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[173789_at] splicing factor

Description C67865 /REP_DB=TREMBL Accession /5_PRIME_EXT_ID=Y111B2A.18 /5_PRIME_EXT_DB=WormBase Gene ID /GB=C67865 /WB_GENE_ID=Y111B2A.18 /WP=CE24139 /CHR=3 /FEA=Genomic Cluster /DEF=splicing factor; C.elegans cDNA clone yk263b9 : 5prime end, single read.
Cluster 6grp_highest_10_10 > 91      6grp_high1_10_10 > 39      4grp_highest_8_8 > 16      4grp_high_8_8 > 52      6grp_highest_nonorm > 84      6grp_total > 39      4grp_total > 59      6grp_cgc > 08      6grp_high1_sub > Cu      6grp_cgc_sub > Cu      6grp_total_sub > Cup      4grp_rule_based > L2      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 923
1 2 3 4 range
A 1019
(1.8)
P 		795.2
(0.4)
P 		1197.3
(3)
P 		274.3
(-3)
P 		923
B 676.5
(-1.5)
P 		1168.1
(3)
P 		667.7
(-1.6)
P 		518.3
(-3)
P 		650
C 878.6
(0.7)
P 		1153.4
(2.9)
P 		1162.3
(3)
P 		435.9
(-3)
P 		726
avr 858
(1.3) 		1038.9
(3) 		1009.1
(2.7) 		409.5
(-3) 		629

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 567
1 2 3 4 5 6 range
A 554.2
(-0.1)
P 		540.7
(-0.3)
P 		464.7
(-1.4)
P 		351.7
(-3)
P 		764.3
(3)
P 		587.8
(0.4)
P 		413
B 740
(1)
P 		588.8
(-0.9)
P 		423.8
(-3)
P 		531.9
(-1.6)
P 		648.8
(-0.1)
P 		892.7
(3)
P 		469
C 717
(3)
P 		556.5
(0.5)
P 		486.5
(-0.5)
P 		377.4
(-2.2)
P 		547.6
(0.4)
P 		325.9
(-3)
P 		391
avr 670.4
(3) 		562
(0.4) 		458.3
(-2.1) 		420.3
(-3) 		653.6
(2.6) 		602.1
(1.4) 		250
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 365
1 2 3 4 range
A 371
(3)
P 		172.6
(-0.6)
P 		313
(1.9)
P 		40.1
(-3)
P 		331
B 215.7
(0.5)
P 		288.5
(3)
P 		154.7
(-1.5)
P 		110.4
(-3)
P 		178
C 290.8
(0.9)
P 		331.6
(1.7)
P 		405.1
(3)
P 		73.5
(-3)
P 		332
avr 292.5
(3) 		264.2
(2.2) 		290.9
(3) 		74.7
(-3) 		218

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 257
1 2 3 4 5 6 range
A 102.2
(-2.4)
P 		192.3
(1.4)
P 		101.2
(-2.5)
P 		89.2
(-3)
P 		230.6
(3)
P 		143.1
(-0.7)
P 		141
B 257.5
(1)
P 		196
(-0.6)
P 		102.9
(-3)
P 		140.9
(-2)
P 		263.6
(1.2)
P 		332.9
(3)
P 		230
C 265.7
(3)
P 		169.8
(-0)
P 		123.8
(-1.5)
P 		75.9
(-3)
P 		177.2
(0.2)
P 		109.1
(-2)
P 		190
avr 208.5
(2.2) 		186
(1.1) 		109.3
(-2.6) 		102
(-3) 		223.8
(3) 		195
(1.6) 		122
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 173789_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.23997
Sequence Type Exemplar sequence
Representative Public ID C67865 NCBI
Target Description C67865 /REP_DB=TREMBL Accession /5_PRIME_EXT_ID=Y111B2A.18 /5_PRIME_EXT_DB=WormBase Gene ID /GB=C67865 /WB_GENE_ID=Y111B2A.18 /WP=CE24139 /CHR=3 /FEA=Genomic Cluster /DEF=splicing factor; C.elegans cDNA clone yk263b9 : 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_067248(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_067248 NCBI Caenorhabditis elegans SR Protein (splicing factor) family member (rsp-3) (rsp-3) mRNA, complete cds. 11/11 A 
Y111B2A.18.1 ENSEMBL cdna:known chromosome:CEL140:III:12686128:12687791:-1 gene:Y111B2A.18 11/11 A 
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
chrIII:12686531-12687778(-) 100.0 100.0
Public Domain and Genome References
Gene Title splicing factor
Gene Symbol rsp-3
Ensembl Y111B2A.18
Entrez Gene 176688 Entrez gene
SwissProt Q9NEW6 EMBL-EBI
WormBase CE31089 Wormbase
Functional Annotations
Ortholog
ID Title Organism
ATH1-121501:262110_AT pre-mRNA splicing factor SF2 (SF2) / SR1 protein at
CANINE:1604184_AT similar to splicing factor, arginine/serine-rich 1 (ASF/SF2) cfa
CANINE_2:CFA.20238.1.S1_AT similar to splicing factor, arginine/serine-rich 1 (ASF/SF2) cfa
CANINE_2:CFA.21121.1.S1_AT similar to splicing factor, arginine/serine-rich 1 (ASF/SF2) cfa
CANINE_2:CFAAFFX.26676.1.S1_S_AT similar to splicing factor, arginine/serine-rich 1 (ASF/SF2) cfa
DROSOPHILA_2:1634975_AT Saccharomyces cerevisiae UAS construct a of Allemand dm
DROSGENOME1:154911_AT Saccharomyces cerevisiae UAS construct a of Allemand dm
HG-U95AV2:36099_AT splicing factor, arginine/serine-rich 1 (splicing factor 2, alternate splicing factor) hs
HG-U133_PLUS_2:208863_S_AT splicing factor, arginine/serine-rich 1 (splicing factor 2, alternate splicing factor) hs
HG-U133A:208863_S_AT splicing factor, arginine/serine-rich 1 (splicing factor 2, alternate splicing factor) hs
HG-FOCUS:208863_S_AT splicing factor, arginine/serine-rich 1 (splicing factor 2, alternate splicing factor) hs
HG-U133A_2:208863_S_AT splicing factor, arginine/serine-rich 1 (splicing factor 2, alternate splicing factor) hs
HG-U133_PLUS_2:201742_X_AT splicing factor, arginine/serine-rich 1 (splicing factor 2, alternate splicing factor) hs
HG-U133A:201742_X_AT splicing factor, arginine/serine-rich 1 (splicing factor 2, alternate splicing factor) hs
HG-U133A_2:201742_X_AT splicing factor, arginine/serine-rich 1 (splicing factor 2, alternate splicing factor) hs
HG-U133A:211784_S_AT splicing factor, arginine/serine-rich 1 (splicing factor 2, alternate splicing factor) hs
HG-U133_PLUS_2:211784_S_AT splicing factor, arginine/serine-rich 1 (splicing factor 2, alternate splicing factor) hs
HG-U133A_2:211784_S_AT splicing factor, arginine/serine-rich 1 (splicing factor 2, alternate splicing factor) hs
U133_X3P:G5902075_3P_S_AT splicing factor, arginine/serine-rich 1 (splicing factor 2, alternate splicing factor) hs
U133_X3P:G13544106_3P_S_AT splicing factor, arginine/serine-rich 1 (splicing factor 2, alternate splicing factor) hs
U133_X3P:HS.73737.0.S2_3P_AT splicing factor, arginine/serine-rich 1 (splicing factor 2, alternate splicing factor) hs
HG-U133A_2:201741_X_AT splicing factor, arginine/serine-rich 1 (splicing factor 2, alternate splicing factor) hs
HG-U133_PLUS_2:201741_X_AT splicing factor, arginine/serine-rich 1 (splicing factor 2, alternate splicing factor) hs
HG-U133A:201741_X_AT splicing factor, arginine/serine-rich 1 (splicing factor 2, alternate splicing factor) hs
HG-U95AV2:36098_AT splicing factor, arginine/serine-rich 1 (splicing factor 2, alternate splicing factor) hs
HG-U95E:91177_S_AT splicing factor, arginine/serine-rich 1 (splicing factor 2, alternate splicing factor) hs
HU35KSUBA:RC_AA256606_AT Splicing factor, arginine/serine-rich 1 (splicing factor 2, alternate splicing factor) hs
HU35KSUBB:RC_N70394_AT Splicing factor, arginine/serine-rich 1 (splicing factor 2, alternate splicing factor) hs
HU35KSUBC:RC_AA460420_AT Splicing factor, arginine/serine-rich 1 (splicing factor 2, alternate splicing factor) hs
U133_X3P:HS.73737.0.S2_3P_S_AT Splicing factor, arginine/serine-rich 1 (splicing factor 2, alternate splicing factor) hs
U133_X3P:HS.44949.0.A1_3P_AT Splicing factor, arginine/serine-rich 1 (splicing factor 2, alternate splicing factor) hs
U133_X3P:HS.36747.0.A1_3P_AT Splicing factor, arginine/serine-rich 1 (splicing factor 2, alternate splicing factor) hs
U133_X3P:HS.238956.1.A1_3P_X_AT Splicing factor, arginine/serine-rich 1 (splicing factor 2, alternate splicing factor) hs
U133_X3P:HS.238956.1.A1_3P_AT Splicing factor, arginine/serine-rich 1 (splicing factor 2, alternate splicing factor) hs
U133_X3P:HS.238956.0.A1_3P_AT Splicing factor, arginine/serine-rich 1 (splicing factor 2, alternate splicing factor) hs
HG-U133_PLUS_2:226419_S_AT Splicing factor, arginine/serine-rich 1 (splicing factor 2, alternate splicing factor) hs
HG-U133B:226419_S_AT Splicing factor, arginine/serine-rich 1 (splicing factor 2, alternate splicing factor) hs
HG-U133_PLUS_2:227164_AT Splicing factor, arginine/serine-rich 1 (splicing factor 2, alternate splicing factor) hs
HG-U133B:227164_AT Splicing factor, arginine/serine-rich 1 (splicing factor 2, alternate splicing factor) hs
HG-U133_PLUS_2:229246_AT Splicing factor, arginine/serine-rich 1 (splicing factor 2, alternate splicing factor) hs
HG-U133B:229246_AT Splicing factor, arginine/serine-rich 1 (splicing factor 2, alternate splicing factor) hs
HG-U133_PLUS_2:239384_AT Splicing factor, arginine/serine-rich 1 (splicing factor 2, alternate splicing factor) hs
HG-U133B:239384_AT Splicing factor, arginine/serine-rich 1 (splicing factor 2, alternate splicing factor) hs
HG-U95B:43496_AT Splicing factor, arginine/serine-rich 1 (splicing factor 2, alternate splicing factor) hs
HG-U95B:43497_G_AT Splicing factor, arginine/serine-rich 1 (splicing factor 2, alternate splicing factor) hs
HG-U95B:46035_AT Splicing factor, arginine/serine-rich 1 (splicing factor 2, alternate splicing factor) hs
HG-U95B:50952_AT Splicing factor, arginine/serine-rich 1 (splicing factor 2, alternate splicing factor) hs
HG-U95B:53598_S_AT Splicing factor, arginine/serine-rich 1 (splicing factor 2, alternate splicing factor) hs
HG-U95B:53602_R_AT Splicing factor, arginine/serine-rich 1 (splicing factor 2, alternate splicing factor) hs
HG-U95C:60888_R_AT Splicing factor, arginine/serine-rich 1 (splicing factor 2, alternate splicing factor) hs
HG-U95C:63834_AT Splicing factor, arginine/serine-rich 1 (splicing factor 2, alternate splicing factor) hs
HG-U95D:82512_AT Splicing factor, arginine/serine-rich 1 (splicing factor 2, alternate splicing factor) hs
HG-U95D:77431_AT Splicing factor, arginine/serine-rich 1 (splicing factor 2, alternate splicing factor) hs
HU35KSUBB:RC_AA086219_AT Splicing factor, arginine/serine-rich 1 (splicing factor 2, alternate splicing factor) hs
MOUSE430_2:1434972_X_AT splicing factor, arginine/serine-rich 1 (ASF/SF2) mm
MOE430A:1434972_X_AT splicing factor, arginine/serine-rich 1 (ASF/SF2) mm
MOUSE430A_2:1434972_X_AT splicing factor, arginine/serine-rich 1 (ASF/SF2) mm
MU11KSUBA:AA189518_S_AT splicing factor, arginine/serine-rich 1 (ASF/SF2) mm
MU11KSUBA:AA182347_AT splicing factor, arginine/serine-rich 1 (ASF/SF2) mm
MU11KSUBB:MSA.40152.0_F_AT splicing factor, arginine/serine-rich 1 (ASF/SF2) mm
MU11KSUBB:MSA.2163.0_G_AT splicing factor, arginine/serine-rich 1 (ASF/SF2) mm
MU11KSUBB:MSA.2163.0_AT splicing factor, arginine/serine-rich 1 (ASF/SF2) mm
MU11KSUBB:MSA.21192.0_F_AT splicing factor, arginine/serine-rich 1 (ASF/SF2) mm
MG-U74AV2:101022_AT splicing factor, arginine/serine-rich 1 (ASF/SF2) mm
MG-U74AV2:104586_AT splicing factor, arginine/serine-rich 1 (ASF/SF2) mm
MG-U74BV2:105797_AT splicing factor, arginine/serine-rich 1 (ASF/SF2) mm
MG-U74AV2:160539_AT splicing factor, arginine/serine-rich 1 (ASF/SF2) mm
MG-U74AV2:160141_R_AT splicing factor, arginine/serine-rich 1 (ASF/SF2) mm
MG-U74CV2:167618_R_AT splicing factor, arginine/serine-rich 1 (ASF/SF2) mm
MG-U74CV2:169749_R_AT splicing factor, arginine/serine-rich 1 (ASF/SF2) mm
MOE430A:1453722_S_AT splicing factor, arginine/serine-rich 1 (ASF/SF2) mm
MOUSE430A_2:1453722_S_AT splicing factor, arginine/serine-rich 1 (ASF/SF2) mm
MOUSE430_2:1453722_S_AT splicing factor, arginine/serine-rich 1 (ASF/SF2) mm
MOE430A:1452430_S_AT splicing factor, arginine/serine-rich 1 (ASF/SF2) mm
MOUSE430A_2:1452430_S_AT splicing factor, arginine/serine-rich 1 (ASF/SF2) mm
MOUSE430_2:1452430_S_AT splicing factor, arginine/serine-rich 1 (ASF/SF2) mm
MOE430A:1428099_A_AT splicing factor, arginine/serine-rich 1 (ASF/SF2) mm
MOUSE430A_2:1428099_A_AT splicing factor, arginine/serine-rich 1 (ASF/SF2) mm
MOUSE430_2:1428099_A_AT splicing factor, arginine/serine-rich 1 (ASF/SF2) mm
MOE430A:1428100_AT splicing factor, arginine/serine-rich 1 (ASF/SF2) mm
MOUSE430A_2:1428100_AT splicing factor, arginine/serine-rich 1 (ASF/SF2) mm
MOUSE430_2:1428100_AT splicing factor, arginine/serine-rich 1 (ASF/SF2) mm
MOE430A:1430982_AT splicing factor, arginine/serine-rich 1 (ASF/SF2) mm
MOUSE430A_2:1430982_AT splicing factor, arginine/serine-rich 1 (ASF/SF2) mm
MOUSE430_2:1430982_AT splicing factor, arginine/serine-rich 1 (ASF/SF2) mm
MOE430B:1457136_AT splicing factor, arginine/serine-rich 1 (ASF/SF2) mm
MOUSE430_2:1457136_AT splicing factor, arginine/serine-rich 1 (ASF/SF2) mm
MU19KSUBA:TC19134_AT ASF mRNA mm
MU19KSUBA:TC19135_S_AT ASF mRNA mm
MU19KSUBA:TC21708_AT ASF mRNA mm
MU19KSUBA:TC23311_F_AT ASF mRNA mm
MU19KSUBA:TC25392_AT ASF mRNA mm
MU19KSUBB:TC30803_AT ASF mRNA mm
MU19KSUBB:TC32978_S_AT ASF mRNA mm
MU19KSUBC:TC36617_S_AT ASF mRNA mm
Gene Ontology
GO Biological Process (view graph)
ID Description Evidence Links
6397 mRNA processing inferred from sequence similarity QuickGO AmiGO
6376 mRNA splice site selection inferred from sequence similarity QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast AAG36874 SF2 [Caenorhabditis elegans] 3.0E-79
blast CAC35847 Hypothetical protein Y111B2A.18 [Caenorhabditis elegans] ref|NP_499649.2| SR Protein (splicing factor) family member (rsp-3) [Caenorhabditis elegans] sp|Q9NEW6|RSP3_CAEEL Probable splicing factor, arginine/serine-rich 3 (CeSF2) (CeSF2/ASF) 4.0E-79
blast CAE60051 Hypothetical protein CBG03563 [Caenorhabditis briggsae] 8.0E-65
Protein Domains
Database ID Description E-Value
Pfam IPR000504 EMBL-EBI RNA-binding region RNP-1 (RNA recognition motif) 1.5E-23
Pfam IPR000504 EMBL-EBI RNA-binding region RNP-1 (RNA recognition motif) 5.3E-15
Sequence
Target Sequence 
>C. ELEGANS:173789_AT
actatatcttgctaatttctttttttttgtgctgtttctaatacaattccatgcctcatg
ttctcctgtttacacacacctttttctttttatcgatctttttggatatatatatccaca
atttcttctattttttatcacctatccttaattcaaacaaccacatccaagtattcatca
gccccacctattattattcaataatttcttttgttggaggaaccacgaataaaatgtttt
gtttcagcctccac

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
ACTATATCTTGCTAATTTCTTTTTT 174 103 793 Antisense
TCTTTTTTTTTGTGCTGTTTCTAAT 200 615 810 Antisense
GTGCTGTTTCTAATACAATTCCATG 671 477 821 Antisense
TTTCTTTTTATCGATCTTTTTGGAT 77 673 875 Antisense
ATATATCCACAATTTCTTCTATTTT 419 19 902 Antisense
TCTATTTTTTATCACCTATCCTTAA 201 615 919 Antisense
ATCACCTATCCTTAATTCAAACAAC 161 29 929 Antisense
TAATTCAAACAACCACATCCAAGTA 74 635 941 Antisense
ATCAGCCCCACCTATTATTATTCAA 696 27 969 Antisense
TATTCAATAATTTCTTTTGTTGGAG 506 661 987 Antisense
TAAAATGTTTTGTTTCAGCCTCCAC 46 639 1022 Antisense
Sequence Source Affymetrix Proprietary Database