.2
(-3)
A 		97.1
(1)
A 		70.3
(-0.4)
A 		136.4
(3)
A 		116
avr 21.7
(-3) 		81.4
(1.1) 		80
(1) 		108.3
(3) 		87

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 2047
1 2 3 4 5 6 range
A 57.3
(-2.9)
A 		13.9
(-3)
A 		54.6
(-2.9)
A 		190.6
(-2.5)
A 		906.6
(-0.4)
P 		2051.4
(3)
P 		2038
B 70.6
(-2.8)
A 		4.6
(-3)
A 		56.3
(-2.8)
A 		175.8
(-2.4)
M 		947.9
(0.4)
P 		1657
(3)
P 		1652
C 26.9
(-3)
A 		15.3
(-3)
A 		114.6
(-2.6)
A 		221.8
(-2.1)
P 		1165.5
(1.8)
P 		1459.6
(3)
P 		1444
avr 51.6
(-2.9) 		11.3
(-3) 		75.2
(-2.8) 		196.1
(-2.4) 		1006.7
(0.5) 		1722.7
(3) 		1711
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 24
1 2 3 4 range
A 12.3
(-3)
A 		16.7
(-0.9)
A 		25
(3)
A 		18.8
(0.1)
A 		13
B 3.5
(-3)
A 		17.4
(3)
A 		17.1
(2.9)
A 		12.8
(1)
A 		14
C 6.7
(-3)
A 		27.9
(3)
A 		24.5
(2)
A 		23
(1.6)
A 		21
avr 7.5
(-3) 		20.7
(2.4) 		22.2
(3) 		18.2
(1.4) 		15

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 616
1 2 3 4 5 6 range
A 10.6
(-2.9)
A 		4.9
(-3)
A 		11.9
(-2.9)
A 		48.3
(-2.5)
A 		273.6
(0.3)
P 		499.5
(3)
P 		495
B 24.6
(-2.8)
A 		1.5
(-3)
A 		13.7
(-2.9)
A 		46.6
(-2.6)
M 		385.1
(0.7)
P 		617.9
(3)
P 		616
C 10
(-2.9)
A 		4.7
(-3)
A 		29.2
(-2.7)
A 		44.6
(-2.5)
P 		377.2
(1.6)
P 		488.6
(3)
P 		484
avr 15.1
(-2.9) 		3.7
(-3) 		18.3
(-2.8) 		46.5
(-2.5) 		345.3
(0.9) 		535.3
(3) 		532
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 194076_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.8802
Sequence Type Exemplar sequence
Representative Public ID Y45F10A.2 NCBI
Target Description Y45F10A.2 /REP_DB=WormBase Gene ID /WP=CE18393 /GEN=puf-3 /TR=Q9U2G4 /GB=CAB63369.1 /SUBMIT=HINXTON /CHR=4 /FEA=Sanger Annotation /DEF=Pumilio-family RNA binding domains (aka PUM-HD, Pumilio homology domain)
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_070205(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_070205 NCBI Caenorhabditis elegans PUF (Pumilio/FBF) domain-containing family member (puf-3) (puf-3) mRNA, complete cds. 11/11 None
SNAP00000021293 ENSEMBL cdna:SNAP chromosome:CEL140:IV:13510487:13515177:-1 11/11 None
GENEFINDER00000021294 ENSEMBL cdna:GeneFinder chromosome:CEL140:IV:13510487:13512114:-1 11/11 None
Y45F10A.2.1 ENSEMBL cdna:known chromosome:CEL140:IV:13510294:13512131:-1 gene:Y45F10A.2 11/11 None
Y45F10A.2.2 ENSEMBL cdna:known chromosome:CEL140:IV:13510301:13512133:-1 gene:Y45F10A.2 11/11 None
Y45F10A.2.3 ENSEMBL cdna:known chromosome:CEL140:IV:13510360:13512137:-1 gene:Y45F10A.2 11/11 None
Annotation Notes
Cross Hybridizing mRNA Matched Probes Nature of Assignment Related Probesets by Grade
NM_171363 1/11 Cross Hyb Matching Probes A 
SNAP00000032059 1/11 Cross Hyb Matching Probes None
GENEFINDER00000032097 1/11 Cross Hyb Matching Probes None
Y73B6BL.38 1/11 Cross Hyb Matching Probes A 
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrIV:13510492-13512120(-) 100.0 100.0
Public Domain and Genome References
Gene Title Pumilio-family RNA binding domains (aka PUM-HD, Pumilio homology domain)
Gene Symbol puf-3
Ensembl Y45F10A.2
Entrez Gene 178320 Entrez gene
SwissProt Q9U2G4 EMBL-EBI
WormBase CE18393 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 CAB63369 Hypothetical protein Y45F10A.2 [Caenorhabditis elegans] ref|NP_502606.1| PUF (Pumilio/FBF) domain-containing family member (puf-3) [Caenorhabditis elegans] 0.0
blast AAN63424 Hypothetical protein Y73B6BL.38 [Caenorhabditis elegans] ref|NP_741425.1| Y73B6BL.38 [Caenorhabditis elegans] 0.0
Protein Domains
Database ID Description E-Value
Pfam IPR001313 EMBL-EBI Pumilio/Puf RNA-binding 9.7E-6
Pfam IPR001313 EMBL-EBI Pumilio/Puf RNA-binding 5.3E-7
Pfam IPR001313 EMBL-EBI Pumilio/Puf RNA-binding 1.6E-6
Pfam IPR001313 EMBL-EBI Pumilio/Puf RNA-binding 9.7E-6
Pfam IPR001313 EMBL-EBI Pumilio/Puf RNA-binding 5.3E-7
Pfam IPR001313 EMBL-EBI Pumilio/Puf RNA-binding 1.6E-6
Sequence
Target Sequence 
>C. ELEGANS:194076_S_AT
tctcatccacgtttgccaggacaaatatgggtgccgtgtcattcaatcgaccgtcgaaac
tttgtcgactgatcaatatgctcagtgctaccagcatcgtgtcattcttcttcgcagttt
gatggctggagtcactcgtaactgcacccagctggcttccaacgagtttgcgaactacgt
ggtacaacacgttatcaagtgtggagatgcgttggctgtctacagagatatcatcattga
gcagtgccttctgcaaaatttgctctcaatgtcacaggagaagtacgctagccacgtggt
cgaagtggcgtttgaatgtgctccatatcgcctcgttgccgagatgatgaacgagatctt
cgaaggatatattccacatccggatacaaatcgtgatgctctcgacattctgctcttcca
tcaatatggaaactacgttgttcagcagatgatccagacttgtgttctcggtcagaatgc
tcgagatcaaaagcaatcggagatgtacggcatgtggctcgagaagattcacggacgagt
gatgcgaaacgcccaccg

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
TCTCATCCACGTTTGCCAGGACAAA 236 613 900 Antisense
ATGGGTGCCGTGTCATTCAATCGAC 97 51 926 Antisense
CAGTGCTACCAGCATCGTGTCATTC 40 209 982 Antisense
GTCATTCTTCTTCGCAGTTTGATGG 328 467 1000 Antisense
GGCTGGAGTCACTCGTAACTGCACC 133 541 1023 Antisense
CTGGCTTCCAACGAGTTTGCGAACT 328 241 1051 Antisense
GTGTGGAGATGCGTTGGCTGTCTAC 561 487 1098 Antisense
GATATCATCATTGAGCAGTGCCTTC 110 427 1126 Antisense
CGTTTGAATGTGCTCCATATCGCCT 550 247 1208 Antisense
CATATCGCCTCGTTGCCGAGATGAT 72 215 1223 Antisense
GACGAGTGATGCGAAACGCCCACCG 384 379 1433 Antisense
Sequence Source Affymetrix Proprietary Database