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[173670_s_at] nucleoporin

Description CEK006B4R_rc /REP_DB=TREMBL Accession /5_PRIME_EXT_ID=C03D6.4 /5_PRIME_EXT_DB=WormBase Gene ID /GB=D27924 /WB_GENE_ID=C03D6.4 /WP=CE05198 /CHR=1 /FEA=Genomic Cluster /DEF=nucleoporin; C.elegans cDNA clone yk6b4 : 3prime end, single read.
Cluster 6grp_highest_10_10 > 75      6grp_high1_10_10 > 56      4grp_highest_8_8 > 43      4grp_high_8_8 > 24      6grp_highest_nonorm > 74      6grp_total > 57      4grp_total > 55      6grp_highest_sub > Cu      6grp_cgc > 27      6grp_high1_sub > Cu      6grp_cgc_sub > Cu      6grp_total_sub > Cup      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 417
1 2 3 4 range
A 907.2
(3)
P 		539.8
(-3)
P 		693.4
(-0.5)
P 		571.9
(-2.5)
P 		367
B 867.5
(3)
P 		641.6
(-2.9)
P 		637.3
(-3)
P 		798.2
(1.2)
P 		230
C 871.5
(3)
P 		489.8
(-3)
P 		611.8
(-1.1)
P 		543.2
(-2.2)
P 		382
avr 882.1
(3) 		557.1
(-3) 		647.5
(-1.3) 		637.8
(-1.5) 		325

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 421
1 2 3 4 5 6 range
A 709.4
(-0.1)
P 		811.1
(1.8)
P 		548.4
(-3)
P 		713.9
(0)
P 		560.5
(-2.8)
P 		879.2
(3)
P 		331
B 825.2
(0.9)
P 		661.1
(-1.6)
P 		675.1
(-1.4)
P 		619.4
(-2.2)
P 		570.4
(-3)
P 		962.1
(3)
P 		392
C 656.6
(-0.3)
P 		664.7
(-0.1)
P 		682.2
(0.3)
P 		541.3
(-3)
P 		591.7
(-1.8)
P 		800.6
(3)
P 		259
avr 730.4
(0.1) 		712.3
(-0.3) 		635.2
(-1.8) 		624.9
(-2) 		574.2
(-3) 		880.6
(3) 		306
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 247
1 2 3 4 range
A 330.3
(3)
P 		117.2
(-2.2)
P 		181.3
(-0.6)
P 		83.7
(-3)
P 		247
B 276.6
(3)
P 		158.5
(-2.5)
P 		147.7
(-3)
P 		170.1
(-2)
P 		129
C 288.5
(3)
P 		140.8
(-1.5)
P 		213.2
(0.7)
P 		91.6
(-3)
P 		197
avr 298.5
(3) 		138.8
(-2.2) 		180.7
(-0.9) 		115.1
(-3) 		183

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 250
1 2 3 4 5 6 range
A 130.8
(-2.6)
P 		288.5
(3)
P 		119.4
(-3)
P 		181.1
(-0.8)
P 		169.1
(-1.2)
P 		214.1
(0.4)
P 		169
B 287.1
(0.8)
P 		220.1
(-1.3)
P 		163.9
(-3)
P 		164.1
(-3)
P 		231.7
(-0.9)
P 		358.8
(3)
P 		195
C 243.4
(2.1)
P 		202.8
(0.5)
P 		173.6
(-0.6)
P 		108.9
(-3)
P 		191.5
(0.1)
P 		268
(3)
P 		159
avr 220.4
(0.2) 		237.1
(1) 		152.3
(-3) 		151.4
(-3) 		197.4
(-0.9) 		280.3
(3) 		129
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 173670_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.22775
Sequence Type Exemplar sequence
Representative Public ID CEK006B4R NCBI
Target Description CEK006B4R_rc /REP_DB=TREMBL Accession /5_PRIME_EXT_ID=C03D6.4 /5_PRIME_EXT_DB=WormBase Gene ID /GB=D27924 /WB_GENE_ID=C03D6.4 /WP=CE05198 /CHR=1 /FEA=Genomic Cluster /DEF=nucleoporin; C.elegans cDNA clone yk6b4 : 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_060167(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_060167 NCBI Caenorhabditis elegans C03D6.4 (nucleoporin) mRNA, complete cds. 11/11 None
SNAP00000028820 ENSEMBL cdna:SNAP chromosome:CEL140:I:9668462:9673034:-1 11/11 None
GENEFINDER00000028828 ENSEMBL cdna:GeneFinder chromosome:CEL140:I:9668462:9673034:-1 11/11 None
C03D6.4 ENSEMBL cdna:known chromosome:CEL140:I:9668307:9673034:-1 gene:C03D6.4 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
chrI:9668258-9672966(-) 100.0 100.0
Public Domain and Genome References
Gene Title nucleoporin
Gene Symbol npp-14
Ensembl C03D6.4
Entrez Gene 172813 Entrez gene
SwissProt Q17602 EMBL-EBI
WormBase CE05198 Wormbase
Functional Annotations
Ortholog
ID Title Organism
ATH1-121501:265074_AT proline-rich family protein at
ATGENOME1:13414_AT proline-rich family protein at
CANINE_2:CFAAFFX.30488.1.S1_S_AT similar to nucleoporin 214kDa cfa
CANINE_2:CFAAFFX.30493.1.S1_AT similar to nucleoporin 214kDa cfa
DROSOPHILA_2:1629305_AT dm
DROSGENOME1:141705_AT dm
CHICKEN:GGA.1904.2.S1_A_AT nucleoporin 214kDa gga
CHICKEN:GGA.19227.1.S1_AT nucleoporin 214kDa gga
CHICKEN:GGA.9861.1.S1_AT nucleoporin 214kDa gga
CHICKEN:GGAAFFX.21363.1.S1_AT nucleoporin 214kDa gga
CHICKEN:GGAAFFX.25980.1.A1_AT nucleoporin 214kDa gga
HG-U133_PLUS_2:202155_S_AT nucleoporin 214kDa hs
HG-U133A:202155_S_AT nucleoporin 214kDa hs
HG-FOCUS:202155_S_AT nucleoporin 214kDa hs
HG-U133A_2:202155_S_AT nucleoporin 214kDa hs
HG-U133_PLUS_2:228902_AT nucleoporin 214kDa hs
HG-U133B:228902_AT nucleoporin 214kDa hs
HU35KSUBB:RC_AA193569_AT nucleoporin 214kDa hs
HU35KSUBC:RC_AA401428_S_AT nucleoporin 214kDa hs
HUGENEFL:D14689_AT nucleoporin 214kDa hs
U133_X3P:G285956_3P_A_AT nucleoporin 214kDa hs
U133_X3P:HS.170285.2.S1_3P_AT nucleoporin 214kDa hs
HG-U95AV2:40768_S_AT nucleoporin 214kDa hs
HG-U95B:54602_AT nucleoporin 214kDa hs
HG-U133_PLUS_2:232454_AT Nucleoporin 214kDa hs
HG-U133B:232454_AT Nucleoporin 214kDa hs
U133_X3P:HS.213891.0.S1_3P_AT Nucleoporin 214kDa hs
HG-U95D:71452_AT Nucleoporin 214kDa hs
HG-U95B:43637_AT Nucleoporin 214kDa hs
HG-U95B:56615_AT Nucleoporin 214kDa hs
HU35KSUBC:RC_AA278887_AT Nucleoporin 214kDa hs
HU35KSUBC:RC_AA287651_AT Nucleoporin 214kDa hs
MOUSE430_2:1456503_AT nucleoporin 214 mm
MOE430B:1456503_AT nucleoporin 214 mm
MG-U74BV2:111967_AT nucleoporin 214 mm
MOE430B:1434351_AT nucleoporin 214 mm
MOUSE430_2:1434351_AT nucleoporin 214 mm
MG-U74BV2:105424_AT Nucleoporin 214, mRNA (cDNA clone MGC:37347 IMAGE:4976266) mm
MG-U74CV2:132811_AT Nucleoporin 214, mRNA (cDNA clone MGC:37347 IMAGE:4976266) mm
MOE430B:1457815_AT Nucleoporin 214, mRNA (cDNA clone MGC:37347 IMAGE:4976266) mm
MOUSE430_2:1457815_AT Nucleoporin 214, mRNA (cDNA clone MGC:37347 IMAGE:4976266) mm
MU19KSUBA:TC14568_S_AT Nucleoporin 214, mRNA (cDNA clone MGC:37347 IMAGE:4976266) mm
MU19KSUBB:TC34740_AT Nucleoporin 214, mRNA (cDNA clone MGC:37347 IMAGE:4976266) mm
MU19KSUBC:TC35467_AT Nucleoporin 214, mRNA (cDNA clone MGC:37347 IMAGE:4976266) mm
RAT230_2:1383092_A_AT similar to mKIAA0023 protein (predicted) rn
RAE230B:1383092_A_AT similar to mKIAA0023 protein (predicted) rn
RG-U34B:RC_AA850592_AT similar to mKIAA0023 protein (predicted) rn
RAE230A:1390074_AT similar to mKIAA0023 protein (predicted) rn
RAT230_2:1390074_AT similar to mKIAA0023 protein (predicted) rn
RAE230B:1395982_AT similar to mKIAA0023 protein (predicted) rn
RAT230_2:1395982_AT similar to mKIAA0023 protein (predicted) rn
RG-U34B:RC_AA944308_AT Similar to mKIAA0023 protein (predicted) rn
RG-U34B:RC_AI070197_AT Similar to mKIAA0023 protein (predicted) rn
Protein Similarities
Method ID Description E-Value
blast CAA99763 Hypothetical protein C03D6.4 [Caenorhabditis elegans] ref|NP_492568.1| C03D6.4 [Caenorhabditis elegans] 0.0
blast CAE60202 Hypothetical protein CBG03763 [Caenorhabditis briggsae] 0.0
blast AAH46835 MGC52541 protein [Xenopus laevis] 4.0E-33
Sequence
Target Sequence 
>C. ELEGANS:173670_S_AT
gggacatcagccagtagcagttcatggctttttggtggtggtggtaatcaacaacaacag
caacagcaaaagccgtcgttttctttcaacactgccggatcgtcagctcaacaagcatct
gcacctgcaacaggaacgtcgtcagtttttggaggagctccgaaattcggatcgcaacca
gcatttggtgctaaaccattcggaggaggggcgaatgcaggattatctaaaaatgcttca
atcttcggaggagcaacatcttccacaaccaacaaccctgccactggtggatttgctcaa
tttgcatcaggccagaagacttcatctttgttcggtggaggtgcaactccacagacgaat
acttctatcttcggtggtggagctaacacaactccagctccgacatcttctgtgtttgga
ggaggagcatctgccaatgccaataaaccgacatctttcacatcatggcg

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GGGACATCAGCCAGTAGCAGTTCAT 154 495 3713 Antisense
GCAGTTCATGGCTTTTTGGTGGTGG 417 311 3729 Antisense
CCGGATCGTCAGCTCAACAAGCATC 459 265 3807 Antisense
AATTCGGATCGCAACCAGCATTTGG 389 177 3876 Antisense
ACAACCCTGCCACTGGTGGATTTGC 79 113 3984 Antisense
GACTTCATCTTTGTTCGGTGGAGGT 131 371 4030 Antisense
GTGCAACTCCACAGACGAATACTTC 659 479 4053 Antisense
ATACTTCTATCTTCGGTGGTGGAGC 205 25 4071 Antisense
AGCTCCGACATCTTCTGTGTTTGGA 111 81 4108 Antisense
GGAGGAGGAGCATCTGCCAATGCCA 141 515 4130 Antisense
AACCGACATCTTTCACATCATGGCG 164 147 4158 Antisense
Sequence Source Affymetrix Proprietary Database