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[174000_at]

Description AV187582 /REP_DB=TREMBL Accession /5_PRIME_EXT_ID=EEED8.7 /5_PRIME_EXT_DB=WormBase Gene ID /GB=AV187582 /WB_GENE_ID=EEED8.7 /WP=CE01891 /CHR=2 /FEA=Genomic Cluster /DEF=splicing factor SC35 (ST.LOUIS) SW:Q09511 protein_id:AAC46767.1; Caenorhabditis elegans cDNA clone:yk513e9 : 5prime end, single read.
Cluster 6grp_highest_10_10 > 95      6grp_high1_10_10 > 68      4grp_highest_8_8 > 10      4grp_high_8_8 > 55      6grp_highest_nonorm > 82      6grp_total > 79      4grp_total > 56      6grp_highest_sub > Cu      6grp_cgc > 29      6grp_high1_sub > Cu      6grp_cgc_sub > Cu      4grp_rule_based > L3      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 573
1 2 3 4 range
A 173.3
(-2.9)
P 		388.4
(-0.5)
P 		699.3
(3)
P 		168.5
(-3)
P 		531
B 265.6
(-3)
P 		496.8
(-0.1)
P 		741.2
(3)
P 		285.5
(-2.7)
P 		476
C 267.2
(-1.7)
P 		589.8
(3)
P 		589.6
(3)
P 		174.2
(-3)
P 		416
avr 235.4
(-2.7) 		491.7
(0.6) 		676.7
(3) 		209.4
(-3) 		467

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 413
1 2 3 4 5 6 range
A 355.8
(-0.8)
P 		433.7
(0.6)
P 		365
(-0.7)
P 		232.1
(-3)
P 		371.9
(-0.5)
P 		572.6
(3)
P 		341
B 342
(-1.4)
P 		417.5
(-0.3)
P 		235.3
(-3)
P 		286.6
(-2.2)
P 		379.8
(-0.9)
P 		645.1
(3)
P 		410
C 329.9
(-2.5)
P 		372.3
(-1.3)
P 		312.8
(-2.9)
P 		310.5
(-3)
P 		383.9
(-1)
P 		528.5
(3)
P 		218
avr 342.6
(-1.7) 		407.8
(-0.4) 		304.4
(-2.5) 		276.4
(-3) 		378.5
(-1) 		582.1
(3) 		306
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 181
1 2 3 4 range
A 63.1
(-1.5)
P 		84.3
(-0.7)
P 		182.8
(3)
P 		24.7
(-3)
P 		158
B 84.7
(-1.7)
P 		122.7
(0.3)
P 		171.7
(3)
P 		60.9
(-3)
P 		111
C 88.4
(-1)
P 		169.6
(1.8)
P 		205.5
(3)
P 		29.4
(-3)
P 		176
avr 78.7
(-1.4) 		125.5
(0.5) 		186.7
(3) 		38.3
(-3) 		148

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 184
1 2 3 4 5 6 range
A 65.6
(-2.6)
P 		154.3
(3)
P 		79.5
(-1.7)
P 		58.9
(-3)
P 		112.2
(0.4)
P 		139.4
(2.1)
P 		95
B 119
(-1)
P 		139
(-0.3)
P 		57.1
(-3)
P 		75.9
(-2.4)
P 		154.3
(0.2)
P 		240.6
(3)
P 		184
C 122.3
(0.1)
P 		113.6
(-0.3)
P 		79.6
(-2.1)
P 		62.4
(-3)
P 		124.2
(0.2)
P 		176.9
(3)
P 		115
avr 102.3
(-1.2) 		135.6
(0.5) 		72.1
(-2.7) 		65.7
(-3) 		130.2
(0.2) 		185.6
(3) 		120
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 174000_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.23560
Sequence Type Exemplar sequence
Representative Public ID AV187582 NCBI
Target Description AV187582 /REP_DB=TREMBL Accession /5_PRIME_EXT_ID=EEED8.7 /5_PRIME_EXT_DB=WormBase Gene ID /GB=AV187582 /WB_GENE_ID=EEED8.7 /WP=CE01891 /CHR=2 /FEA=Genomic Cluster /DEF=splicing factor SC35 (ST.LOUIS) SW:Q09511 protein_id:AAC46767.1; Caenorhabditis elegans cDNA clone:yk513e9 : 5prime 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_062612(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_062612 NCBI Caenorhabditis elegans SR Protein (splicing factor) family member (rsp-4) (rsp-4) mRNA, complete cds. 11/11 None
EEED8.7a ENSEMBL cdna:known chromosome:CEL140:II:5387389:5388796:-1 gene:EEED8.7 11/11 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
173915 2 1 NM_062612 174000_at (11), 190239_s_at (11)
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrII:5387397-5388795(-) 100.0 100.0
Public Domain and Genome References
Ensembl EEED8.7
Functional Annotations
Protein Similarities
Method ID Description E-Value
blast AAK68298 Sr protein (splicing factor) protein 4, isoform b [Caenorhabditis elegans] ref|NP_495014.1| SR Protein (splicing factor) family member (rsp-4) [Caenorhabditis elegans] 2.0E-44
blast AAC46767 Sr protein (splicing factor) protein 4, isoform a [Caenorhabditis elegans] ref|NP_495013.1| SR Protein (splicing factor) family member (rsp-4) [Caenorhabditis elegans] sp|Q09511|RSP4_CAEEL Probable splicing factor, arginine/serine-rich 4 (RNA-binding protein srp-2) (CeSC35) 2.0E-44
blast CAE59091 Hypothetical protein CBG02383 [Caenorhabditis briggsae] 1.0E-43
Protein Domains
Database ID Description E-Value
Pfam IPR000504 EMBL-EBI RNA-binding region RNP-1 (RNA recognition motif) 8.2E-22
Sequence
Target Sequence 
>C. ELEGANS:174000_AT
gaaaaaatttcctcttcgatttctgattatttttcgttttcgttttcgtttttactatga
tttactcactgatcctgaaatttcaaacgtcttttttttccagttgcctccaacaagaca
agtaatatatatgatttccaattttccatctaatttctccaa

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GAAAAAATTTCCTCTTCGATTTCTG 143 331 610 Antisense
ATTTCCTCTTCGATTTCTGATTATT 587 17 616 Antisense
CTTCGATTTCTGATTATTTTTCGTT 323 219 623 Antisense
TTCGTTTTTACTATGATTTACTCAC 368 695 654 Antisense
TATGATTTACTCACTGATCCTGAAA 267 657 665 Antisense
GATCCTGAAATTTCAAACGTCTTTT 491 415 680 Antisense
TTTTTTTCCAGTTGCCTCCAACAAG 571 673 702 Antisense
TTTCCAGTTGCCTCCAACAAGACAA 445 669 706 Antisense
AGTTGCCTCCAACAAGACAAGTAAT 436 63 711 Antisense
GACAAGTAATATATATGATTTCCAA 609 361 726 Antisense
CCAATTTTCCATCTAATTTCTCCAA 308 277 747 Antisense
Sequence Source Affymetrix Proprietary Database