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[171761_x_at]

Description AV185416_rc /REP_DB=TREMBL Accession /GB=AV185416 /CHR=2 /FEA=Genomic Cluster /DEF=Caenorhabditis elegans cDNA clone:yk678b1 : 3prime end, single read.
Cluster 6grp_highest_10_10 > 78      6grp_high1_10_10 > 87      4grp_highest_8_8 > 63      4grp_high_8_8 > 28      6grp_highest_nonorm > 94      6grp_total > 77      4grp_total > 36      6grp_highest_sub > In      6grp_cgc > 49      6grp_high1_sub > In      6grp_cgc_sub > Da      6grp_total_sub > Increase      6grp_rule_based > S6      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 228
1 2 3 4 range
A 433.9
(-3)
P 		602.7
(1.5)
P 		497.2
(-1.3)
P 		661.4
(3)
P 		228
B 621.9
(3)
P 		622
(3)
P 		512.9
(-3)
P 		512.5
(-3)
P 		110
C 575.4
(3)
P 		572.2
(2.9)
P 		439.3
(-3)
P 		458.7
(-2.1)
P 		136
avr 543.7
(0.1) 		599
(3) 		483.1
(-3) 		544.2
(0.2) 		116

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 796
1 2 3 4 5 6 range
A 316.1
(-3)
P 		463.9
(-1.9)
P 		338.9
(-2.8)
P 		503.8
(-1.6)
P 		586.6
(-1)
P 		1112.1
(3)
P 		796
B 355.3
(-2.8)
P 		382.1
(-2.6)
P 		334.2
(-3)
P 		424.6
(-2.2)
P 		636.6
(-0.5)
P 		1046.4
(3)
P 		712
C 416.4
(-2.4)
P 		365.3
(-3)
P 		457.5
(-2)
P 		360.3
(-3)
P 		684.2
(0.2)
P 		965.6
(3)
P 		605
avr 362.6
(-3) 		403.8
(-2.6) 		376.9
(-2.9) 		429.6
(-2.4) 		635.8
(-0.6) 		1041.4
(3) 		679
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 121
1 2 3 4 range
A 158
(3)
P 		130.8
(0.3)
P 		130
(0.3)
P 		96.8
(-3)
P 		61
B 198.3
(3)
P 		153.6
(-0)
P 		118.9
(-2.3)
P 		109.2
(-3)
P 		89
C 190.5
(3)
P 		164.5
(1.6)
P 		153.1
(1)
P 		77.3
(-3)
P 		113
avr 182.3
(3) 		149.6
(0.8) 		134
(-0.3) 		94.4
(-3) 		88

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 332
1 2 3 4 5 6 range
A 58.3
(-3)
P 		165
(0)
P 		73.8
(-2.6)
P 		127.8
(-1)
P 		177
(0.4)
P 		270.8
(3)
P 		213
B 123.6
(-2.2)
P 		127.2
(-2.1)
P 		81.2
(-3)
P 		112.5
(-2.4)
P 		258.6
(0.4)
P 		390.2
(3)
P 		309
C 154.3
(-1)
P 		111.5
(-2.1)
P 		116.4
(-1.9)
P 		72.5
(-3)
P 		221.4
(0.6)
P 		323.2
(3)
P 		251
avr 112.1
(-2.5) 		134.6
(-1.9) 		90.5
(-3) 		104.3
(-2.7) 		219
(0.2) 		328.1
(3) 		238
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 171761_x_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.20823
Sequence Type Exemplar sequence
Representative Public ID AV185416 NCBI
Target Description AV185416_rc /REP_DB=TREMBL Accession /GB=AV185416 /CHR=2 /FEA=Genomic Cluster /DEF=Caenorhabditis elegans cDNA clone:yk678b1 : 3prime 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_062907(9), NM_062908(10), NM_062906(9), NM_062909(11)
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. 9/11 A 
NM_062908 NCBI Caenorhabditis elegans SR Protein (splicing factor) family member (rsp-5) (rsp-5) mRNA, complete cds. 10/11 None
NM_062906 NCBI Caenorhabditis elegans SR Protein (splicing factor) family member (rsp-5) (rsp-5) mRNA, complete cds. 9/11 A 
NM_062909 NCBI Caenorhabditis elegans SR Protein (splicing factor) family member (rsp-5) (rsp-5) mRNA, complete cds. 11/11 A 
T28D9.2d ENSEMBL cdna:known chromosome:CEL140:II:6490105:6491216:1 gene:T28D9.2 9/11 A 
T28D9.2a ENSEMBL cdna:known chromosome:CEL140:II:6490116:6491255:1 gene:T28D9.2 9/11 A 
T28D9.2b ENSEMBL cdna:known chromosome:CEL140:II:6490116:6491292:1 gene:T28D9.2 10/11 A 
T28D9.2c ENSEMBL cdna:known chromosome:CEL140:II:6490255:6491216:1 gene:T28D9.2 11/11 A 
Annotation Notes
Cross Hybridizing mRNA Matched Probes Nature of Assignment Related Probesets by Grade
SNAP00000011382 8/11 Cross Hyb Matching Probes None
GENEFINDER00000011385 8/11 Cross Hyb Matching Probes None
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrII:6490774-6491242(+) 100.0 100.0
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
blast AAK68399 Sr protein (splicing factor) protein 5, isoform b [Caenorhabditis elegans] ref|NP_495309.3| SR Protein (splicing factor) family member (rsp-5) [Caenorhabditis elegans] 1.0E-50
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:171761_X_AT
tccccacagttaccaaaagccgctgtttcgattaaaagagaagcgtgaagcgtcgagatc
tcgttcaccactgccagcaaaagatcgaagcagaacccgaagtggatctcccccaaagaa
cggcggagatagaaagcgcagcgtgagccgtggaagaagtcacagccgagatggcagcaa
tcgcagtgtgtctcgctctccgtctccaggatctccaaaggattaaaattgtgtttttat
accgtttactgttgttcatttaccacttcta

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
TCCCCACAGTTACCAAAAGCCGCTG 566 595 26 Antisense
AAAGCCGCTGTTTCGATTAAAAGAG 363 123 41 Antisense
GAAGCGTCGAGATCTCGTTCACCAC 121 343 72 Antisense
CGTTCACCACTGCCAGCAAAAGATC 644 247 87 Antisense
AAGCAGAACCCGAAGTGGATCTCCC 100 151 113 Antisense
GATCTCCCCCAAAGAACGGCGGAGA 424 417 130 Antisense
GCGCAGCGTGAGCCGTGGAAGAAGT 532 287 161 Antisense
GGAAGAAGTCACAGCCGAGATGGCA 172 531 177 Antisense
ATGGCAGCAATCGCAGTGTGTCTCG 309 53 196 Antisense
TCCGTCTCCAGGATCTCCAAAGGAT 244 595 224 Antisense
TACTGTTGTTCATTTACCACTTCTA 452 647 272 Antisense
Sequence Source Affymetrix Proprietary Database