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[191768_at] pumilio-repeat like domain

Description ZK945.3 /REP_DB=WormBase Gene ID /WP=CE01734 /TR=SW:Q09622 /GB=CAA88437.1 /SUBMIT=HINXTON /CHR=2 /FEA=Sanger Annotation /DEF=pumilio-repeat like domain
Cluster 6grp_highest_10_10 > 75      6grp_high1_10_10 > 56      4grp_highest_8_8 > 30      4grp_high_8_8 > 05      6grp_highest_nonorm > 67      6grp_total > 57      4grp_total > 03      6grp_highest_sub > Cu      6grp_high1_sub > Cu      6grp_total_sub > Cup      4grp_rule_based > L4      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 7177
1 2 3 4 range
A 2776
(-1.8)
P 		1734
(-3)
P 		2006.4
(-2.7)
P 		7057.4
(3)
P 		5323
B 2915.4
(-1.9)
P 		1670.8
(-3)
P 		1800.9
(-2.9)
P 		8618.5
(3)
P 		6948
C 2502.8
(-2.1)
P 		1441.9
(-3)
P 		2117.9
(-2.4)
P 		8156.4
(3)
P 		6715
avr 2731.4
(-1.9) 		1615.6
(-3) 		1975.1
(-2.7) 		7944.1
(3) 		6329

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 1245
1 2 3 4 5 6 range
A 1970.6
(0.8)
P 		1812.9
(-0.5)
P 		1507.7
(-3)
P 		1663.9
(-1.7)
P 		1570
(-2.5)
P 		2245.2
(3)
P 		738
B 1948.1
(0)
P 		1555
(-2.8)
P 		1822
(-0.9)
P 		1727.5
(-1.6)
P 		1529.3
(-3)
P 		2356.3
(3)
P 		827
C 1730.5
(-0.7)
P 		1837.2
(-0.2)
P 		1679.9
(-1)
P 		1978.1
(0.5)
P 		1255.7
(-3)
P 		2501
(3)
P 		1245
avr 1883.1
(-0.2) 		1735
(-1.1) 		1669.9
(-1.6) 		1789.8
(-0.8) 		1451.7
(-3) 		2367.5
(3) 		916
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 1460
1 2 3 4 range
A 1010.8
(2.8)
P 		376.4
(-3)
P 		524.5
(-1.6)
P 		1033.1
(3)
P 		657
B 929.7
(-0.8)
P 		412.7
(-3)
P 		417.3
(-3)
P 		1836.6
(3)
P 		1424
C 828.5
(-0.4)
P 		414.5
(-3)
P 		738.2
(-1)
P 		1375.3
(3)
P 		961
avr 923
(0.1) 		401.2
(-3) 		560
(-2.1) 		1415
(3) 		1014

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 550
1 2 3 4 5 6 range
A 363.3
(-2.3)
P 		644.8
(3)
P 		328.4
(-3)
P 		422
(-1.2)
P 		473.8
(-0.2)
P 		546.6
(1.1)
P 		316
B 677.9
(0.2)
P 		517.6
(-2)
P 		442.4
(-3)
P 		457.5
(-2.8)
P 		621.3
(-0.5)
P 		878.7
(3)
P 		436
C 641.4
(0.3)
P 		560.6
(-0.8)
P 		427.6
(-2.6)
P 		397.8
(-3)
P 		406.3
(-2.9)
P 		837.2
(3)
P 		439
avr 560.9
(-0.3) 		574.3
(-0) 		399.5
(-3) 		425.8
(-2.6) 		500.5
(-1.3) 		754.2
(3) 		355
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 191768_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.3690
Sequence Type Exemplar sequence
Representative Public ID ZK945.3 NCBI
Target Description ZK945.3 /REP_DB=WormBase Gene ID /WP=CE01734 /TR=SW:Q09622 /GB=CAA88437.1 /SUBMIT=HINXTON /CHR=2 /FEA=Sanger Annotation /DEF=pumilio-repeat like domain
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_063777(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_063777 NCBI Caenorhabditis elegans ZK945.3 (ZK945.3) mRNA, complete cds. 11/11 None
SNAP00000015334 ENSEMBL cdna:SNAP chromosome:CEL140:II:10100240:10102782:1 11/11 None
GENEFINDER00000015342 ENSEMBL cdna:GeneFinder chromosome:CEL140:II:10100240:10102782:1 11/11 None
ZK945.3 ENSEMBL cdna:known chromosome:CEL140:II:10100221:10102964:1 gene:ZK945.3 11/11 None
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:10100236-10102779(+) 100.0 100.0
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:191768_AT
tggacagttgtacgccggtattaccgagaacttgtatccttatttggctgctaacttcga
agagcttgttttcgaggccaacaagtcaaaattcgtggctgcatgtctcgaaaccacctc
aagcttcgatttgttcgatcgacaagtcccagcagaagctcgcaagagttgcaaccaagc
gatcgttgaattggcgaagaaggactttgtaccaatggaccaggaaggcttccacattat
tgaacaccaatcgggcaatttcattctcatggcagtcatgcgctgtgatgccgctctaca
agaagatgaacgtttgtcagttgcattggcagaaggacttacgagcaagcagcttggctc
gtgggtg

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
TGGACAGTTGTACGCCGGTATTACC 333 547 1782 Antisense
GTATCCTTATTTGGCTGCTAACTTC 521 455 1815 Antisense
GAAGAGCTTGTTTTCGAGGCCAACA 382 337 1840 Antisense
GTGGCTGCATGTCTCGAAACCACCT 168 491 1876 Antisense
GAAACCACCTCAAGCTTCGATTTGT 381 359 1891 Antisense
GTTCGATCGACAAGTCCCAGCAGAA 698 441 1914 Antisense
GAAGGCTTCCACATTATTGAACACC 500 333 2005 Antisense
AATCGGGCAATTTCATTCTCATGGC 435 169 2030 Antisense
TTCTCATGGCAGTCATGCGCTGTGA 342 689 2045 Antisense
GCTGTGATGCCGCTCTACAAGAAGA 110 295 2063 Antisense
GAGCAAGCAGCTTGGCTCGTGGGTG 367 391 2124 Antisense
Sequence Source Affymetrix Proprietary Database