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[172000_x_at]

Description g459659 /REP_DB=GenBank Identifier /GB=U06932.1 /PROTEIN_GB=AAA64937.1 /CHR=3 /FEA=Mapped Transcript /DEF=CeSWAP
Cluster 6grp_highest_10_10 > 85      6grp_high1_10_10 > 68      4grp_highest_8_8 > 45      4grp_high_8_8 > 09      6grp_highest_nonorm > 82      6grp_total > 57      4grp_total > 23      6grp_highest_sub > Cu      6grp_cgc > 28      6grp_high1_sub > Cu      6grp_cgc_sub > Cu      6grp_total_sub > Cup      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 445
1 2 3 4 range
A 673
(3)
P 		295.2
(-2.4)
P 		254.2
(-3)
P 		541.5
(1.1)
P 		419
B 489.6
(1.8)
P 		255.9
(-3)
P 		299
(-2.1)
P 		548.3
(3)
P 		292
C 575.3
(3)
P 		228.5
(-3)
P 		318.8
(-1.4)
P 		443.7
(0.7)
P 		347
avr 579.3
(3) 		259.9
(-3) 		290.7
(-2.4) 		511.2
(1.7) 		319

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 303
1 2 3 4 5 6 range
A 321.5
(-2.5)
P 		455.3
(0.1)
P 		297.4
(-3)
P 		364.3
(-1.7)
P 		354.7
(-1.9)
P 		600.3
(3)
P 		303
B 326.7
(-3)
P 		425.9
(1)
P 		354.6
(-1.9)
P 		465
(2.5)
P 		371.3
(-1.2)
P 		476.9
(3)
P 		150
C 481.5
(3)
P 		393.4
(-0.2)
P 		368.2
(-1.1)
P 		316.5
(-3)
P 		367.1
(-1.2)
P 		473.1
(2.7)
P 		165
avr 376.6
(-1.8) 		424.9
(-0.1) 		340.1
(-3) 		381.9
(-1.6) 		364.4
(-2.2) 		516.8
(3) 		177
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 182
1 2 3 4 range
A 245.1
(3)
P 		64.1
(-3)
P 		66.5
(-2.9)
P 		79.3
(-2.5)
P 		181
B 156.1
(3)
P 		63.2
(-3)
P 		69.3
(-2.6)
P 		116.9
(0.5)
P 		93
C 190.4
(3)
P 		65.7
(-3)
P 		111.1
(-0.8)
P 		74.8
(-2.6)
P 		125
avr 197.2
(3) 		64.3
(-3) 		82.3
(-2.2) 		90.3
(-1.8) 		133

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 119
1 2 3 4 5 6 range
A 59.3
(-3)
P 		161.9
(3)
P 		64.8
(-2.7)
P 		92.4
(-1.1)
P 		107
(-0.2)
P 		146.1
(2.1)
P 		103
B 113.7
(-1.2)
P 		141.8
(0.6)
P 		86.1
(-3)
P 		123.2
(-0.6)
P 		150.8
(1.2)
P 		177.8
(3)
P 		92
C 178.5
(3)
P 		120
(-0.1)
P 		93.7
(-1.4)
P 		63.7
(-3)
P 		118.8
(-0.1)
P 		158.4
(1.9)
P 		115
avr 117.2
(-0.3) 		141.2
(1.5) 		81.5
(-3) 		93.1
(-2.1) 		125.5
(0.3) 		160.8
(3) 		79
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 172000_x_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.19817
Sequence Type Exemplar sequence
Representative Public ID 459659 NCBI
Target Description g459659 /REP_DB=GenBank Identifier /GB=U06932.1 /PROTEIN_GB=AAA64937.1 /CHR=3 /FEA=Mapped Transcript /DEF=CeSWAP
Cluster Evidence This cluster is supported by a Mapped Transcript.
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_001025951(9), NM_001025949(9), NM_171132(9)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_001025951 NCBI Caenorhabditis elegans splicing factor (Suppressor of White aPricot) related family member (swp-1) (swp-1) mRNA, complete cds. 9/11 None
NM_001025949 NCBI Caenorhabditis elegans splicing factor (Suppressor of White aPricot) related family member (swp-1) (swp-1) mRNA, complete cds. 9/11 None
NM_171132 NCBI Caenorhabditis elegans splicing factor (Suppressor of White aPricot) related family member (swp-1) (swp-1) mRNA, complete cds. 9/11 A 
GENEFINDER00000008885 ENSEMBL cdna:GeneFinder chromosome:CEL140:III:5702273:5705410:-1 11/11 None
SNAP00000008876 ENSEMBL cdna:SNAP chromosome:CEL140:III:5702292:5705410:-1 9/11 None
B0336.9b.1 ENSEMBL cdna:known chromosome:CEL140:III:5702219:5704676:-1 gene:B0336.9 11/11 A 
B0336.9d ENSEMBL cdna:known chromosome:CEL140:III:5702292:5705410:-1 gene:B0336.9 9/11 A 
B0336.9a ENSEMBL cdna:known chromosome:CEL140:III:5702292:5705313:-1 gene:B0336.9 9/11 A 
B0336.9b.2 ENSEMBL cdna:known chromosome:CEL140:III:5702292:5705407:-1 gene:B0336.9 9/11 A 
Annotation Notes
There are no noteworthy cross hybridizing mRNAs found for this probe set.
Splice Variants
Entrez Total Refseq Isoforms Total Detected By This Probeset Refseq Probesets
175795 5 3 NM_001025949 172000_x_at (9), 187991_s_at (11)
NM_001025951 172000_x_at (9), 187991_s_at (11)
NM_171132 172000_x_at (9), 187991_s_at (11)
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrIII:5702201-5705312(-) 100.0 100.0
Public Domain and Genome References
Ensembl B0336.9
Functional Annotations
Protein Similarities
Method ID Description E-Value
blast AAM75380 Splicing factor (suppressor of white apricot) related protein 1, isoform d [Caenorhabditis elegans] ref|NP_001021122.1| splicing factor (Suppressor of White aPricot) related family member (swp-1) [Caenorhabditis elegans] 0.0
blast T15336 hypothetical protein B0336.9 - Caenorhabditis elegans 0.0
blast AAM75378 Splicing factor (suppressor of white apricot) related protein 1, isoform a [Caenorhabditis elegans] ref|NP_741149.1| splicing factor (Suppressor of White aPricot) related family member (swp-1) [Caenorhabditis elegans] sp|Q10580|SWAP_CAEEL SWAP protein (Suppressor of white apricot protein homolog) gb|AAA64937.1| CeSWAP 0.0
blast AAL50323 Splicing factor (suppressor of white apricot) related protein 1, isoform b [Caenorhabditis elegans] ref|NP_001021120.1| splicing factor (Suppressor of White aPricot) related family member (swp-1) [Caenorhabditis elegans] 0.0
Protein Domains
Database ID Description E-Value
Pfam IPR000061 EMBL-EBI SWAP/Surp 8.0E-20
Pfam IPR000061 EMBL-EBI SWAP/Surp 0.019
Pfam IPR000061 EMBL-EBI SWAP/Surp 8.0E-20
Pfam IPR000061 EMBL-EBI SWAP/Surp 0.019
Pfam IPR000061 EMBL-EBI SWAP/Surp 8.0E-20
Pfam IPR000061 EMBL-EBI SWAP/Surp 0.019
Sequence
Target Sequence 
>C. ELEGANS:172000_X_AT
ccaccatccactcaaatgcaagtcgatcggaaggaaaaagcgagaattttcatggagaag
ttgcttcaagagaagaaagcaaagaaattacaagaagaagaagaacgatcaaaattagag
gaagagacacggaagaaggctgaaaagatatcagaatcattgtcagaacggaaaaatact
ggtagatcggatcggagagaagaagcacccaaaggggcgagatctctcgatgaaataatt
aataataggatcaacagtttgctatccgaatctggttttgaacccgttgaggagatgaag
agaacagacgaggatagggagagaaaaagacatcgaaaacgaagccgttcacgacgacga
tctcgctcctgtagccccagagaccgatcacgagagcacaaaaaatcccgaaaatccggt
agacatcatcgatctcgctctcgttcctcatccagagatcgtcatcgtcgaaatcgcagt
agaagtcgggatagacggcggtgatttcttgtggaata

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
CCACCATCCACTCAAATGCAAGTCG 288 273 1759 Antisense
GCACCCAAAGGGGCGAGATCTCTCG 380 315 1963 Antisense
GATCAACAGTTTGCTATCCGAATCT 517 421 2007 Antisense
GCTATCCGAATCTGGTTTTGAACCC 12 301 2019 Antisense
AAACGAAGCCGTTCACGACGACGAT 447 125 2095 Antisense
CCCCAGAGACCGATCACGAGAGCAC 314 259 2133 Antisense
TCCGGTAGACATCATCGATCTCGCT 258 591 2173 Antisense
CTCGTTCCTCATCCAGAGATCGTCA 365 233 2198 Antisense
GAGATCGTCATCGTCGAAATCGCAG 39 397 2213 Antisense
GAAGTCGGGATAGACGGCGGTGATT 424 331 2240 Antisense
GACGGCGGTGATTTCTTGTGGAATA 326 375 2252 Antisense
Sequence Source GenBank