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[176576_at]

Description R13A5.1 /REP_DB=WormBase Gene ID /WP=CE25082 /GEN=cup-5 /SUBMIT=ST.LOUIS /CHR=3 /FEA=Sanger Annotation
Cluster 6grp_highest_10_10 > 87      6grp_high1_10_10 > 77      4grp_highest_8_8 > 44      4grp_high_8_8 > 08      6grp_highest_nonorm > 82      6grp_total > 77      4grp_total > 31      6grp_highest_sub > Da      6grp_cgc > 49      6grp_high1_sub > Da      6grp_cgc_sub > Da      6grp_total_sub > Increase      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 184
1 2 3 4 range
A 307.7
(3)
P 		233.4
(-3)
P 		283.5
(1)
P 		268
(-0.2)
P 		74
B 385.8
(3)
P 		201.6
(-3)
P 		294
(0)
P 		267.5
(-0.9)
P 		184
C 318.4
(2.7)
P 		296.1
(1.4)
P 		215.9
(-3)
P 		324.3
(3)
P 		108
avr 337.3
(3) 		243.7
(-3) 		264.5
(-1.7) 		286.6
(-0.2) 		94

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 319
1 2 3 4 5 6 range
A 291.7
(-2)
P 		279.8
(-2.4)
P 		281.8
(-2.3)
P 		257.5
(-3)
P 		316.3
(-1.3)
P 		467.5
(3)
P 		210
B 454.4
(1.8)
P 		410.4
(0.5)
P 		284.7
(-3)
P 		346.7
(-1.3)
P 		425
(1)
P 		497.6
(3)
P 		213
C 251.1
(-3)
P 		350.9
(-1.1)
P 		272.4
(-2.6)
P 		458.5
(0.9)
P 		375.9
(-0.7)
P 		570
(3)
P 		319
avr 332.4
(-1.6) 		347
(-1.3) 		279.6
(-3) 		354.2
(-1.1) 		372.4
(-0.6) 		511.7
(3) 		232
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 84
1 2 3 4 range
A 112
(3)
P 		50.7
(-2.1)
P 		74.1
(-0.1)
P 		39.2
(-3)
P 		73
B 123
(3)
P 		49.8
(-3)
P 		68.1
(-1.5)
P 		57
(-2.4)
P 		73
C 105.4
(3)
P 		85.1
(0.6)
P 		75.3
(-0.6)
P 		54.7
(-3)
P 		51
avr 113.5
(3) 		61.9
(-1.9) 		72.5
(-0.9) 		50.3
(-3) 		63

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 137
1 2 3 4 5 6 range
A 53.8
(-3)
P 		99.5
(1.6)
P 		61.4
(-2.2)
P 		65.3
(-1.9)
P 		95.5
(1.2)
P 		113.8
(3)
P 		60
B 158.1
(1.6)
P 		136.6
(0.5)
P 		69.1
(-3)
P 		91.8
(-1.8)
P 		172.7
(2.3)
P 		185.6
(3)
P 		117
C 93.1
(-1.8)
P 		107.1
(-1.1)
P 		69.3
(-3)
P 		92.2
(-1.9)
P 		121.7
(-0.4)
P 		190.8
(3)
P 		122
avr 101.7
(-0.8) 		114.4
(-0) 		66.6
(-3) 		83.1
(-2) 		130
(0.9) 		163.4
(3) 		97
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 176576_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.7307
Sequence Type Exemplar sequence
Representative Public ID R13A5.1 NCBI
Target Description R13A5.1 /REP_DB=WormBase Gene ID /WP=CE25082 /GEN=cup-5 /SUBMIT=ST.LOUIS /CHR=3 /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_001027548(9), NM_066263(10), NM_001027551(9)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_001027548 NCBI Caenorhabditis elegans Coelomocyte UPtake defective family member (cup-5) (cup-5) mRNA, complete cds. 9/11 None
NM_066263 NCBI Caenorhabditis elegans Coelomocyte UPtake defective family member (cup-5) (cup-5) mRNA, complete cds. 10/11 None
NM_001027551 NCBI Caenorhabditis elegans Coelomocyte UPtake defective family member (cup-5) (cup-5) mRNA, complete cds. 9/11 None
GENEFINDER00000038259 ENSEMBL cdna:GeneFinder chromosome:CEL140:III:7584607:7591252:1 9/11 None
SNAP00000038252 ENSEMBL cdna:SNAP chromosome:CEL140:III:7589359:7591252:1 9/11 None
R13A5.1a.2 ENSEMBL cdna:known chromosome:CEL140:III:7584257:7591481:1 gene:R13A5.1 9/11 None
R13A5.1b ENSEMBL cdna:known chromosome:CEL140:III:7584607:7591476:1 gene:R13A5.1 10/11 None
R13A5.1a.1 ENSEMBL cdna:known chromosome:CEL140:III:7584607:7591483:1 gene:R13A5.1 9/11 None
R13A5.1d ENSEMBL cdna:known chromosome:CEL140:III:7584607:7591438:1 gene:R13A5.1 9/11 None
Annotation Notes
Cross Hybridizing mRNA Matched Probes Nature of Assignment Related Probesets by Grade
NM_001027550 7/11 Cross Hyb Matching Probes None
R13A5.1c 7/11 Cross Hyb Matching Probes None
Splice Variants
Entrez Total Refseq Isoforms Total Detected By This Probeset Refseq Probesets
176074 4 3 NM_001027548 176576_at (9)
NM_001027551 176576_at (9)
NM_066263 176576_at (10)
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrIII:7584096-7591250(+) 100.0 100.0
Public Domain and Genome References
Ensembl R13A5.1
Functional Annotations
Protein Similarities
Method ID Description E-Value
blast AAM15596 Coelomocyte uptake defective protein 5, isoform a [Caenorhabditis elegans] ref|NP_001022719.1| Coelomocyte UPtake defective family member (cup-5) [Caenorhabditis elegans] gb|AAK19624.1| CUP-5 [Caenorhabditis elegans] 0.0
blast AAP82643 Coelomocyte uptake defective protein 5, isoform d [Caenorhabditis elegans] ref|NP_001022722.1| Coelomocyte UPtake defective family member (cup-5) [Caenorhabditis elegans] gb|AAL89754.1| CUP-5L [Caenorhabditis elegans] 0.0
blast AAP82642 Coelomocyte uptake defective protein 5, isoform c [Caenorhabditis elegans] ref|NP_001022721.1| Coelomocyte UPtake defective family member (cup-5) [Caenorhabditis elegans] 0.0
blast AAL38965 Coelomocyte uptake defective protein 5, isoform b [Caenorhabditis elegans] ref|NP_498664.3| Coelomocyte UPtake defective family member (cup-5) [Caenorhabditis elegans] 0.0
Protein Domains
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_001022719.1 6 70-92,332-354,384-403,418-440,460-482,527-549
NP_498664.3 6 70-92,324-346,382-404,424-446,466-488,533-555
NP_001022722.1 6 70-92,332-354,384-403,418-440,460-482,527-549
R13A5.1a.2 6 70-92,332-354,384-403,418-440,460-482,527-549
R13A5.1b 6 70-92,324-346,382-404,424-446,466-488,533-555
R13A5.1a.1 6 70-92,332-354,384-403,418-440,460-482,527-549
R13A5.1d 6 70-92,332-354,384-403,418-440,460-482,527-549
GENEFINDER00000038259 6 70-92,359-381,411-430,445-467,487-509,554-576
SNAP00000038252 2 12-34,78-100
Sequence
Target Sequence 
>C. ELEGANS:176576_AT
gaagttccgtacactggcagaatcatcggaagctctattttcgcttctcaacggtgacga
tatgttcgccacgttttacactattaatgattccaatacagttatcaaggtatttgggac
agtgtacatctacctattcgtgtcactctttatctatgtagtattatcactgttcattgc
aattatcatggatgcatatgaagtcgtcaaggatcgctactcagacggtcttcgagccat
cgaaaaacgtggatgtcttcgcgatttcgtggaatcgaatccaccgccgtcggaactcgg
ctcaccgacgactcgatccgcctacgcaccgtctaatctgctcaatctggttgttcatca
gttcgttcgaaaacattcagtttctctaatttcagcggctggcaacgactcgagtagagc
tcttcgtgctcttcatgccattgacaatgc

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GAAGTTCCGTACACTGGCAGAATCA 304 337 1533 Antisense
CTCTATTTTCGCTTCTCAACGGTGA 83 229 1565 Antisense
GATATGTTCGCCACGTTTTACACTA 544 425 1591 Antisense
GTACATCTACCTATTCGTGTCACTC 294 461 1656 Antisense
GAAGTCGTCAAGGATCGCTACTCAG 675 335 1732 Antisense
CTACTCAGACGGTCTTCGAGCCATC 19 227 1749 Antisense
AAAACGTGGATGTCTTCGCGATTTC 434 131 1776 Antisense
CGTCTAATCTGCTCAATCTGGTTGT 494 245 1862 Antisense
AGTTTCTCTAATTTCAGCGGCTGGC 419 63 1911 Antisense
CGACTCGAGTAGAGCTCTTCGTGCT 662 249 1938 Antisense
GTGCTCTTCATGCCATTGACAATGC 541 479 1958 Antisense
Sequence Source Affymetrix Proprietary Database