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[175573_s_at] --- /// Pumilio-family RNA binding domains (aka PUM-HD, Pumilio homology domain) (6 domains)

Description CE952_rc /REP_DB=TREMBL Accession /GB=T00952 /CHR=2 /FEA=Genomic Cluster /DEF=wEST01673 Early embryo, Stratagene (cat. no. 937007) Caenorhabditis elegans cDNA clone CEESL04, mRNA sequence.
Cluster 6grp_high1_10_10 > 88      6grp_total > 88      4grp_total > 06      6grp_cgc > 59      6grp_high1_sub > Da      6grp_cgc_sub > Da      6grp_total_sub > Increase      6grp_rule_based > S6      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 260
1 2 3 4 range
A 149.9
(2)
A 		24.1
(-3)
A 		92.9
(-0.3)
A 		174.9
(3)
P 		151
B 132.3
(-1.5)
A 		80.7
(-3)
A 		103
(-2.3)
A 		283.9
(3)
P 		203
C 156
(0.9)
A 		65.3
(-3)
A 		100.3
(-1.5)
A 		205.3
(3)
P 		140
avr 146.1
(0.3) 		56.7
(-3) 		98.7
(-1.5) 		221.4
(3) 		165

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 4509
1 2 3 4 5 6 range
A 124.8
(-2.9)
A 		96.6
(-3)
A 		137.3
(-2.9)
P 		200.4
(-2.8)
P 		2404.9
(1.5)
P 		3179.9
(3)
P 		3083
B 179.8
(-2.9)
M 		181.1
(-2.9)
A 		69.4
(-3)
A 		468.9
(-2.5)
P 		2130.1
(-0.3)
P 		4578.4
(3)
P 		4509
C 89.1
(-3)
P 		138.9
(-2.9)
P 		161.7
(-2.9)
P 		343
(-2.6)
P 		1753.7
(-0.6)
P 		4271
(3)
P 		4182
avr 131.2
(-3) 		138.9
(-3) 		122.8
(-3) 		337.4
(-2.7) 		2096.2
(0) 		4009.8
(3) 		3887
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 55
1 2 3 4 range
A 54.6
(3)
A 		5.2
(-3)
A 		24.3
(-0.7)
A 		25.6
(-0.5)
P 		49
B 42.2
(0.3)
A 		19.9
(-3)
A 		23.9
(-2.4)
A 		60.5
(3)
P 		41
C 51.7
(3)
A 		18.8
(-3)
A 		35
(-0)
A 		34.6
(-0.1)
P 		33
avr 49.5
(3) 		14.6
(-3) 		27.7
(-0.7) 		40.2
(1.4) 		35

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 1690
1 2 3 4 5 6 range
A 23
(-3)
A 		34.4
(-2.9)
A 		29.9
(-2.9)
P 		50.8
(-2.8)
P 		725.7
(2.6)
P 		774.2
(3)
P 		751
B 62.6
(-2.8)
M 		60.3
(-2.8)
A 		16.9
(-3)
A 		124.2
(-2.6)
P 		865.4
(0)
P 		1707.3
(3)
P 		1690
C 33
(-3)
P 		42.4
(-3)
P 		41.2
(-3)
P 		69
(-2.8)
P 		567.5
(-0.7)
P 		1429.7
(3)
P 		1397
avr 39.5
(-3) 		45.7
(-2.9) 		29.3
(-3) 		81.3
(-2.8) 		719.5
(0.2) 		1303.7
(3) 		1274
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 175573_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.20568
Sequence Type Exemplar sequence
Representative Public ID CE952 NCBI
Target Description CE952_rc /REP_DB=TREMBL Accession /GB=T00952 /CHR=2 /FEA=Genomic Cluster /DEF=wEST01673 Early embryo, Stratagene (cat. no. 937007) Caenorhabditis elegans cDNA clone CEESL04, mRNA sequence.
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_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
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
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
chrIV:5489991-5490541(+) 95.45 97.16
chrI:211673-212229(-) 98.58 98.58
chrII:13039694-13040046(-) 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
blast CAE57668 Hypothetical protein CBG00661 [Caenorhabditis briggsae] 1.0E-147
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
Sequence
Target Sequence 
>C. ELEGANS:175573_S_AT
ttcacaaaattctaaccgtaatccagcgtaattcatgtgtaatggtaatcgatagataat
aacccacatttctactcgccccagcaatcacctactgctcctgtattatgcaaatttaca
tatcattattcattatatatacatatagcttcacaatattgccacgtgtacattttccct
gttgtcatctttgtttgtgagttgtaggtcgccaccagaatct

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
TTCACAAAATTCTAACCGTAATCCA 582 681 37 Antisense
AATTCTAACCGTAATCCAGCGTAAT 478 175 44 Antisense
AACCGTAATCCAGCGTAATTCATGT 614 145 50 Antisense
AATCCAGCGTAATTCATGTGTAATG 611 167 56 Antisense
TCATGTGTAATGGTAATCGATAGAT 237 623 69 Antisense
GATAATAACCCACATTTCTACTCGC 136 421 91 Antisense
GCAAATTTACATATCATTATTCATT 690 317 146 Antisense
TTTCCCTGTTGTCATCTTTGTTTGT 543 669 210 Antisense
CCTGTTGTCATCTTTGTTTGTGAGT 159 267 214 Antisense
GTTTGTGAGTTGTAGGTCGCCACCA 15 453 229 Antisense
GAGTTGTAGGTCGCCACCAGAATCT 324 525 235 Antisense
Sequence Source Affymetrix Proprietary Database