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[194080_s_at] --- /// Pumilio-family RNA binding domains (aka PUM-HD, Pumilio homology domain) (6 domains)

Description F18A11.1 /REP_DB=WormBase Gene ID /WP=CE09451 /GEN=puf-6 /TR=O01322 /GB=CAB04133.1 /SUBMIT=HINXTON /CHR=2 /FEA=Sanger Annotation /DEF=Pumilio-family RNA binding domains (aka PUM-HD, Pumilio homology domain) (6 domains)
Cluster 6grp_total > 87      4grp_total > 34      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.
4 116
1 2 3 4 range
A 151
(-3)
A 		232
(1.8)
A 		194.6
(-0.4)
A 		252.5
(3)
A 		102
B 145.1
(-3)
A 		171
(-0.6)
M 		177.1
(0)
P 		208.6
(3)
P 		64
C 152.3
(-3)
M 		260.9
(3)
M 		185.8
(-1.1)
P 		225.3
(1)
P 		109
avr 149.5
(-3) 		221.3
(2.4) 		185.8
(-0.3) 		228.8
(3) 		79

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 1416
1 2 3 4 5 6 range
A 145.8
(-3)
A 		165.5
(-2.9)
P 		155.7
(-3)
P 		211.4
(-2.7)
P 		786.3
(-0.3)
P 		1555.5
(3)
P 		1410
B 152
(-2.9)
A 		187.2
(-2.8)
P 		139.1
(-3)
A 		275.9
(-2.4)
P 		805.2
(0.1)
P 		1435.7
(3)
P 		1297
C 155.7
(-3)
M 		178.2
(-2.9)
A 		237.2
(-2.6)
P 		241.6
(-2.5)
P 		772.4
(0.2)
P 		1296.7
(3)
P 		1141
avr 151.2
(-3) 		177
(-2.9) 		177.3
(-2.9) 		243
(-2.6) 		788
(-0) 		1429.3
(3) 		1278
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 38
1 2 3 4 range
A 55
(3)
A 		50.4
(1.5)
A 		50.9
(1.6)
A 		37
(-3)
A 		18
B 46.3
(3)
A 		42.2
(-1.6)
M 		41
(-3)
P 		44.5
(1)
P 		5
C 50.4
(-1)
M 		75
(3)
M 		64.8
(1.3)
P 		38
(-3)
P 		37
avr 50.6
(1) 		55.9
(3) 		52.2
(1.6) 		39.8
(-3) 		16

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 509
1 2 3 4 5 6 range
A 26.9
(-3)
A 		58.9
(-2.5)
P 		33.9
(-2.9)
P 		53.6
(-2.5)
P 		237.3
(0.6)
P 		378.7
(3)
P 		352
B 52.9
(-2.8)
A 		62.3
(-2.7)
P 		33.8
(-3)
A 		73.1
(-2.5)
P 		327.1
(0.5)
P 		535.4
(3)
P 		502
C 57.7
(-2.9)
M 		54.4
(-2.9)
A 		60.4
(-2.8)
P 		48.6
(-3)
P 		249.9
(0.1)
P 		434.1
(3)
P 		386
avr 45.8
(-3) 		58.5
(-2.8) 		42.7
(-3) 		58.4
(-2.8) 		271.4
(0.4) 		449.4
(3) 		407
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 194080_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.3790
Sequence Type Exemplar sequence
Representative Public ID F18A11.1 NCBI
Target Description F18A11.1 /REP_DB=WormBase Gene ID /WP=CE09451 /GEN=puf-6 /TR=O01322 /GB=CAB04133.1 /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_058293(11), NM_064372(11), NM_068419(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_058293 NCBI Caenorhabditis elegans PUF (Pumilio/FBF) domain-containing family member (puf-10) (puf-10) mRNA, complete cds. 11/11 None
NM_064372 NCBI Caenorhabditis elegans PUF (Pumilio/FBF) domain-containing family member (puf-6) (puf-6) mRNA, complete cds. 11/11 None
NM_068419 NCBI Caenorhabditis elegans PUF (Pumilio/FBF) domain-containing family member (puf-7) (puf-7) mRNA, complete cds. 11/11 None
SNAP00000016208 ENSEMBL cdna:SNAP chromosome:CEL140:I:212256:215491:-1 11/11 None
GENEFINDER00000016214 ENSEMBL cdna:GeneFinder chromosome:CEL140:I:212256:214005:-1 11/11 None
SNAP00000029956 ENSEMBL cdna:SNAP chromosome:CEL140:II:13040076:13043270:-1 11/11 None
GENEFINDER00000029959 ENSEMBL cdna:GeneFinder chromosome:CEL140:II:13040076:13043306:-1 11/11 None
SNAP00000012461 ENSEMBL cdna:SNAP chromosome:CEL140:IV:5486771:5489959:1 11/11 None
GENEFINDER00000012469 ENSEMBL cdna:GeneFinder chromosome:CEL140:IV:5486735:5489959:1 11/11 None
Y48G1BL.3 ENSEMBL cdna:known chromosome:CEL140:I:211907:214050:-1 gene:Y48G1BL.3 11/11 A 
F18A11.1 ENSEMBL cdna:known chromosome:CEL140:II:13039688:13043341:-1 gene:F18A11.1 11/11 A 
B0273.2 ENSEMBL cdna:known chromosome:CEL140:IV:5486680:5490318:1 gene:B0273.2 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
chrIV:5486740-5489965(+) 98.49 98.49
chrI:212255-215491(-) 98.15 98.42
chrII:13040072-13043303(-) 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-7
puf-6
Ensembl Y48G1BL.3
F18A11.1
B0273.2
Entrez Gene 174947 Entrez gene
177332 Entrez gene
SwissProt O44169 EMBL-EBI
O01322 EMBL-EBI
WormBase CE16788 Wormbase
CE09451 Wormbase
Functional Annotations
Gene Ontology
GO Biological Process (view graph)
ID Description Evidence Links
16478 negative regulation of translation inferred from sequence similarity QuickGO AmiGO
6402 mRNA catabolism inferred from sequence similarity QuickGO AmiGO
GO Cellular Component (view graph)
ID Description Evidence Links
5737 cytoplasm inferred from sequence similarity QuickGO AmiGO
GO Molecular Function (view graph)
ID Description Evidence Links
3723 RNA binding inferred from electronic annotation QuickGO AmiGO
3723 RNA binding inferred from sequence similarity QuickGO AmiGO
3730 mRNA 3'-UTR binding inferred from sequence similarity QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast CAB04133 Hypothetical protein F18A11.1 [Caenorhabditis elegans] ref|NP_496773.1| PUF (Pumilio/FBF) domain-containing family member (puf-6) [Caenorhabditis elegans] 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] 0.0
Protein Domains
Database ID Description E-Value
Pfam IPR001313 EMBL-EBI Pumilio/Puf RNA-binding 3.1E-6
Pfam IPR001313 EMBL-EBI Pumilio/Puf RNA-binding 3.8E-7
Pfam IPR001313 EMBL-EBI Pumilio/Puf RNA-binding 3.1E-6
Pfam IPR001313 EMBL-EBI Pumilio/Puf RNA-binding 3.8E-7
Sequence
Target Sequence 
>C. ELEGANS:194080_S_AT
gttgcattctctgatgacgtgtatcgtccgcaactgctaccggctgtcttccaacgagtt
cgccaactacgtcatccaatacgtcatcaaatcgtcgggcatcatggaaatgtacagaga
cactatcatcgataaatgcctgctccgtaacttgctctcaatgtcacaggacaagtacgc
gtcgcacgtcatcgagggagcgttcttgtttgcaccgcccgcgttgcttcacgagatgat
ggaggagattttcagtggatatgtgaaggatgtcgagttgaatcgtgatgcgttggatat
tcttctgttccatcagtatggcaactatgtcgtccagcaaatgatttcgatttgcaccgc
cgctttaattggcaaagaagaacgtcaacttccaccagctattctgcttctctactctgg
atggtacgagaaaatgaagcagcgtgtgctccaacacgcctcccgtctcgagcgtttctc
atctggaaagaagattatcgattcggtgatgaggcatggagtccctactgctgcagcaat
caatgcacaagctgcaccatcattaatggaattgaccgcccagtttgac

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GTTGCATTCTCTGATGACGTGTATC 266 439 852 Antisense
TGTCTTCCAACGAGTTCGCCAACTA 105 505 896 Antisense
CGCCAACTACGTCATCCAATACGTC 82 259 912 Antisense
CGATAAATGCCTGCTCCGTAACTTG 312 249 981 Antisense
TCGAGGGAGCGTTCTTGTTTGCACC 370 601 1043 Antisense
CCCGCGTTGCTTCACGAGATGATGG 677 259 1069 Antisense
TGATGCGTTGGATATTCTTCTGTTC 56 567 1137 Antisense
AAGCAGCGTGTGCTCCAACACGCCT 414 151 1288 Antisense
TCTCGAGCGTTTCTCATCTGGAAAG 633 611 1317 Antisense
TGATGAGGCATGGAGTCCCTACTGC 196 567 1358 Antisense
AATGGAATTGACCGCCCAGTTTGAC 673 161 1416 Antisense
Sequence Source Affymetrix Proprietary Database