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[171835_x_at] pre-mRNA splicing factor like protein

Description CEC836_rc /REP_DB=TREMBL Accession /GB=C07836 /FEA=Transcript Cluster /DEF=C.elegans cDNA clone yk167c1 : 3prime end, single read.
Cluster 6grp_highest_10_10 > 95      6grp_high1_10_10 > 58      4grp_highest_8_8 > 10      4grp_high_8_8 > 54      6grp_highest_nonorm > 74      6grp_total > 49      4grp_total > 57      6grp_highest_sub > Cu      6grp_cgc > 18      6grp_high1_sub > Cu      6grp_cgc_sub > Cu      6grp_total_sub > Cup      4grp_rule_based > L3      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 437
1 2 3 4 range
A 849.5
(-1.2)
P 		1002
(1.7)
P 		1066.3
(3)
P 		760.2
(-3)
P 		306
B 737.7
(-3)
P 		1141.9
(2.7)
P 		1162
(3)
P 		802.1
(-2.1)
P 		424
C 872.7
(-0.1)
P 		948
(1.3)
P 		1032.5
(3)
P 		725.4
(-3)
P 		307
avr 820
(-1.9) 		1030.6
(2) 		1086.9
(3) 		762.6
(-3) 		324

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 411
1 2 3 4 5 6 range
A 555
(-2.2)
P 		746.3
(1.8)
P 		657.1
(-0.1)
P 		518.8
(-3)
P 		633.2
(-0.6)
P 		805
(3)
P 		286
B 836.8
(2.7)
P 		690.3
(0.2)
P 		610.3
(-1.2)
P 		504.4
(-3)
P 		637.8
(-0.7)
P 		854.1
(3)
P 		350
C 913.7
(3)
P 		611.4
(-1.4)
P 		595.3
(-1.6)
P 		502.5
(-3)
P 		837.2
(1.9)
P 		879.7
(2.5)
P 		411
avr 768.5
(1.6) 		682.7
(0.1) 		620.9
(-1) 		508.6
(-3) 		702.7
(0.4) 		846.3
(3) 		338
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 249
1 2 3 4 range
A 309.3
(3)
P 		217.5
(0.2)
P 		278.8
(2.1)
P 		111.3
(-3)
P 		198
B 235.2
(0.5)
P 		282
(3)
P 		269.3
(2.3)
P 		170.9
(-3)
P 		111
C 288.9
(1.2)
P 		272.6
(0.8)
P 		359.8
(3)
P 		122.3
(-3)
P 		238
avr 277.8
(2.1) 		257.4
(1.4) 		302.6
(3) 		134.8
(-3) 		168

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 238
1 2 3 4 5 6 range
A 102.3
(-3)
P 		265.4
(3)
P 		143.1
(-1.5)
P 		131.6
(-1.9)
P 		191.1
(0.3)
P 		196
(0.4)
P 		163
B 291.2
(2.1)
P 		229.8
(0.1)
P 		148.2
(-2.5)
P 		133.6
(-3)
P 		259.1
(1.1)
P 		318.5
(3)
P 		185
C 338.7
(3)
P 		186.5
(-0.8)
P 		151.5
(-1.7)
P 		101.1
(-3)
P 		270.9
(1.3)
P 		294.5
(1.9)
P 		238
avr 244.1
(2) 		227.2
(1.3) 		147.6
(-2) 		122.1
(-3) 		240.4
(1.8) 		269.7
(3) 		148
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 171835_x_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.27702
Sequence Type Exemplar sequence
Representative Public ID CEC836 NCBI
Target Description CEC836_rc /REP_DB=TREMBL Accession /GB=C07836 /FEA=Transcript Cluster /DEF=C.elegans cDNA clone yk167c1 : 3prime end, single read.
Cluster Evidence This cluster is supported by a Transcript Cluster.
Annotation Method Description
Annotation Description This probe set was annotated using the Genome Target Overlap based pipeline to a RefSeq identifier using 1 transcript(s).
Annotation Grade This is a grade B annotation.
Annotation Transcript Cluster (# of Matching Probes) NM_064040
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
SNAP00000002906 ENSEMBL cdna:SNAP chromosome:CEL140:II:11451568:11452850:-1 None
W02B12.2.1 ENSEMBL cdna:known chromosome:CEL140:II:11451289:11452860:-1 gene:W02B12.2 A 
GENEFINDER00000002923 ENSEMBL cdna:GeneFinder chromosome:CEL140:II:11451568:11452850:-1 None
NM_064040 NCBI Caenorhabditis elegans SR Protein (splicing factor) family member (rsp-2) (rsp-2) mRNA, complete cds. A 
W02B12.2.2 ENSEMBL cdna:known chromosome:CEL140:II:11451349:11452860:-1 gene:W02B12.2 A 
W02B12.2.3 ENSEMBL cdna:known chromosome:CEL140:II:11451568:11452866:-1 gene:W02B12.2 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
chrII:11451451-11451764(-) 87.67 87.67
Public Domain and Genome References
Gene Title pre-mRNA splicing factor like protein
Gene Symbol rsp-2
Ensembl W02B12.2
Entrez Gene 174747 Entrez gene
SwissProt Q23120 EMBL-EBI
WormBase CE03762 Wormbase
Functional Annotations
Ortholog
ID Title Organism
CANINE:1589333_AT similar to Splicing factor, arginine/serine-rich 5 (Pre-mRNA splicing factor SRP40) (Insulin-induced growth response protein CL-4) (Delayed-early protein HRS) cfa
CANINE:1587887_AT similar to Splicing factor, arginine/serine-rich 5 (Pre-mRNA splicing factor SRP40) (Insulin-induced growth response protein CL-4) (Delayed-early protein HRS) cfa
CANINE:1587542_AT similar to Splicing factor, arginine/serine-rich 5 (Pre-mRNA splicing factor SRP40) (Insulin-induced growth response protein CL-4) (Delayed-early protein HRS) cfa
CANINE_2:CFA.12115.3.A1_AT similar to Splicing factor, arginine/serine-rich 5 (Pre-mRNA splicing factor SRP40) (Insulin-induced growth response protein CL-4) (Delayed-early protein HRS) cfa
CANINE_2:CFA.12115.3.A1_S_AT similar to Splicing factor, arginine/serine-rich 5 (Pre-mRNA splicing factor SRP40) (Insulin-induced growth response protein CL-4) (Delayed-early protein HRS) cfa
CANINE_2:CFA.4157.1.S1_AT similar to Splicing factor, arginine/serine-rich 5 (Pre-mRNA splicing factor SRP40) (Insulin-induced growth response protein CL-4) (Delayed-early protein HRS) cfa
CANINE_2:CFAAFFX.25382.1.S1_S_AT similar to Splicing factor, arginine/serine-rich 5 (Pre-mRNA splicing factor SRP40) (Insulin-induced growth response protein CL-4) (Delayed-early protein HRS) cfa
CHICKEN:GGA.15313.1.S1_AT similar to Sfrs4 protein gga
HG-U133_PLUS_2:242837_AT splicing factor, arginine/serine-rich 4 hs
HG-U133B:242837_AT splicing factor, arginine/serine-rich 4 hs
HG-U133_PLUS_2:201696_AT splicing factor, arginine/serine-rich 4 hs
HG-FOCUS:201696_AT splicing factor, arginine/serine-rich 4 hs
HG-U133A:201696_AT splicing factor, arginine/serine-rich 4 hs
HG-U133A_2:201696_AT splicing factor, arginine/serine-rich 4 hs
HG-U95AV2:36991_AT splicing factor, arginine/serine-rich 4 hs
HUGENEFL:L14076_AT splicing factor, arginine/serine-rich 4 hs
U133_X3P:G5032088_3P_AT splicing factor, arginine/serine-rich 4 hs
U133_X3P:HS.115472.2.A1_3P_AT splicing factor, arginine/serine-rich 4 hs
U133_X3P:HS.115472.0.S1_3P_AT splicing factor, arginine/serine-rich 4 hs
HG-U133_PLUS_2:239511_S_AT splicing factor, arginine/serine-rich 4 hs
HG-U133B:239511_S_AT splicing factor, arginine/serine-rich 4 hs
HG-U133_PLUS_2:239512_AT splicing factor, arginine/serine-rich 4 hs
HG-U133B:239512_AT splicing factor, arginine/serine-rich 4 hs
HG-U95E:81073_AT splicing factor, arginine/serine-rich 4 hs
HG-U133_PLUS_2:241245_AT Splicing factor, arginine/serine-rich 4 hs
HG-U133B:241245_AT Splicing factor, arginine/serine-rich 4 hs
HG-U95C:57121_R_AT Splicing factor, arginine/serine-rich 4 hs
U133_X3P:HS.115472.1.A1_3P_AT Splicing factor, arginine/serine-rich 4 hs
RAE230B:1381623_AT similar to Sfrs4 protein rn
RAT230_2:1381623_AT similar to Sfrs4 protein rn
RAE230B:1396759_AT Similar to Sfrs4 protein rn
RAT230_2:1396759_AT Similar to Sfrs4 protein rn
Protein Similarities
Method ID Description E-Value
blast CAA91394 Hypothetical protein W02B12.2 [Caenorhabditis elegans] ref|NP_496441.1| SR Protein (splicing factor) family member (rsp-2) [Caenorhabditis elegans] sp|Q23120|RSP2_CAEEL Probable splicing factor, arginine/serine-rich 2 (RNA-binding protein srp-4) (CeSRp40) 1.0E-106
blast CAE59505 Hypothetical protein CBG02891 [Caenorhabditis briggsae] 1.0E-102
Protein Domains
Database ID Description E-Value
Pfam IPR000504 EMBL-EBI RNA-binding region RNP-1 (RNA recognition motif) 8.4E-16
Pfam IPR000504 EMBL-EBI RNA-binding region RNP-1 (RNA recognition motif) 6.3E-9
Sequence
Target Sequence 
>C. ELEGANS:171835_X_AT
acgatccgacaagagagctcgcagtgagagcaagagccgttctcgttccggcggaagacg
ttcccgctccaactctccaccaaaccgttctccatcaccaaagaaaagacgcgacnnnnn
nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnncacctctcatgtga
aatttcctgttccatctannnnnnnatcgtaacgtcagtaactcgtgcccaaagccgaat
catgtaatcgaccaatctaat

BLASTn GenBank NR
Note: "n"'s represent regions that are not probed by the probe sequences.
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
ACGATCCGACAAGAGAGCTCGCAGT 157 93 14 Antisense
GAGCTCGCAGTGAGAGCAAGAGCCG 249 387 28 Antisense
TGAGAGCAAGAGCCGTTCTCGTTCC 443 567 38 Antisense
ACCGTTCTCCATCACCAAAGAAAAG 262 89 97 Antisense
TCCATCACCAAAGAAAAGACGCGAC 370 591 104 Antisense
CACCTCTCATGTGAAATTTCCTGTT 643 201 180 Antisense
CATGTGAAATTTCCTGTTCCATCTA 88 211 187 Antisense
TCGTAACGTCAGTAACTCGTGCCCA 106 603 220 Antisense
TAACTCGTGCCCAAAGCCGAATCAT 527 637 232 Antisense
GTGCCCAAAGCCGAATCATGTAATC 689 477 238 Antisense
GAATCATGTAATCGACCAATCTAAT 648 327 250 Antisense
Sequence Source Affymetrix Proprietary Database