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[171989_x_at] pumilio-repeat like domain

Description AV181490_rc /REP_DB=TREMBL Accession /GB=AV181490 /FEA=Transcript Cluster /DEF=Caenorhabditis elegans cDNA clone:yk621a8 : 3prime end, single read.
Cluster 6grp_highest_10_10 > 76      6grp_high1_10_10 > 66      4grp_highest_8_8 > 30      4grp_high_8_8 > 05      6grp_highest_nonorm > 82      6grp_total > 67      4grp_total > 03      6grp_highest_sub > Da      6grp_high1_sub > Da      6grp_total_sub > Increase      6grp_rule_based > S6      4grp_rule_based > L4      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 1978
1 2 3 4 range
A 499.1
(-2.2)
P 		274.7
(-3)
P 		282.6
(-3)
P 		1922.5
(3)
P 		1648
B 576.9
(-2.2)
P 		342
(-3)
P 		340.3
(-3)
P 		2190.2
(3)
P 		1850
C 690.2
(-1.7)
P 		274.3
(-3)
P 		442.2
(-2.5)
P 		2251.8
(3)
P 		1978
avr 588.7
(-2) 		297
(-3) 		355
(-2.8) 		2121.5
(3) 		1825

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 467
1 2 3 4 5 6 range
A 270.4
(-2.8)
P 		298
(-2)
P 		338.3
(-0.8)
P 		263.4
(-3)
P 		368.4
(0)
P 		471.5
(3)
P 		208
B 368.9
(-1.8)
P 		286.4
(-3)
P 		464.4
(-0.4)
P 		380.4
(-1.6)
P 		313.2
(-2.6)
P 		704
(3)
P 		418
C 388.4
(-0.7)
P 		405.3
(-0.4)
P 		259.8
(-2.6)
P 		280
(-2.3)
P 		236.8
(-3)
P 		624.3
(3)
P 		388
avr 342.6
(-2.3) 		329.9
(-2.5) 		354.2
(-2) 		307.9
(-3) 		306.1
(-3) 		599.9
(3) 		294
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 407
1 2 3 4 range
A 181.7
(0.3)
P 		59.6
(-3)
P 		73.9
(-2.6)
P 		281.4
(3)
P 		222
B 184
(-1.4)
P 		84.5
(-2.9)
P 		78.9
(-3)
P 		466.7
(3)
P 		388
C 228.5
(-0)
P 		78.9
(-3)
P 		154.1
(-1.5)
P 		379.7
(3)
P 		301
avr 198.1
(-0.5) 		74.3
(-3) 		102.3
(-2.4) 		375.9
(3) 		302

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 213
1 2 3 4 5 6 range
A 49.8
(-3)
P 		106
(2.2)
P 		73.7
(-0.8)
P 		66.8
(-1.4)
P 		111.2
(2.7)
P 		114.8
(3)
P 		65
B 128.4
(-1.8)
P 		95.3
(-3)
P 		112.8
(-2.4)
P 		100.8
(-2.8)
P 		127.2
(-1.9)
P 		262.5
(3)
P 		167
C 144
(0.4)
P 		123.7
(-0.4)
P 		66.1
(-2.6)
P 		56.3
(-3)
P 		76.6
(-2.2)
P 		209
(3)
P 		153
avr 107.4
(-1.4) 		108.3
(-1.3) 		84.2
(-2.5) 		74.6
(-3) 		105
(-1.5) 		195.4
(3) 		121
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 171989_x_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.27695
Sequence Type Exemplar sequence
Representative Public ID AV181490 NCBI
Target Description AV181490_rc /REP_DB=TREMBL Accession /GB=AV181490 /FEA=Transcript Cluster /DEF=Caenorhabditis elegans cDNA clone:yk621a8 : 3prime end, single read.
Cluster Evidence This cluster is supported by a Transcript Cluster.
Annotation Method Description
Annotation Description This probe set was annotated using the Genome Target Overlap based pipeline to a RefSeq identifier using 1 transcript(s).
Annotation Grade This is a grade B annotation.
Annotation Transcript Cluster (# of Matching Probes) NM_063777
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
GENEFINDER00000015342 ENSEMBL cdna:GeneFinder chromosome:CEL140:II:10100240:10102782:1 None
NM_063777 NCBI Caenorhabditis elegans ZK945.3 (ZK945.3) mRNA, complete cds. A 
SNAP00000015334 ENSEMBL cdna:SNAP chromosome:CEL140:II:10100240:10102782:1 None
ZK945.3 ENSEMBL cdna:known chromosome:CEL140:II:10100221:10102964:1 gene:ZK945.3 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
chrII:10102604-10102799(+) 63.67 63.67
Public Domain and Genome References
Gene Title pumilio-repeat like domain
Ensembl ZK945.3
Entrez Gene 174572 Entrez gene
SwissProt Q09622 EMBL-EBI
WormBase CE01734 Wormbase
Functional Annotations
Ortholog
ID Title Organism
ATH1-121501:257652_AT pumilio/Puf RNA-binding domain-containing protein at
CANINE:1606152_AT similar to D19Bwg1357e protein cfa
CANINE_2:CFA.20109.1.S1_S_AT similar to D19Bwg1357e protein cfa
CANINE_2:CFA.3371.1.S1_AT similar to D19Bwg1357e protein cfa
CANINE_2:CFA.3371.1.S1_S_AT similar to D19Bwg1357e protein cfa
CANINE_2:CFAAFFX.3979.1.S1_AT similar to D19Bwg1357e protein cfa
DROSOPHILA_2:1623956_AT penguin dm
DROSGENOME1:154002_AT penguin dm
CHICKEN:GGA.8109.1.S1_S_AT similar to Protein KIAA0020 gga
HUGENEFL:D13645_AT KIAA0020 hs
HG-U133A:203712_AT KIAA0020 hs
HG-U133_PLUS_2:203712_AT KIAA0020 hs
HG-U133A_2:203712_AT KIAA0020 hs
U133_X3P:G7661865_3P_AT KIAA0020 hs
HG-U95AV2:34765_AT KIAA0020 hs
HG-U133_PLUS_2:242580_AT KIAA0020 hs
HG-U133B:242580_AT KIAA0020 hs
U133_X3P:HS.208019.0.A1_3P_AT KIAA0020 hs
MG-U74AV2:160310_AT DNA segment, Chr 19, Brigham & Women's Genetics 1357 expressed mm
MOE430B:1434173_S_AT DNA segment, Chr 19, Brigham & Women's Genetics 1357 expressed mm
MOUSE430_2:1434173_S_AT DNA segment, Chr 19, Brigham & Women's Genetics 1357 expressed mm
MU11KSUBA:AA220521_AT DNA segment, Chr 19, Brigham & Women's Genetics 1357 expressed mm
MG-U74BV2:107802_AT DNA segment, Chr 19, Brigham & Women's Genetics 1357 expressed mm
MOE430A:1426932_AT DNA segment, Chr 19, Brigham & Women's Genetics 1357 expressed mm
MOUSE430A_2:1426932_AT DNA segment, Chr 19, Brigham & Women's Genetics 1357 expressed mm
MOUSE430_2:1426932_AT DNA segment, Chr 19, Brigham & Women's Genetics 1357 expressed mm
MOE430A:1426931_S_AT DNA segment, Chr 19, Brigham & Women's Genetics 1357 expressed mm
MOUSE430A_2:1426931_S_AT DNA segment, Chr 19, Brigham & Women's Genetics 1357 expressed mm
MOUSE430_2:1426931_S_AT DNA segment, Chr 19, Brigham & Women's Genetics 1357 expressed mm
MU19KSUBB:TC27166_AT MKIAA0020 protein mm
MU19KSUBB:TC32718_AT MKIAA0020 protein mm
MU19KSUBB:TC32718_G_AT MKIAA0020 protein mm
RAE230A:1376408_AT similar to DNA segment, Chr 19, Brigham & Womens Genetics 1357 expressed (predicted) rn
RAT230_2:1376408_AT similar to DNA segment, Chr 19, Brigham & Womens Genetics 1357 expressed (predicted) rn
RAE230B:1385020_AT similar to DNA segment, Chr 19, Brigham & Womens Genetics 1357 expressed (predicted) rn
RAT230_2:1385020_AT similar to DNA segment, Chr 19, Brigham & Womens Genetics 1357 expressed (predicted) rn
YEAST_2:1771126_AT Pumilio-homology domain protein that binds ASH1 mRNA at PUF consensus sequences in the 3' UTR and represses its translation, resulting in proper asymmetric localization of ASH1 mRNA Sc
Gene Ontology
GO Biological Process (view graph)
ID Description Evidence Links
6118 electron transport inferred from electronic annotation QuickGO AmiGO
GO Molecular Function (view graph)
ID Description Evidence Links
3723 RNA binding inferred from electronic annotation QuickGO AmiGO
5489 electron transporter activity inferred from electronic annotation QuickGO AmiGO
5507 copper ion binding inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast CAA88437 Hypothetical protein ZK945.3 [Caenorhabditis elegans] ref|NP_496178.1| ZK945.3 [Caenorhabditis elegans] sp|Q09622|YS83_CAEEL Hypothetical protein ZK945.3 in chromosome II 0.0
blast CAE67820 Hypothetical protein CBG13400 [Caenorhabditis briggsae] 0.0
blast XP_788454 PREDICTED: similar to D19Bwg1357e protein [Strongylocentrotus purpuratus] 5.0E-80
Sequence
Target Sequence 
>C. ELEGANS:171989_X_AT
gacttgcaatcgcggttgccatgttctcttgaaaatgcttcaagttggaggaccgaaagt
tattgnnnnnttgaaggcttcgatcagcagaaaacacttggatggctataactctaaagg
agcttatcttctgaaggctcagctcgacggaaatgtcaagaagtgagaatgcaaggtata
cgaa

BLASTn GenBank NR
Note: "n"'s represent regions that are not probed by the probe sequences.
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GACTTGCAATCGCGGTTGCCATGTT 164 371 22 Antisense
GGTTGCCATGTTCTCTTGAAAATGC 268 507 35 Antisense
GCCATGTTCTCTTGAAAATGCTTCA 341 281 39 Antisense
AAATGCTTCAAGTTGGAGGACCGAA 64 117 54 Antisense
GAAGGCTTCGATCAGCAGAAAACAC 503 333 94 Antisense
AACACTTGGATGGCTATAACTCTAA 10 137 114 Antisense
ATAACTCTAAAGGAGCTTATCTTCT 389 23 129 Antisense
GCTTATCTTCTGAAGGCTCAGCTCG 425 305 143 Antisense
GAAGGCTCAGCTCGACGGAAATGTC 604 331 154 Antisense
GGCTCAGCTCGACGGAAATGTCAAG 473 537 157 Antisense
GAAGTGAGAATGCAAGGTATACGAA 668 333 181 Antisense
Sequence Source Affymetrix Proprietary Database