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[183498_s_at] integral membrane protein /// ---

Description Y39B6B.C /REP_DB=WormBase Gene ID /WP=CE21673 /TR=Q9NEV6 /GB=CAB60908.1 /SUBMIT=HINXTON /CHR=5 /FEA=Sanger Annotation
Cluster 6grp_highest_10_10 > 64      6grp_high1_10_10 > 45      4grp_highest_8_8 > 16      4grp_high_8_8 > 52      6grp_highest_nonorm > 72      6grp_total > 46      4grp_total > 52      6grp_highest_sub > Cu      6grp_cgc > 26      4grp_rule_based > L2      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 423
1 2 3 4 range
A 535.6
(1.1)
P 		618
(3)
P 		549.3
(1.4)
P 		360.9
(-3)
P 		257
B 552.3
(1.7)
P 		636
(3)
P 		589.6
(2.3)
P 		253.3
(-3)
P 		383
C 560.7
(1)
P 		676.5
(3)
P 		590.6
(1.5)
P 		322
(-3)
P 		355
avr 549.5
(1.3) 		643.5
(3) 		576.5
(1.8) 		312.1
(-3) 		331

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 300
1 2 3 4 5 6 range
A 378
(-1.3)
P 		554.7
(3)
P 		307.5
(-3)
P 		422.6
(-0.2)
P 		388.4
(-1)
P 		520.2
(2.2)
P 		247
B 461.6
(3)
P 		406.7
(1.4)
P 		423.5
(1.9)
P 		417.2
(1.7)
P 		254.3
(-3)
P 		448.6
(2.6)
P 		207
C 454.6
(1.8)
P 		451.6
(1.7)
P 		491
(3)
P 		428.6
(0.9)
P 		313.5
(-3)
P 		466.9
(2.2)
P 		178
avr 431.4
(1.2) 		471
(2.7) 		407.3
(0.3) 		422.8
(0.9) 		318.7
(-3) 		478.6
(3) 		160
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 153
1 2 3 4 range
A 195
(3)
P 		134.1
(0.4)
P 		143.6
(0.8)
P 		52.8
(-3)
P 		142
B 176.1
(3)
P 		157.1
(2.1)
P 		136.6
(1.1)
P 		54
(-3)
P 		122
C 185.6
(2.2)
P 		194.5
(2.6)
P 		205.8
(3)
P 		54.3
(-3)
P 		152
avr 185.6
(3) 		161.9
(1.9) 		162
(1.9) 		53.7
(-3) 		132

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 130
1 2 3 4 5 6 range
A 69.7
(-2.9)
P 		197.3
(3)
P 		67
(-3)
P 		107.2
(-1.1)
P 		117.2
(-0.7)
P 		126.6
(-0.3)
P 		130
B 160.6
(2.4)
P 		135.4
(0)
P 		102.8
(-3)
P 		110.5
(-2.3)
P 		103.3
(-3)
P 		167.3
(3)
P 		65
C 168.5
(3)
P 		137.8
(0.8)
P 		125
(-0.2)
P 		86.2
(-3)
P 		101.5
(-1.9)
P 		156.3
(2.1)
P 		82
avr 132.9
(0.5) 		156.8
(3) 		98.3
(-3) 		101.3
(-2.7) 		107.3
(-2.1) 		150.1
(2.3) 		59
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 183498_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.19427
Sequence Type Exemplar sequence
Representative Public ID Y39B6B.C NCBI
Target Description Y39B6B.C /REP_DB=WormBase Gene ID /WP=CE21673 /TR=Q9NEV6 /GB=CAB60908.1 /SUBMIT=HINXTON /CHR=5 /FEA=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_171591(11), NM_059454(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_171591 NCBI Caenorhabditis elegans Y39B6A.47 (Y39B6A.47) mRNA, complete cds. 11/11 None
NM_059454 NCBI Caenorhabditis elegans Nuclear Pore complex Protein family member (npp-12) (npp-12) mRNA, complete cds. 11/11 A 
GENEFINDER00000032988 ENSEMBL cdna:GeneFinder chromosome:CEL140:I:6454768:6461732:1 11/11 None
SNAP00000032985 ENSEMBL cdna:SNAP chromosome:CEL140:I:6455467:6461732:1 11/11 None
GENEFINDER00000030709 ENSEMBL cdna:GeneFinder chromosome:CEL140:V:19090297:19099412:1 11/11 None
T23H2.1 ENSEMBL cdna:known chromosome:CEL140:I:6455467:6462077:1 gene:T23H2.1 11/11 A 
Y39B6A.47 ENSEMBL cdna:known chromosome:CEL140:V:19090297:19099412:1 gene:Y39B6A.47 11/11 None
Annotation Notes
Cross Hybridizing mRNA Matched Probes Nature of Assignment Related Probesets by Grade
SNAP00000030548 2/11 Cross Hyb Matching Probes None
SNAP00000030549 8/11 Cross Hyb Matching Probes None
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrV:19090296-19099412(+) 100.0 100.0
chrI:6457924-6460221(+) 49.43 49.43
Public Domain and Genome References
Gene Title integral membrane protein

Gene Symbol npp-12
nhr-145
Ensembl T23H2.1
Y39B6A.47
Entrez Gene 172348 Entrez gene
180255 Entrez gene
SwissProt P91495 EMBL-EBI
Q9NEV6 EMBL-EBI
WormBase CE14106 Wormbase
CE36621 Wormbase
Functional Annotations
Ortholog
ID Title Organism
ATH1-121501:249354_AT expressed protein at
CANINE:1600355_AT similar to nucleoporin 210 cfa
CANINE_2:CFA.13989.1.A1_AT similar to nucleoporin 210 cfa
CANINE_2:CFAAFFX.7449.1.S1_AT similar to nucleoporin 210 cfa
CANINE_2:CFAAFFX.7509.1.S1_AT similar to nucleoporin 210 cfa
CANINE_2:CFAAFFX.7516.1.S1_AT similar to nucleoporin 210 cfa
CANINE_2:CFAAFFX.7516.1.S1_S_AT similar to nucleoporin 210 cfa
DROSGENOME1:151321_AT dm
DROSOPHILA_2:1629125_AT dm
DROSOPHILA_2:1628986_AT dm
DROSGENOME1:154094_AT dm
CHICKEN:GGAAFFX.3178.1.S1_AT similar to Nup210 protein gga
CHICKEN:GGAAFFX.3178.2.S1_S_AT similar to Nup210 protein gga
HG-U133_PLUS_2:220035_AT nucleoporin 210kDa hs
HG-U133A:220035_AT nucleoporin 210kDa hs
HG-U133A_2:220035_AT nucleoporin 210kDa hs
HU35KSUBA:RC_AA279841_AT nucleoporin 210kDa hs
HU35KSUBA:AA250870_S_AT nucleoporin 210kDa hs
HU35KSUBC:RC_AA478999_AT nucleoporin 210kDa hs
U133_X3P:G13376397_3P_AT nucleoporin 210kDa hs
U133_X3P:HS.56966.1.S1_3P_A_AT nucleoporin 210kDa hs
U133_X3P:HS.56966.0.S1_3P_X_AT nucleoporin 210kDa hs
U133_X3P:HS.56966.0.S1_3P_A_AT nucleoporin 210kDa hs
HG-U133A_2:212315_S_AT nucleoporin 210kDa hs
HG-U133_PLUS_2:212315_S_AT nucleoporin 210kDa hs
HG-U133A:212315_S_AT nucleoporin 210kDa hs
HG-U133A_2:212316_AT nucleoporin 210kDa hs
HG-U133_PLUS_2:212316_AT nucleoporin 210kDa hs
HG-U133A:212316_AT nucleoporin 210kDa hs
HG-U133A_2:213947_S_AT nucleoporin 210kDa hs
HG-U133_PLUS_2:213947_S_AT nucleoporin 210kDa hs
HG-U133A:213947_S_AT nucleoporin 210kDa hs
HG-U95AV2:41812_S_AT nucleoporin 210kDa hs
HG-U95D:90651_AT nucleoporin 210kDa hs
U133_X3P:HS2.385676.1.S1_3P_AT Nucleoporin 210kDa hs
HG-U133_PLUS_2:1562723_AT Nucleoporin 210kDa hs
HG-U95C:54754_R_AT Nucleoporin 210kDa hs
MG-U74BV2:108076_AT nucleoporin 210 mm
MOE430A:1417585_AT nucleoporin 210 mm
MOUSE430A_2:1417585_AT nucleoporin 210 mm
MOUSE430_2:1417585_AT nucleoporin 210 mm
MOE430B:1443310_AT nucleoporin 210 mm
MOUSE430_2:1443310_AT nucleoporin 210 mm
MG-U74BV2:117230_AT Nucleoporin 210 (Nup210), mRNA mm
MU19KSUBA:TC23639_AT Nucleoporin 210 (Nup210), mRNA mm
MU19KSUBA:TC23639_G_AT Nucleoporin 210 (Nup210), mRNA mm
MU19KSUBB:TC33364_AT Nucleoporin 210 (Nup210), mRNA mm
MU19KSUBC:TC40310_AT Nucleoporin 210 (Nup210), mRNA mm
RG-U34A:Y00826_AT nuclear pore membrane glycoprotein 210 rn
RAE230A:1367919_AT nuclear pore membrane glycoprotein 210 rn
RAT230_2:1367919_AT nuclear pore membrane glycoprotein 210 rn
RAE230B:1384596_AT Nuclear pore membrane glycoprotein 210 rn
RAT230_2:1384596_AT Nuclear pore membrane glycoprotein 210 rn
RG-U34C:RC_AI073013_AT Nuclear pore membrane glycoprotein 210 rn
Gene Ontology
GO Biological Process (view graph)
ID Description Evidence Links
6355 regulation of transcription, DNA-dependent inferred from electronic annotation QuickGO AmiGO
GO Cellular Component (view graph)
ID Description Evidence Links
5634 nucleus inferred from electronic annotation QuickGO AmiGO
GO Molecular Function (view graph)
ID Description Evidence Links
3677 DNA binding inferred from electronic annotation QuickGO AmiGO
3700 transcription factor activity inferred from electronic annotation QuickGO AmiGO
3707 steroid hormone receptor activity inferred from electronic annotation QuickGO AmiGO
4879 ligand-dependent nuclear receptor activity inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast CAC51060 Hypothetical protein Y39B6A.47 [Caenorhabditis elegans] ref|NP_741681.2| Y39B6A.47 [Caenorhabditis elegans] 0.0
blast AAC48199 Nuclear pore complex protein protein 12 [Caenorhabditis elegans] ref|NP_491855.1| Nuclear Pore complex Protein family member (npp-12) [Caenorhabditis elegans] 0.0
blast CAE67193 Hypothetical protein CBG12629 [Caenorhabditis briggsae] 0.0
Protein Domains
Database ID Description E-Value
Pfam IPR001628 EMBL-EBI Zn-finger, C4-type steroid receptor 2.2E-19
Pfam IPR003343 EMBL-EBI Bacterial Ig-like, group 2 5.3E-18
Pfam IPR003343 EMBL-EBI Bacterial Ig-like, group 2 5.3E-18
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_491855.1 1 1749-1771
T23H2.1 1 1749-1771
GENEFINDER00000032988 1 1795-1817
SNAP00000032985 1 1749-1771
Sequence
Target Sequence 
>C. ELEGANS:183498_S_AT
ttgcctctctcggtggaattattctgtcagcgtcaagcaggaaagtggaaactggtggaa
gagtaaacttacgattaagaggagtgatcgccggagctgaagacgaagaaccatttgctt
ttggtgaagccatttacccgttcaaacttaatgagaaggcaagaaagcatttcactggaa
gaacctctactttcaccgctgaaacaacaattacagtggaagatggactttcattagttc
aaccagaaatggatattaatactgtcagagtggcgccaaattctcaattgaagatggtca
ctgcatggtctcaagcatctttctcagttcgttctgatttctcgagccggattgtcattt
ctgcggacggtcatttgagaacaaacggaaaagaaggatcagctgcaattaccgttcgta
atgtgaacagcccggataatgaaactgttctcattcctgtgactgtttctcgtgtcgctt
ccctcgatgttcacccaacaattgaacttaaaagtgcttttgagaattctccactcatac
atcttc

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
TTGCCTCTCTCGGTGGAATTATTCT 624 701 2132 Antisense
AGGAGTGATCGCCGGAGCTGAAGAC 284 57 2211 Antisense
ACTGGAAGAACCTCTACTTTCACCG 666 89 2305 Antisense
GTCAGAGTGGCGCCAAATTCTCAAT 197 465 2395 Antisense
GAAGATGGTCACTGCATGGTCTCAA 302 339 2421 Antisense
TGCATGGTCTCAAGCATCTTTCTCA 468 577 2433 Antisense
GTCATTTCTGCGGACGGTCATTTGA 21 469 2485 Antisense
AGGATCAGCTGCAATTACCGTTCGT 482 57 2526 Antisense
TGAAACTGTTCTCATTCCTGTGACT 386 573 2571 Antisense
CATTCCTGTGACTGTTTCTCGTGTC 335 217 2583 Antisense
GAGAATTCTCCACTCATACATCTTC 454 391 2653 Antisense
Sequence Source Affymetrix Proprietary Database