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[192771_at] WD domain, G-beta repeat (2 domains)

Description Y43F4B.4 /REP_DB=WormBase Gene ID /WP=CE16629 /TR=O45933 /GB=CAA16333.1 /SUBMIT=HINXTON /CHR=3 /FEA=Sanger Annotation /DEF=WD domain, G-beta repeat (2 domains)
Cluster 6grp_highest_10_10 > 59      6grp_high1_10_10 > 94      4grp_highest_8_8 > 12      4grp_high_8_8 > 31      6grp_highest_nonorm > 97      6grp_total > 85      4grp_total > 32      6grp_highest_sub > In      6grp_cgc > 67      6grp_high1_sub > In      6grp_cgc_sub > In      4grp_rule_based > L3      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 317
1 2 3 4 range
A 752.4
(-2.7)
P 		734.9
(-3)
P 		1050.6
(3)
P 		1020.8
(2.4)
P 		316
B 867
(-3)
P 		978.2
(0.6)
P 		1034.2
(2.4)
P 		1051.8
(3)
P 		185
C 800.7
(-3)
P 		1049.8
(3)
P 		1045
(2.9)
P 		1043.9
(2.9)
P 		249
avr 806.7
(-3) 		921
(-0.1) 		1043.3
(3) 		1038.8
(2.9) 		237

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 925
1 2 3 4 5 6 range
A 508.3
(-3)
P 		789.6
(-0.7)
P 		875.3
(0.1)
P 		1026
(1.3)
P 		1134
(2.2)
P 		1229.9
(3)
P 		722
B 566.1
(-3)
P 		810.2
(-1.1)
P 		730
(-1.7)
P 		1104.3
(1.2)
P 		1219.7
(2.1)
P 		1329.9
(3)
P 		764
C 652.4
(-3)
P 		736.2
(-2.4)
P 		748.6
(-2.3)
P 		1337.2
(2.3)
P 		982.2
(-0.5)
P 		1433.2
(3)
P 		781
avr 575.6
(-3) 		778.7
(-1.4) 		784.6
(-1.3) 		1155.8
(1.6) 		1112
(1.3) 		1331
(3) 		755
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 215
1 2 3 4 range
A 273.9
(3)
P 		159.5
(-2.5)
P 		274.7
(3)
P 		149.4
(-3)
P 		125
B 276.5
(3)
P 		241.6
(-1)
P 		239.7
(-1.2)
P 		224.1
(-3)
P 		52
C 265.1
(-0.2)
P 		301.8
(1)
P 		364.2
(3)
P 		176
(-3)
P 		188
avr 271.8
(1.8) 		234.3
(-0.2) 		292.9
(3) 		183.2
(-3) 		110

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 402
1 2 3 4 5 6 range
A 93.7
(-3)
P 		280.8
(1.5)
P 		190.6
(-0.7)
P 		260.2
(1)
P 		342.2
(3)
P 		299.4
(2)
P 		249
B 197
(-2.6)
P 		269.7
(-1.3)
P 		177.3
(-3)
P 		292.5
(-0.8)
P 		495.6
(3)
P 		495.9
(3)
P 		319
C 241.8
(-1.9)
P 		224.6
(-2.3)
P 		190.5
(-3)
P 		268.9
(-1.4)
P 		317.8
(-0.4)
P 		479.8
(3)
P 		289
avr 177.5
(-3) 		258.4
(-1) 		186.1
(-2.8) 		273.9
(-0.7) 		385.2
(2) 		425
(3) 		248
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 192771_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.7502
Sequence Type Exemplar sequence
Representative Public ID Y43F4B.4 NCBI
Target Description Y43F4B.4 /REP_DB=WormBase Gene ID /WP=CE16629 /TR=O45933 /GB=CAA16333.1 /SUBMIT=HINXTON /CHR=3 /FEA=Sanger Annotation /DEF=WD domain, G-beta repeat (2 domains)
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_067339(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_067339 NCBI Caenorhabditis elegans Nuclear Pore complex Protein family member (npp-18) (npp-18) mRNA, complete cds. 11/11 None
SNAP00000007799 ENSEMBL cdna:SNAP chromosome:CEL140:III:13296373:13298302:1 11/11 None
GENEFINDER00000007809 ENSEMBL cdna:GeneFinder chromosome:CEL140:III:13296373:13298302:1 11/11 None
Y43F4B.4 ENSEMBL cdna:known chromosome:CEL140:III:13296368:13298453:1 gene:Y43F4B.4 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
chrIII:13296368-13298298(+) 100.0 100.0
Public Domain and Genome References
Gene Title WD domain, G-beta repeat (2 domains)
Gene Symbol npp-18
Ensembl Y43F4B.4
Entrez Gene 176748 Entrez gene
SwissProt O45933 EMBL-EBI
WormBase CE16629 Wormbase
Functional Annotations
Ortholog
ID Title Organism
CANINE_2:CFA.18120.1.S1_S_AT similar to Nucleoporin SEH1-like (SEC13-like protein) cfa
CANINE_2:CFAAFFX.28817.1.S1_S_AT similar to Nucleoporin SEH1-like (SEC13-like protein) cfa
CHICKEN:GGAAFFX.24299.1.S1_AT similar to Nucleoporin SEH1 (SEC13-like protein) gga
HG-U133_PLUS_2:221931_S_AT SEH1-like (S. cerevisiae) hs
HG-U133A_2:221931_S_AT SEH1-like (S. cerevisiae) hs
HG-U133A:221931_S_AT SEH1-like (S. cerevisiae) hs
HU35KSUBA:HUM_ALU_AT SEH1-like (S. cerevisiae) hs
HU35KSUBB:HUM_ALU_AT SEH1-like (S. cerevisiae) hs
HU35KSUBC:HUM_ALU_AT SEH1-like (S. cerevisiae) hs
HU35KSUBD:HUM_ALU_AT SEH1-like (S. cerevisiae) hs
HUGENEFL:HUM_ALU_AT SEH1-like (S. cerevisiae) hs
HC-G110:HUM_ALU_AT SEH1-like (S. cerevisiae) hs
HU35KSUBA:RC_AA398109_AT SEH1-like (S. cerevisiae) hs
HU35KSUBC:RC_AA443918_AT SEH1-like (S. cerevisiae) hs
U133_X3P:HS.301048.1.A1_3P_S_AT SEH1-like (S. cerevisiae) hs
U133_X3P:HS.301048.0.S1_3P_S_AT SEH1-like (S. cerevisiae) hs
HG-U133B:223225_S_AT SEH1-like (S. cerevisiae) hs
HG-U133_PLUS_2:223225_S_AT SEH1-like (S. cerevisiae) hs
HG-U95C:62547_AT SEH1-like (S. cerevisiae) hs
HG-U95C:63808_AT SEH1-like (S. cerevisiae) hs
HU35KSUBD:RC_AA598420_AT SEH1-like (S. cerevisiae) hs
YEAST_2:1774765_AT Nuclear pore protein that is part of the evolutionarily conserved Nup84p complex (Nup84p, Nup85p, Nup120p, Nup145p, and Seh1p); homologous to Sec13p Sc
Protein Similarities
Method ID Description E-Value
blast CAA16333 Hypothetical protein Y43F4B.4 [Caenorhabditis elegans] ref|NP_499740.1| Nuclear Pore complex Protein family member (npp-18) [Caenorhabditis elegans] 0.0
blast CAE60058 Hypothetical protein CBG03573 [Caenorhabditis briggsae] 0.0
blast AAH99027 Unknown (protein for MGC:115524) [Xenopus laevis] 1.0E-75
Protein Domains
Database ID Description E-Value
Pfam IPR001680 EMBL-EBI G-protein beta WD-40 repeat 6.3E-9
Pfam IPR001680 EMBL-EBI G-protein beta WD-40 repeat 7.5E-7
Pfam IPR001680 EMBL-EBI G-protein beta WD-40 repeat 0.096
Pfam IPR001680 EMBL-EBI G-protein beta WD-40 repeat 0.32
Sequence
Target Sequence 
>C. ELEGANS:192771_AT
gcttcaagcgtttcatacccgatgtggatgtgtcacatggtcactttctcgtatgcaccg
cccgttgattgctgttggttcggatgagaagaaggcagagaacaagaaacgagttgtgat
ctatgagaatattgatggattgaggaaatggcagcgaatcaactcattagtcttcgatct
accatgcccgattactgatttgaaattctcgccgatatcgatggtggattcgcatcaatt
agccgttgcatcaggcgatgttcacgtctacaacatcaaagtggctcgttcggcgattct
cgaagaagacggtgtcgagaatccgattcagctggcggattacaatctgatcaaggtggc
actgctcggggatcatcgaaaagcatggaggcttcgatataatctcatgggatcagtcat
ctcgtcgacgagcttggatggaacactgagatcctggaaatcactcttcgtgaaccaatg
ggtaaagctgagtgagatgaatgtcgacgactacgttccatcgcctgaagaagttcgcgc
cttcatctca

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GCTTCAAGCGTTTCATACCCGATGT 594 303 504 Antisense
ACATGGTCACTTTCTCGTATGCACC 388 107 538 Antisense
TCATTAGTCTTCGATCTACCATGCC 703 619 667 Antisense
CTACCATGCCCGATTACTGATTTGA 171 225 682 Antisense
ATCAGGCGATGTTCACGTCTACAAC 327 29 753 Antisense
TCAAAGTGGCTCGTTCGGCGATTCT 258 629 779 Antisense
TGATCAAGGTGGCACTGCTCGGGGA 2 565 851 Antisense
GGATCAGTCATCTCGTCGACGAGCT 690 509 913 Antisense
GAGATCCTGGAAATCACTCTTCGTG 44 397 951 Antisense
GAATGTCGACGACTACGTTCCATCG 570 331 1002 Antisense
TGAAGAAGTTCGCGCCTTCATCTCA 271 575 1029 Antisense
Sequence Source Affymetrix Proprietary Database