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[187948_s_at]

Description T01G9.4 /REP_DB=WormBase Gene ID /WP=CE06341 /GEN=kup-2 /TR=Q22078 /GB=CAB00054.1 /SUBMIT=HINXTON /CHR=1 /FEA=Sanger Annotation
Cluster 6grp_highest_10_10 > 68      6grp_high1_10_10 > 96      4grp_highest_8_8 > 18      4grp_high_8_8 > 62      6grp_highest_nonorm > 97      6grp_total > 86      4grp_total > 59      6grp_highest_sub > In      6grp_cgc > 67      6grp_high1_sub > In      6grp_cgc_sub > In      6grp_total_sub > Increase      6grp_rule_based > S6      4grp_rule_based > L3      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 431
1 2 3 4 range
A 735.2
(0.2)
P 		854.1
(2.7)
P 		869.9
(3)
P 		580
(-3)
P 		290
B 815.1
(-0.5)
P 		900.3
(1)
P 		1011.4
(3)
P 		678.8
(-3)
P 		333
C 801.1
(-0.5)
P 		768.1
(-2.2)
P 		868.4
(3)
P 		752.1
(-3)
P 		116
avr 783.8
(-0.2) 		840.8
(1.2) 		916.6
(3) 		670.3
(-3) 		246

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 1056
1 2 3 4 5 6 range
A 730.2
(-2.4)
P 		672.8
(-3)
P 		933.9
(-0.3)
P 		820
(-1.5)
P 		1057
(0.9)
P 		1257
(3)
P 		584
B 665.2
(-3)
P 		762.7
(-2.3)
P 		1049.6
(-0.3)
P 		992.2
(-0.7)
P 		1181.9
(0.6)
P 		1524.5
(3)
P 		859
C 620.1
(-3)
P 		772.3
(-2.1)
P 		718.7
(-2.4)
P 		1160.9
(0.1)
P 		882
(-1.5)
P 		1675.8
(3)
P 		1056
avr 671.8
(-3) 		735.9
(-2.5) 		900.7
(-1.3) 		991
(-0.6) 		1040.3
(-0.3) 		1485.8
(3) 		814
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 218
1 2 3 4 range
A 267.7
(3)
P 		185.4
(0.3)
P 		227.4
(1.7)
P 		84.9
(-3)
P 		183
B 259.9
(3)
P 		222.3
(1)
P 		234.4
(1.7)
P 		144.7
(-3)
P 		115
C 265.2
(1.7)
P 		220.8
(0.2)
P 		302.7
(3)
P 		126.8
(-3)
P 		176
avr 264.3
(3) 		209.5
(0.7) 		254.8
(2.6) 		118.8
(-3) 		146

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 434
1 2 3 4 5 6 range
A 134.6
(-3)
P 		239.3
(0.4)
P 		203.4
(-0.8)
P 		208
(-0.6)
P 		318.9
(3)
P 		306
(2.6)
P 		184
B 231.5
(-3)
P 		253.9
(-2.6)
P 		254.9
(-2.6)
P 		262.8
(-2.4)
P 		480.2
(1.4)
P 		568.5
(3)
P 		337
C 229.8
(-2.3)
P 		235.6
(-2.2)
P 		182.9
(-3)
P 		233.4
(-2.2)
P 		285.4
(-1.4)
P 		561
(3)
P 		378
avr 198.6
(-3) 		242.9
(-2.1) 		213.7
(-2.7) 		234.7
(-2.2) 		361.5
(0.5) 		478.5
(3) 		280
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 187948_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.1566
Sequence Type Exemplar sequence
Representative Public ID T01G9.4 NCBI
Target Description T01G9.4 /REP_DB=WormBase Gene ID /WP=CE06341 /GEN=kup-2 /TR=Q22078 /GB=CAB00054.1 /SUBMIT=HINXTON /CHR=1 /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_059855(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_059855 NCBI Caenorhabditis elegans Nuclear Pore complex Protein family member (npp-2) (npp-2) mRNA, complete cds. 11/11 None
SNAP00000040994 ENSEMBL cdna:SNAP chromosome:CEL140:I:8297325:8301764:-1 11/11 None
GENEFINDER00000041001 ENSEMBL cdna:GeneFinder chromosome:CEL140:I:8297325:8301764:-1 11/11 None
T01G9.4 ENSEMBL cdna:known chromosome:CEL140:I:8299430:8301764:-1 gene:T01G9.4 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:8299460-8301695(-) 99.94 100.0
Public Domain and Genome References
Gene Title
Gene Symbol npp-2
Ensembl T01G9.4
Entrez Gene 172611 Entrez gene
SwissProt Q22078 EMBL-EBI
WormBase CE06341 Wormbase
Functional Annotations
Ortholog
ID Title Organism
ATGENOME1:20602_AT expressed protein at
ATH1-121501:253388_AT expressed protein at
CANINE:1604289_AT similar to pericentrin 1 cfa
CANINE:1591944_AT similar to pericentrin 1 cfa
CANINE_2:CFA.17130.1.S1_S_AT similar to pericentrin 1 cfa
CANINE_2:CFA.17130.2.S1_AT similar to pericentrin 1 cfa
DROSOPHILA_2:1636645_AT dm
DROSGENOME1:154498_AT dm
CHICKEN:GGAAFFX.4995.2.S1_S_AT pericentrin 1 gga
HG-U133A:218014_AT pericentrin 1 hs
HG-U133_PLUS_2:218014_AT pericentrin 1 hs
HG-U133A_2:218014_AT pericentrin 1 hs
HU35KSUBA:RC_AA464853_AT pericentrin 1 hs
U133_X3P:G13376258_3P_AT pericentrin 1 hs
HG-U95B:45268_AT pericentrin 1 hs
HG-U95E:70469_AT Pericentrin 1 hs
MG-U74AV2:99663_G_AT pericentrin 1 mm
MG-U74AV2:99662_AT pericentrin 1 mm
MOE430A:1437520_A_AT pericentrin 1 mm
MOUSE430A_2:1437520_A_AT pericentrin 1 mm
MOUSE430_2:1437520_A_AT pericentrin 1 mm
MOE430A:1416073_A_AT pericentrin 1 mm
MOUSE430A_2:1416073_A_AT pericentrin 1 mm
MOUSE430_2:1416073_A_AT pericentrin 1 mm
MU19KSUBA:TC19963_AT Pericentrin 1, mRNA (cDNA clone MGC:105225 IMAGE:6403446) mm
MU19KSUBA:TC19963_G_AT Pericentrin 1, mRNA (cDNA clone MGC:105225 IMAGE:6403446) mm
RAE230A:1390650_AT pericentrin 1 (predicted) rn
RAT230_2:1390650_AT pericentrin 1 (predicted) rn
Protein Similarities
Method ID Description E-Value
blast CAB00054 Hypothetical protein T01G9.4 [Caenorhabditis elegans] ref|NP_492256.1| Nuclear Pore complex Protein family member (npp-2) [Caenorhabditis elegans] 0.0
blast CAE60475 Hypothetical protein CBG04087 [Caenorhabditis briggsae] 0.0
blast CAB00053 Hypothetical protein T01G9.6b [Caenorhabditis elegans] ref|NP_492254.1| protein KINase family member (kin-10) [Caenorhabditis elegans] 1.0E-110
Protein Domains
Database ID Description E-Value
Pfam IPR000704 EMBL-EBI Casein kinase II, regulatory subunit 1.0E-126
Pfam IPR000704 EMBL-EBI Casein kinase II, regulatory subunit 1.0E-126
Sequence
Target Sequence 
>C. ELEGANS:187948_S_AT
atgactttccggtatctgaagcaaggacattggagttcaacactcgcttgggcgttgaaa
actggatccaaaaagacaattgactggacagtatctcgaattgttggttcaagttcgaag
gatgaattggctgcattaagagttttatcttcaataaccaatcattctgtactctcactt
ccatctcttaccttcctctactcttatcaacgatttgtgaagatgatgcactgtggtgat
gtactggactgtgttcaacatctgataccgcttattatgatgcctgatgttccaactcag
tattactatgatctcttcgattatttaatcacgattatcaaagaggatgggcgtgctgga
atccgattttccaaggagattctctatgagctctcaacctttttgtcaacgtt

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
ATGACTTTCCGGTATCTGAAGCAAG 195 43 1279 Antisense
AGTTCAACACTCGCTTGGGCGTTGA 556 59 1312 Antisense
AACCAATCATTCTGTACTCTCACTT 268 149 1434 Antisense
CTTCCTCTACTCTTATCAACGATTT 39 219 1470 Antisense
GCACTGTGGTGATGTACTGGACTGT 232 315 1506 Antisense
CTGTGTTCAACATCTGATACCGCTT 163 241 1527 Antisense
GATACCGCTTATTATGATGCCTGAT 256 425 1542 Antisense
ATTATGATGCCTGATGTTCCAACTC 526 13 1552 Antisense
CAGTATTACTATGATCTCTTCGATT 388 207 1576 Antisense
ATGGGCGTGCTGGAATCCGATTTTC 495 49 1625 Antisense
AGCTCTCAACCTTTTTGTCAACGTT 176 81 1667 Antisense
Sequence Source Affymetrix Proprietary Database