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[174989_at] pumilo repeats

Description CEK132F7R_rc /REP_DB=TREMBL Accession /GB=D65196 /CHR=X /FEA=Genomic Cluster /DEF=C.elegans cDNA clone yk132f7 : 3prime end, single read.
Cluster 6grp_highest_10_10 > 64      6grp_high1_10_10 > 46      4grp_highest_8_8 > 47      4grp_high_8_8 > 12      6grp_highest_nonorm > 76      6grp_total > 46      4grp_total > 13      6grp_highest_sub > Cu      6grp_cgc > 27      6grp_high1_sub > Cu      6grp_cgc_sub > Cu      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 1266
1 2 3 4 range
A 1836.3
(2.7)
P 		1583.5
(0.3)
P 		1229.7
(-3)
P 		1872.1
(3)
P 		642
B 1655.5
(-0.8)
P 		1418.2
(-1.9)
P 		1185.3
(-3)
P 		2451.4
(3)
P 		1266
C 1580.9
(-1.1)
P 		1522.9
(-1.6)
P 		1359.5
(-3)
P 		2076.9
(3)
P 		717
avr 1690.9
(-0) 		1508.2
(-1.3) 		1258.2
(-3) 		2133.5
(3) 		875

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 847
1 2 3 4 5 6 range
A 1229.3
(3)
P 		1214
(2.8)
P 		876.9
(-1.5)
P 		762.8
(-3)
P 		1014.7
(0.2)
P 		1116.9
(1.6)
P 		467
B 1307.6
(3)
P 		1233.6
(2.2)
P 		1097.7
(0.8)
P 		1013.3
(-0)
P 		725.4
(-3)
P 		1281.5
(2.7)
P 		582
C 1099.9
(-1.1)
P 		1299.4
(0.7)
P 		1023.5
(-1.7)
P 		1041
(-1.6)
P 		872.8
(-3)
P 		1572.4
(3)
P 		700
avr 1212.3
(1.5) 		1249
(2) 		999.4
(-1.3) 		939
(-2.1) 		871
(-3) 		1323.6
(3) 		453
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 395
1 2 3 4 range
A 668.6
(3)
P 		343.7
(-1.9)
P 		321.5
(-2.3)
P 		274
(-3)
P 		395
B 527.9
(3)
P 		350.3
(-1.2)
P 		274.7
(-3)
P 		522.4
(2.9)
P 		253
C 523.3
(3)
P 		437.8
(0)
P 		473.8
(1.3)
P 		350.2
(-3)
P 		173
avr 573.3
(3) 		377.3
(-2.4) 		356.7
(-3) 		382.2
(-2.3) 		217

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 335
1 2 3 4 5 6 range
A 226.6
(-2.1)
P 		431.8
(3)
P 		191
(-3)
P 		193.5
(-2.9)
P 		306.2
(-0.1)
P 		271.9
(-1)
P 		241
B 455
(2.3)
P 		410.6
(1.1)
P 		266.6
(-3)
P 		268.4
(-2.9)
P 		294.7
(-2.2)
P 		477.9
(3)
P 		211
C 407.7
(0.8)
P 		396.5
(0.5)
P 		260.5
(-2)
P 		209.3
(-3)
P 		282.4
(-1.6)
P 		526.4
(3)
P 		317
avr 363.1
(1.1) 		413
(2.6) 		239.4
(-2.5) 		223.7
(-3) 		294.4
(-0.9) 		425.4
(3) 		202
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 174989_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.22248
Sequence Type Exemplar sequence
Representative Public ID CEK132F7R NCBI
Target Description CEK132F7R_rc /REP_DB=TREMBL Accession /GB=D65196 /CHR=X /FEA=Genomic Cluster /DEF=C.elegans cDNA clone yk132f7 : 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_076579(11)
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. 11/11 None
W06B11.2 ENSEMBL cdna:known chromosome:CEL140:X:5841550:5845928:1 gene:W06B11.2 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
chrX:5845590-5845914(+) 100.0 100.0
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:174989_AT
gttgagtatcgcttgaattatgtatacatagctgtaaatctcttgttacaatgtcatttt
tgttcgatattcatattcatggaaagggagggtcttacttgctcttcgttctttttgtgt
cgtttttttggttctgctttttgtcccccttttctcattgatgccctaattcatttcgct
ccagtatcagagattatgaactttaacgactactgttttcctatctctgccattttcagc
acagcatttccaa

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GTTGAGTATCGCTTGAATTATGTAT 692 435 14 Antisense
ATACATAGCTGTAAATCTCTTGTTA 120 25 37 Antisense
GTCATTTTTGTTCGATATTCATATT 24 469 66 Antisense
GAAAGGGAGGGTCTTACTTGCTCTT 636 121 95 Antisense
TTTGTGTCGTTTTTTTGGTTCTGCT 545 665 127 Antisense
CCCTTTTCTCATTGATGCCCTAATT 177 259 160 Antisense
ATTGATGCCCTAATTCATTTCGCTC 341 5 170 Antisense
TAATTCATTTCGCTCCAGTATCAGA 323 633 180 Antisense
TAACGACTACTGTTTTCCTATCTCT 591 637 217 Antisense
CTATCTCTGCCATTTTCAGCACAGC 258 223 234 Antisense
GCCATTTTCAGCACAGCATTTCCAA 580 281 242 Antisense
Sequence Source Affymetrix Proprietary Database