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[189363_at]

Description T28D9.2 /REP_DB=WormBase Gene ID /WP=CE02067 /CHR=2 /FEA=Sanger Annotation /DEF=splicing factor (ST.LOUIS) SW:Q10021 protein_id:AAA68314.1
Cluster 6grp_highest_10_10 > 88      6grp_high1_10_10 > 88      4grp_highest_8_8 > 09      4grp_high_8_8 > 54      6grp_highest_nonorm > 97      6grp_total > 88      4grp_total > 58      6grp_highest_sub > Da      6grp_cgc > 59      6grp_high1_sub > Da      6grp_cgc_sub > Da      6grp_total_sub > Increase      6grp_rule_based > S6      4grp_rule_based > L3      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 440
1 2 3 4 range
A 835.2
(-3)
P 		1108
(2.5)
P 		1132
(3)
P 		848.3
(-2.7)
P 		297
B 950.1
(1.6)
P 		1002.6
(3)
P 		972.2
(2.2)
P 		771.6
(-3)
P 		231
C 822.3
(-1)
P 		987.5
(1.6)
P 		1075.4
(3)
P 		691.9
(-3)
P 		384
avr 869.2
(-1) 		1032.7
(2.4) 		1059.9
(3) 		770.6
(-3) 		289

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 1252
1 2 3 4 5 6 range
A 701.2
(-2.5)
P 		740.7
(-2.3)
P 		592.8
(-3)
P 		859.2
(-1.7)
P 		1087.8
(-0.5)
P 		1788.4
(3)
P 		1196
B 697.6
(-2.1)
P 		588.2
(-2.7)
P 		536.2
(-3)
P 		690.1
(-2.1)
P 		1093.6
(0.1)
P 		1602.2
(3)
P 		1066
C 720.8
(-2.2)
P 		595.1
(-3)
P 		738
(-2.1)
P 		739.4
(-2.1)
P 		1223.6
(0.9)
P 		1568
(3)
P 		973
avr 706.5
(-2.5) 		641.3
(-2.9) 		622.3
(-3) 		762.9
(-2.2) 		1135
(-0) 		1652.9
(3) 		1031
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 258
1 2 3 4 range
A 304.1
(3)
P 		240.5
(0.9)
P 		295.9
(2.7)
P 		124.2
(-3)
P 		180
B 303
(3)
P 		247.6
(0.6)
P 		225.3
(-0.4)
P 		164.4
(-3)
P 		139
C 272.2
(0.6)
P 		283.9
(0.9)
P 		374.8
(3)
P 		116.7
(-3)
P 		258
avr 293.1
(2.8) 		257.3
(1.5) 		298.7
(3) 		135.1
(-3) 		164

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 468
1 2 3 4 5 6 range
A 129.3
(-3)
P 		263.4
(-0.4)
P 		129.1
(-3)
P 		217.9
(-1.3)
P 		328.3
(0.9)
P 		435.4
(3)
P 		306
B 242.7
(-1.6)
P 		195.8
(-2.2)
P 		130.2
(-3)
P 		182.8
(-2.3)
P 		444.3
(1)
P 		597.5
(3)
P 		467
C 267.2
(-1.1)
P 		181.6
(-2.5)
P 		187.8
(-2.4)
P 		148.7
(-3)
P 		395.9
(0.9)
P 		524.9
(3)
P 		376
avr 213.1
(-2) 		213.6
(-2) 		149
(-3) 		183.1
(-2.4) 		389.5
(0.9) 		519.3
(3) 		370
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 189363_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.4617
Sequence Type Exemplar sequence
Representative Public ID T28D9.2 NCBI
Target Description T28D9.2 /REP_DB=WormBase Gene ID /WP=CE02067 /CHR=2 /FEA=Sanger Annotation /DEF=splicing factor (ST.LOUIS) SW:Q10021 protein_id:AAA68314.1
Cluster Evidence This cluster is supported by a 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_062907(11), NM_062908(11), NM_062906(11), NM_062909(9)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_062907 NCBI Caenorhabditis elegans SR Protein (splicing factor) family member (rsp-5) (rsp-5) mRNA, complete cds. 11/11 None
NM_062908 NCBI Caenorhabditis elegans SR Protein (splicing factor) family member (rsp-5) (rsp-5) mRNA, complete cds. 11/11 None
NM_062906 NCBI Caenorhabditis elegans SR Protein (splicing factor) family member (rsp-5) (rsp-5) mRNA, complete cds. 11/11 None
NM_062909 NCBI Caenorhabditis elegans SR Protein (splicing factor) family member (rsp-5) (rsp-5) mRNA, complete cds. 9/11 A 
SNAP00000011381 ENSEMBL cdna:SNAP chromosome:CEL140:II:6490116:6490610:1 11/11 None
GENEFINDER00000011385 ENSEMBL cdna:GeneFinder chromosome:CEL140:II:6490116:6491165:1 11/11 None
T28D9.2d ENSEMBL cdna:known chromosome:CEL140:II:6490105:6491216:1 gene:T28D9.2 11/11 A 
T28D9.2a ENSEMBL cdna:known chromosome:CEL140:II:6490116:6491255:1 gene:T28D9.2 11/11 A 
T28D9.2b ENSEMBL cdna:known chromosome:CEL140:II:6490116:6491292:1 gene:T28D9.2 11/11 A 
T28D9.2c ENSEMBL cdna:known chromosome:CEL140:II:6490255:6491216:1 gene:T28D9.2 9/11 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
chrII:6490112-6491162(+) 99.84 99.84
Public Domain and Genome References
Ensembl T28D9.2
Functional Annotations
Protein Similarities
Method ID Description E-Value
blast AAK68400 Sr protein (splicing factor) protein 5, isoform c [Caenorhabditis elegans] ref|NP_495310.1| SR Protein (splicing factor) family member (rsp-5) [Caenorhabditis elegans] 2.0E-88
blast AAK72066 Sr protein (splicing factor) protein 5, isoform d [Caenorhabditis elegans] ref|NP_495308.3| SR Protein (splicing factor) family member (rsp-5) [Caenorhabditis elegans] 1.0E-66
blast AAA68314 Sr protein (splicing factor) protein 5, isoform a [Caenorhabditis elegans] ref|NP_495307.3| SR Protein (splicing factor) family member (rsp-5) [Caenorhabditis elegans] sp|Q10021|RSP5_CAEEL Probable splicing factor, arginine/serine-rich 5 (RNA-binding protein srp-3) (CeSC35-2) 2.0E-64
blast T16953 hypothetical protein T28D9.2 - Caenorhabditis elegans 2.0E-63
Protein Domains
Database ID Description E-Value
Pfam IPR000504 EMBL-EBI RNA-binding region RNP-1 (RNA recognition motif) 1.5E-16
Sequence
Target Sequence 
>C. ELEGANS:189363_AT
tgccgcgcctctatctaggaaaaattccatacaattgtcacgaacgcgacgttgagcgat
tcttaaaaggatatggcaaaattaataacatctcaatgaagtatggatttgcctttgtcg
attttgaagattctcgtgatgctgaagacgcatgccatgatttggatggaaaaaccatgg
aaggaagctctatgcgccttgtcgtggaaatggctcgcggaaaaccacgcggcaatgacc
gtcatggatcgagatcaccacgacgacgttcccgctctcctagacgtcgttcacgtactc
caccaagaagacgttcccgctctcgtgatcgcaaacgttctcgcagatcccgttccagaa
gctcctccagatccagatcaccagttcgtgaaagtcgtcgcagaagcgaatcccgttcgc
c

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
TGCCGCGCCTCTATCTAGGAAAAAT 656 583 14 Antisense
GTATGGATTTGCCTTTGTCGATTTT 62 457 114 Antisense
GGAAGGAAGCTCTATGCGCCTTGTC 550 531 192 Antisense
GCGCCTTGTCGTGGAAATGGCTCGC 283 287 207 Antisense
AACCACGCGGCAATGACCGTCATGG 39 147 236 Antisense
TGGATCGAGATCACCACGACGACGT 551 543 258 Antisense
TCTCCTAGACGTCGTTCACGTACTC 659 607 289 Antisense
GTTCACGTACTCCACCAAGAAGACG 303 443 302 Antisense
GATCGCAAACGTTCTCGCAGATCCC 595 417 340 Antisense
TCCTCCAGATCCAGATCACCAGTTC 249 593 376 Antisense
GTCGCAGAAGCGAATCCCGTTCGCC 629 473 410 Antisense
Sequence Source Affymetrix Proprietary Database