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[191350_s_at] polyA RNA export protein

Description F10G8.3 /REP_DB=WormBase Gene ID /WP=CE09338 /TR=SW:Q93454 /GB=CAB02280.1 /SUBMIT=HINXTON /CHR=1 /FEA=Sanger Annotation /DEF=polyA RNA export protein
Cluster 6grp_highest_10_10 > 10      6grp_high1_10_10 > 0      4grp_highest_8_8 > 09      4grp_high_8_8 > 61      6grp_highest_nonorm > 73      6grp_total > 03      4grp_total > 58      6grp_cgc > 50      4grp_rule_based > L3      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 313
1 2 3 4 range
A 675.4
(-0.5)
P 		817
(2.3)
P 		852.5
(3)
P 		545.9
(-3)
P 		307
B 663.6
(-2.9)
P 		740.6
(0.4)
P 		803
(3)
P 		660.9
(-3)
P 		142
C 738.7
(0.1)
P 		859
(3)
P 		848.5
(2.7)
P 		607.3
(-3)
P 		252
avr 692.6
(-0.7) 		805.5
(2.2) 		834.7
(3) 		604.7
(-3) 		230

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 163
1 2 3 4 5 6 range
A 636.6
(2.5)
P 		604.5
(1.4)
P 		486.5
(-3)
P 		648.9
(3)
P 		553.8
(-0.5)
P 		520.7
(-1.7)
P 		162
B 572.7
(-0.1)
P 		644.6
(3)
P 		617.1
(1.8)
P 		599.9
(1.1)
P 		535.6
(-1.7)
P 		505.9
(-3)
P 		139
C 649.4
(3)
P 		580.4
(0.3)
P 		611.9
(1.5)
P 		596.8
(1)
P 		583.9
(0.5)
P 		494.3
(-3)
P 		155
avr 619.6
(3) 		609.8
(2.5) 		571.8
(0.5) 		615.2
(2.8) 		557.8
(-0.3) 		507
(-3) 		113
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 216
1 2 3 4 range
A 245.9
(3)
P 		177.4
(0.5)
P 		222.9
(2.2)
P 		79.9
(-3)
P 		166
B 211.6
(3)
P 		182.9
(0.6)
P 		186.1
(0.8)
P 		140.8
(-3)
P 		71
C 244.5
(1.4)
P 		247
(1.5)
P 		295.7
(3)
P 		102.4
(-3)
P 		193
avr 234
(3) 		202.4
(1.5) 		234.9
(3) 		107.7
(-3) 		127

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 135
1 2 3 4 5 6 range
A 117.4
(-2.4)
P 		215
(3)
P 		105.9
(-3)
P 		164.6
(0.2)
P 		167.1
(0.4)
P 		126.8
(-1.9)
P 		109
B 199.3
(1.4)
P 		214.6
(2.7)
P 		149.8
(-3)
P 		158.9
(-2.2)
P 		217.6
(3)
P 		188.7
(0.4)
P 		68
C 240.7
(3)
P 		177.1
(-0.2)
P 		155.7
(-1.2)
P 		120
(-3)
P 		189
(0.4)
P 		165.5
(-0.7)
P 		121
avr 185.8
(1.5) 		202.2
(3) 		137.1
(-3) 		147.8
(-2) 		191.2
(2) 		160.3
(-0.9) 		65
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 191350_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.559
Sequence Type Exemplar sequence
Representative Public ID F10G8.3 NCBI
Target Description F10G8.3 /REP_DB=WormBase Gene ID /WP=CE09338 /TR=SW:Q93454 /GB=CAB02280.1 /SUBMIT=HINXTON /CHR=1 /FEA=Sanger Annotation /DEF=polyA RNA export protein
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_060249(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_060249 NCBI Caenorhabditis elegans Nuclear Pore complex Protein family member (npp-17) (npp-17) mRNA, complete cds. 11/11 None
SNAP00000036093 ENSEMBL cdna:SNAP chromosome:CEL140:I:10034765:10037849:1 11/11 None
GENEFINDER00000036106 ENSEMBL cdna:GeneFinder chromosome:CEL140:I:10034765:10037849:1 11/11 None
F10G8.3.2 ENSEMBL cdna:known chromosome:CEL140:I:10034762:10038178:1 gene:F10G8.3 11/11 None
F10G8.3.1 ENSEMBL cdna:known chromosome:CEL140:I:10034764:10038179:1 gene:F10G8.3 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
chrI:10034695-10037780(+) 100.0 100.0
Public Domain and Genome References
Gene Title polyA RNA export protein
Gene Symbol npp-17
Ensembl F10G8.3
Entrez Gene 172864 Entrez gene
SwissProt Q93454 EMBL-EBI
WormBase CE09338 Wormbase
Functional Annotations
Ortholog
ID Title Organism
ATH1-121501:261896_AT transducin family protein / WD-40 repeat family protein at
ATGENOME1:20492_AT transducin family protein / WD-40 repeat family protein at
CANINE_2:CFA.12299.1.A1_AT similar to RAE1 RNA export 1 homolog cfa
CANINE_2:CFAAFFX.18719.1.S1_AT similar to RAE1 RNA export 1 homolog cfa
CANINE_2:CFAAFFX.18719.1.S1_S_AT similar to RAE1 RNA export 1 homolog cfa
DROSOPHILA_2:1636291_AT dm
DROSGENOME1:154923_AT dm
CHICKEN:GGAAFFX.12629.1.S1_S_AT RAE1 RNA export 1 homolog (S. pombe) gga
HG-U133_PLUS_2:211318_S_AT RAE1 RNA export 1 homolog (S. pombe) hs
HG-U133A:211318_S_AT RAE1 RNA export 1 homolog (S. pombe) hs
HG-U133A_2:211318_S_AT RAE1 RNA export 1 homolog (S. pombe) hs
HG-U133_PLUS_2:201558_AT RAE1 RNA export 1 homolog (S. pombe) hs
HG-FOCUS:201558_AT RAE1 RNA export 1 homolog (S. pombe) hs
HG-U133A:201558_AT RAE1 RNA export 1 homolog (S. pombe) hs
HG-U133A_2:201558_AT RAE1 RNA export 1 homolog (S. pombe) hs
HUGENEFL:U84720_AT RAE1 RNA export 1 homolog (S. pombe) hs
U133_X3P:G4506398_3P_AT RAE1 RNA export 1 homolog (S. pombe) hs
U133_X3P:G2231591_3P_X_AT RAE1 RNA export 1 homolog (S. pombe) hs
U133_X3P:G2231591_3P_A_AT RAE1 RNA export 1 homolog (S. pombe) hs
HG-U95AV2:32757_AT RAE1 RNA export 1 homolog (S. pombe) hs
HG-U95AV2:32758_G_AT RAE1 RNA export 1 homolog (S. pombe) hs
HG-U95B:48245_AT RAE1 RNA export 1 homolog (S. pombe) hs
HU35KSUBB:RC_AA180163_S_AT RAE1 RNA export 1 homolog (S. pombe) hs
HU35KSUBD:RC_N20080_AT RAE1 RNA export 1 homolog (S. pombe) hs
MOUSE430_2:1459822_AT RAE1 RNA export 1 homolog (S. pombe) mm
MOE430B:1459822_AT RAE1 RNA export 1 homolog (S. pombe) mm
MU11KSUBA:AA420161_AT RAE1 RNA export 1 homolog (S. pombe) mm
MU11KSUBB:MSA.8428.0_AT RAE1 RNA export 1 homolog (S. pombe) mm
MG-U74AV2:161455_R_AT RAE1 RNA export 1 homolog (S. pombe) mm
MG-U74AV2:160466_AT RAE1 RNA export 1 homolog (S. pombe) mm
MG-U74BV2:165126_I_AT RAE1 RNA export 1 homolog (S. pombe) mm
MG-U74CV2:169537_AT RAE1 RNA export 1 homolog (S. pombe) mm
MOE430A:1429528_AT RAE1 RNA export 1 homolog (S. pombe) mm
MOUSE430A_2:1429528_AT RAE1 RNA export 1 homolog (S. pombe) mm
MOUSE430_2:1429528_AT RAE1 RNA export 1 homolog (S. pombe) mm
MOE430B:1444256_AT RAE1 RNA export 1 homolog (S. pombe) mm
MOUSE430_2:1444256_AT RAE1 RNA export 1 homolog (S. pombe) mm
MU19KSUBB:TC27593_AT RAE1 RNA export 1 homolog (S. pombe), mRNA (cDNA clone MGC:73449 IMAGE:5718934) mm
RG-U34B:RC_AI029703_AT RAE1 RNA export 1 homolog (S. pombe) (predicted) rn
RG-U34C:RC_AI145539_AT RAE1 RNA export 1 homolog (S. pombe) (predicted) rn
YEAST_2:1777821_AT Component of the nuclear pore complex required for polyadenylated RNA export but not for protein import, homologous to S. pombe Rae1p Sc
Protein Similarities
Method ID Description E-Value
blast CAB02280 Hypothetical protein F10G8.3 [Caenorhabditis elegans] ref|NP_492650.1| Nuclear Pore complex Protein family member (npp-17) [Caenorhabditis elegans] sp|Q93454|NPP17_CAEEL Nucleoporin-17 (Nuclear pore complex protein 17) (CeRAE1) 0.0
blast CAE60216 Hypothetical protein CBG03784 [Caenorhabditis briggsae] 0.0
Protein Domains
Database ID Description E-Value
Pfam IPR001680 EMBL-EBI G-protein beta WD-40 repeat 8.1E-8
Pfam IPR001680 EMBL-EBI G-protein beta WD-40 repeat 7.9E-4
Pfam IPR001680 EMBL-EBI G-protein beta WD-40 repeat 1.7E-8
Pfam IPR001680 EMBL-EBI G-protein beta WD-40 repeat 0.019
Sequence
Target Sequence 
>C. ELEGANS:191350_S_AT
atgcagccgatgtgctatatccgatggcagttgttgcactagctaacaagcatatcaaag
tttataatctggaaaatggaccaacagaagtgaaagatattgaaagtcaattaaagttcc
agatcagatgtatctcaattttcaaggataaatcgaatcaaaatcccgctggattcgctc
taggatctattgaaggtcgagtagctgtacaatacgtggatgttgcaaatccaaaagaca
acttcacattcaaatgtcatcgatcagctgaacttgtgaacggatttcaagaaatttacg
ctgtcaatgatatttgcttccatccacaacacggaactctggtcacaattggttcagatg
gccgttattcaatgtgggacaaggatgcacggacaaagctgaagacatcagaaccacatc
caatgccgttgacatgctgtgatgttcatagttcgggtgctttccttgtctatgcattgg
gctatgattggagtcgaggtcacgaaggaaacactcaaccaggatcga

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
ATGCAGCCGATGTGCTATATCCGAT 458 43 551 Antisense
CGCTGGATTCGCTCTAGGATCTATT 150 255 717 Antisense
ATGATATTTGCTTCCATCCACAACA 280 47 857 Antisense
ACAACACGGAACTCTGGTCACAATT 183 111 876 Antisense
GGTCACAATTGGTTCAGATGGCCGT 561 503 891 Antisense
GATGGCCGTTATTCAATGTGGGACA 655 405 907 Antisense
TGAAGACATCAGAACCACATCCAAT 75 575 950 Antisense
CACATCCAATGCCGTTGACATGCTG 160 197 965 Antisense
GATGTTCATAGTTCGGGTGCTTTCC 575 409 991 Antisense
GCTTTCCTTGTCTATGCATTGGGCT 52 305 1009 Antisense
GAAGGAAACACTCAACCAGGATCGA 75 333 1054 Antisense
Sequence Source Affymetrix Proprietary Database