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[194176_x_at]

Description AV177573_rc /REP_DB=TREMBL Accession /5_PRIME_EXT_ID=Y48G1BL.E /5_PRIME_EXT_DB=WormBase Gene ID /GB=AV177573 /WB_GENE_ID=Y48G1BL.E /WP=CE22182 /CHR=1 /FEA=Genomic Cluster /DEF=locus:puf-10 (ST.LOUIS) protein_id:AAF60691.1; Caenorhabditis elegans cDNA clone:yk530e8 : 3prime end, single read.
Cluster 6grp_highest_10_10 > 87      6grp_high1_10_10 > 88      4grp_high_8_8 > 13      6grp_highest_nonorm > 99      6grp_total > 88      4grp_total > 11      6grp_highest_sub > Da      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.
4 209
1 2 3 4 range
A 246.8
(-3)
P 		256.2
(-2.6)
P 		320.8
(0.3)
P 		379.6
(3)
P 		133
B 308.7
(0.9)
P 		342.4
(3)
P 		245.8
(-3)
P 		288.6
(-0.3)
P 		97
C 313.9
(-1.1)
P 		260.8
(-2.6)
M 		246.8
(-3)
P 		454.8
(3)
P 		208
avr 289.8
(-1.9) 		286.5
(-2.1) 		271.1
(-3) 		374.3
(3) 		103

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 3276
1 2 3 4 5 6 range
A 291.8
(-3)
P 		307.4
(-3)
P 		290.8
(-3)
P 		447.1
(-2.7)
P 		1603.8
(-0.5)
P 		3467.2
(3)
P 		3176
B 280
(-3)
P 		274.2
(-3)
P 		280.1
(-3)
P 		388.1
(-2.7)
P 		1347.8
(-0.5)
P 		2802.5
(3)
P 		2528
C 253.9
(-2.9)
P 		191.4
(-3)
P 		332.3
(-2.7)
P 		348.3
(-2.7)
P 		1488.4
(-0.2)
P 		3014.3
(3)
P 		2823
avr 275.2
(-3) 		257.7
(-3) 		301.1
(-2.9) 		394.5
(-2.7) 		1480
(-0.4) 		3094.7
(3) 		2837
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 48
1 2 3 4 range
A 89.9
(3)
P 		55.6
(-3)
P 		83.9
(2)
P 		55.6
(-3)
P 		34
B 98.5
(3)
P 		84.6
(1)
P 		56.9
(-3)
P 		61.5
(-2.3)
P 		42
C 103.9
(3)
P 		75
(-3)
M 		86
(-0.7)
P 		76.7
(-2.6)
P 		29
avr 97.4
(3) 		71.7
(-1.7) 		75.6
(-1) 		64.6
(-3) 		33

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 991
1 2 3 4 5 6 range
A 53.8
(-3)
P 		109.3
(-2.6)
P 		63.3
(-2.9)
P 		113.4
(-2.5)
P 		484
(0.3)
P 		844.2
(3)
P 		790
B 97.4
(-2.8)
P 		91.3
(-2.9)
P 		68
(-3)
P 		102.8
(-2.8)
P 		547.6
(-0.1)
P 		1045.1
(3)
P 		977
C 94.1
(-2.8)
P 		58.4
(-3)
P 		84.6
(-2.8)
P 		70
(-2.9)
P 		481.6
(-0.3)
P 		1009.1
(3)
P 		951
avr 81.8
(-2.9) 		86.3
(-2.9) 		72
(-3) 		95.4
(-2.8) 		504.4
(-0.1) 		966.1
(3) 		894
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 194176_x_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.23167
Sequence Type Exemplar sequence
Representative Public ID AV177573 NCBI
Target Description AV177573_rc /REP_DB=TREMBL Accession /5_PRIME_EXT_ID=Y48G1BL.E /5_PRIME_EXT_DB=WormBase Gene ID /GB=AV177573 /WB_GENE_ID=Y48G1BL.E /WP=CE22182 /CHR=1 /FEA=Genomic Cluster /DEF=locus:puf-10 (ST.LOUIS) protein_id:AAF60691.1; Caenorhabditis elegans cDNA clone:yk530e8 : 3prime end, single read.
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(10), NM_068419(9)
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. 10/11 A 
NM_068419 NCBI Caenorhabditis elegans PUF (Pumilio/FBF) domain-containing family member (puf-7) (puf-7) mRNA, complete cds. 9/11 A 
Y48G1BL.3 ENSEMBL cdna:known chromosome:CEL140:I:211907:214050:-1 gene:Y48G1BL.3 10/11 A 
B0273.2 ENSEMBL cdna:known chromosome:CEL140:IV:5486680:5490318:1 gene:B0273.2 9/11 A 
Annotation Notes
Cross Hybridizing mRNA Matched Probes Nature of Assignment Related Probesets by Grade
NM_064372 7/11 Cross Hyb Matching Probes A 
SNAP00000016208 4/11 Cross Hyb Matching Probes None
GENEFINDER00000016214 4/11 Cross Hyb Matching Probes None
SNAP00000029956 3/11 Cross Hyb Matching Probes None
GENEFINDER00000029959 3/11 Cross Hyb Matching Probes None
SNAP00000012461 4/11 Cross Hyb Matching Probes None
GENEFINDER00000012469 4/11 Cross Hyb Matching Probes None
F18A11.1 7/11 Cross Hyb Matching Probes A 
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrIV:5486739-5490238(+) 98.21 98.38
chrII:13039799-13043304(-) 97.34 97.69
chrI:211980-215492(-) 100.0 100.0
Public Domain and Genome References
Gene Title
Gene Symbol puf-7
Ensembl Y48G1BL.3
B0273.2
Entrez Gene 177332 Entrez gene
SwissProt O44169 EMBL-EBI
WormBase CE16788 Wormbase
Functional Annotations
Gene Ontology
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
Protein Similarities
Method ID Description E-Value
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 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 CAE57668 Hypothetical protein CBG00661 [Caenorhabditis briggsae] 1.0E-147
blast NP_490694 PUF (Pumilio/FBF) domain-containing family member (puf-10) [Caenorhabditis elegans] 1.0E-139
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-138
Protein Domains
Database ID Description E-Value
Pfam IPR001313 EMBL-EBI Pumilio/Puf RNA-binding 3.1E-6
Sequence
Target Sequence 
>C. ELEGANS:194176_X_AT
gatattcttctgttccaccagtatggcaactatgtcgttcagcaaatgatttcgatttgc
accgccgctttgattggcacaggagaacgtcaacttccaccagctattctgcttctctac
tctggatggtacgagaaaatgaagcagcgtgtgctccaacacgcctcccgtctcgagcgt
ttctcatctggaaagaagattatcgattcggtgatgaggcatggagtccctactgctgca
gcaatcaatgcacaagctgcaccatcattaatggaattgaccgcccagtttgacgcaatg
ttcccctcgttcctggctcgttgagcatcttcgacaattatagatttatagccccagcgt
tttactcattttttttcacaaaattctaaccgtaatccagcgtaattcatgtgtaatggt
aatcgatagataataacccacatttctactcgccccagcaatcacgtactgttcctgtat
tatgcaaatttacatatcattattcattatatatacatatagcttcaccatattgccacg
tgtacattttccct

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GATATTCTTCTGTTCCACCAGTATG 212 427 1145 Antisense
ACCGCCGCTTTGATTGGCACAGGAG 524 87 1205 Antisense
CTGCTTCTCTACTCTGGATGGTACG 280 237 1253 Antisense
AAGCAGCGTGTGCTCCAACACGCCT 415 151 1286 Antisense
TGATGAGGCATGGAGTCCCTACTGC 197 567 1356 Antisense
TCCTGGCTCGTTGAGCATCTTCGAC 49 595 1455 Antisense
TAGATTTATAGCCCCAGCGTTTTAC 329 653 1485 Antisense
GATAATAACCCACATTTCTACTCGC 137 421 1573 Antisense
CCCCAGCAATCACGTACTGTTCCTG 511 259 1597 Antisense
CACGTACTGTTCCTGTATTATGCAA 619 199 1607 Antisense
ATATTGCCACGTGTACATTTTCCCT 667 17 1674 Antisense
Sequence Source Affymetrix Proprietary Database