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[191234_at] pumilo repeats

Description W06B11.2 /REP_DB=WormBase Gene ID /WP=CE05044 /GEN=puf-9 /TR=Q23191 /GB=AAA81077.1 /SUBMIT=ST.LOUIS /CHR=X /FEA=Sanger Annotation /DEF=pumilo repeats
Cluster 6grp_highest_10_10 > 53      6grp_high1_10_10 > 25      4grp_highest_8_8 > 30      4grp_high_8_8 > 04      6grp_highest_nonorm > 71      6grp_total > 26      4grp_total > 05      6grp_highest_sub > 02      6grp_cgc > 25      6grp_high1_sub > 01_02      6grp_total_sub > Cup      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 420
1 2 3 4 range
A 331.2
(-0.3)
P 		221.8
(-2.6)
P 		203.9
(-3)
P 		484.1
(3)
P 		280
B 400.7
(-0.5)
P 		243.8
(-3)
P 		323.3
(-1.7)
P 		623.8
(3)
P 		380
C 341.5
(-1.4)
P 		243.1
(-3)
P 		287.4
(-2.3)
P 		603.5
(3)
P 		360
avr 357.8
(-0.8) 		236.2
(-3) 		271.5
(-2.4) 		570.5
(3) 		334

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 465
1 2 3 4 5 6 range
A 426.7
(3)
P 		245.2
(-2.3)
P 		315.1
(-0.3)
P 		222.3
(-3)
P 		358.6
(1)
P 		347
(0.7)
P 		204
B 502.5
(3)
P 		503.8
(3)
P 		360.1
(0.4)
P 		382.8
(0.8)
P 		177.9
(-3)
P 		289
(-1)
P 		326
C 345
(-0.5)
P 		617.3
(3)
P 		152.2
(-3)
P 		444.2
(0.8)
P 		173.2
(-2.7)
P 		271.4
(-1.5)
P 		465
avr 424.7
(2.2) 		455.4
(3) 		275.8
(-1.9) 		349.8
(0.1) 		236.6
(-3) 		302.5
(-1.2) 		219
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 85
1 2 3 4 range
A 120.6
(3)
P 		48.1
(-3)
P 		53.3
(-2.6)
P 		70.9
(-1.1)
P 		73
B 127.8
(2.6)
P 		60.2
(-3)
P 		74.9
(-1.8)
P 		132.9
(3)
P 		73
C 113
(3)
P 		69.9
(-3)
P 		100.2
(1.2)
P 		101.8
(1.4)
P 		43
avr 120.5
(3) 		59.4
(-3) 		76.1
(-1.4) 		101.9
(1.2) 		61

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 150
1 2 3 4 5 6 range
A 78.7
(-0.4)
P 		87.2
(0.6)
P 		68.6
(-1.6)
P 		56.4
(-3)
P 		108.2
(3)
P 		84.5
(0.3)
P 		52
B 174.9
(3)
P 		167.7
(2.6)
P 		87.4
(-2.1)
P 		101.4
(-1.3)
P 		72.3
(-3)
P 		107.8
(-0.9)
P 		103
C 127.9
(0.6)
P 		188.4
(3)
P 		38.7
(-3)
P 		89.3
(-1)
P 		56
(-2.3)
P 		90.8
(-0.9)
P 		150
avr 127.2
(1.5) 		147.8
(3) 		64.9
(-3) 		82.4
(-1.7) 		78.8
(-2) 		94.4
(-0.9) 		83
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 191234_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.16625
Sequence Type Exemplar sequence
Representative Public ID W06B11.2 NCBI
Target Description W06B11.2 /REP_DB=WormBase Gene ID /WP=CE05044 /GEN=puf-9 /TR=Q23191 /GB=AAA81077.1 /SUBMIT=ST.LOUIS /CHR=X /FEA=Sanger Annotation /DEF=pumilo repeats
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_076579(10)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_076579 NCBI Caenorhabditis elegans PUF (Pumilio/FBF) domain-containing family member (puf-9) (puf-9) mRNA, complete cds. 10/11 None
SNAP00000035430 ENSEMBL cdna:SNAP chromosome:CEL140:X:5841575:5844333:1 9/11 None
GENEFINDER00000035434 ENSEMBL cdna:GeneFinder chromosome:CEL140:X:5841575:5844333:1 9/11 None
W06B11.2 ENSEMBL cdna:known chromosome:CEL140:X:5841550:5845928:1 gene:W06B11.2 10/11 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
chrX:5841574-5844760(+) 96.75 100.0
Public Domain and Genome References
Gene Title pumilo repeats
Gene Symbol puf-9
Ensembl W06B11.2
Entrez Gene 180850 Entrez gene
SwissProt Q23191 EMBL-EBI
WormBase CE31253 Wormbase
Functional Annotations
Ortholog
ID Title Organism
CHICKEN:GGA.1780.1.S1_AT similar to pumilio homolog 2; pumilio (Drosphila) homolog 2 gga
YEAST_2:1773003_AT Protein that regulates degradation of specific mRNAs such as COX17, binds almost exclusively to cytoplasmic mRNAs encoding mitochondrial proteins, member of the PUF protein family that contains Pumilio homology domains Sc
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
3730 mRNA 3'-UTR binding inferred from sequence similarity QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast AAA81077 Puf (pumilio/fbf) domain-containing protein 9 [Caenorhabditis elegans] ref|NP_508980.2| PUF (Pumilio/FBF) domain-containing family member (puf-9) [Caenorhabditis elegans] 0.0
blast CAE68810 Hypothetical protein CBG14762 [Caenorhabditis briggsae] 0.0
blast XP_857938 PREDICTED: similar to pumilio homolog 2 isoform 3 [Canis familiaris] 1.0E-113
Protein Domains
Database ID Description E-Value
Pfam IPR001313 EMBL-EBI Pumilio/Puf RNA-binding 4.4E-8
Pfam IPR001313 EMBL-EBI Pumilio/Puf RNA-binding 2.1E-9
Pfam IPR001313 EMBL-EBI Pumilio/Puf RNA-binding 2.6E-8
Pfam IPR001313 EMBL-EBI Pumilio/Puf RNA-binding 2.7E-11
Pfam IPR001313 EMBL-EBI Pumilio/Puf RNA-binding 1.9E-11
Pfam IPR001313 EMBL-EBI Pumilio/Puf RNA-binding 4.8E-12
Pfam IPR001313 EMBL-EBI Pumilio/Puf RNA-binding 7.5E-7
Pfam IPR001313 EMBL-EBI Pumilio/Puf RNA-binding 1.7E-8
Sequence
Target Sequence 
>C. ELEGANS:191234_AT
cgttcatccatacggttgtcgtgttattcaacgtgttctcgaatattgcaatgaagagca
gaagcagccagtgttagacgctcttcagattcatttgaaacaacttgttcttgatcaata
cggaaactatgtcatccaacatgtcattgaacatggaagtcccagcgacaaggaacaaat
cgtgcaagacgtgatttcggatgatttgctcaaattcgctcaacacaaatttgcttcaaa
tgttattgagaaatgtctcacgttcggaggacatgcagaaagaaacctgataattgacaa
agtttgtggagacccgaatgacccatcaccaccactactacaaatgatgaaggatccatt
cgccaactacgttgtccagaagatgcttgacgttgccgatccacaacaccgaaagaagat
cacgctgactatcaagccccacattgcaactctgcgcaagtacaactttggaaagcacat
cctgcgtaagtacatcctgaaactcgagaagtactttgcaaagcaagcgcccgccaactc
ttccaactcatcttccaacgaccaaatctac

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
CGTTCATCCATACGGTTGTCGTGTT 148 247 1509 Antisense
GTCGTGTTATTCAACGTGTTCTCGA 505 471 1526 Antisense
AGCAGCCAGTGTTAGACGCTCTTCA 528 77 1571 Antisense
GTCTCACGTTCGGAGGACATGCAGA 595 467 1763 Antisense
TGTGGAGACCCGAATGACCCATCAC 400 555 1813 Antisense
CATTCGCCAACTACGTTGTCCAGAA 164 217 1865 Antisense
AGAAGATGCTTGACGTTGCCGATCC 356 75 1886 Antisense
AAGATCACGCTGACTATCAAGCCCC 435 155 1924 Antisense
GCAACTCTGCGCAAGTACAACTTTG 74 321 1954 Antisense
GCACATCCTGCGTAAGTACATCCTG 10 317 1983 Antisense
CTCATCTTCCAACGACCAAATCTAC 539 229 2055 Antisense
Sequence Source Affymetrix Proprietary Database