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[173352_s_at] RNA recognition motif. (aka RRM, RBD, or RNP domain)

Description AV184592_rc /REP_DB=TREMBL Accession /GB=AV184592 /FEA=Transcript Cluster /DEF=Caenorhabditis elegans cDNA clone:yk666g3 : 3prime end, single read.
Cluster 6grp_highest_10_10 > 81      6grp_high1_10_10 > 28      4grp_highest_8_8 > 48      4grp_high_8_8 > 42      6grp_highest_nonorm > 30      6grp_total > 28      4grp_total > 45      6grp_highest_sub > Cu      6grp_cgc > 12      6grp_high1_sub > De      6grp_cgc_sub > De      6grp_total_sub > Cup      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 381
1 2 3 4 range
A 1222.1
(3)
P 		1040.3
(0.1)
P 		920.1
(-1.8)
P 		840.8
(-3)
P 		381
B 988.7
(-3)
P 		1027.8
(-1.9)
P 		1067.2
(-0.8)
P 		1202.5
(3)
P 		214
C 1196.3
(3)
P 		1176.7
(2.5)
P 		1128.2
(1.1)
P 		982.3
(-3)
P 		214
avr 1135.7
(3) 		1081.6
(0.4) 		1038.5
(-1.6) 		1008.5
(-3) 		127

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 884
1 2 3 4 5 6 range
A 1044.5
(3)
P 		877.5
(-0.7)
P 		813.4
(-2.2)
P 		804.1
(-2.4)
P 		776.5
(-3)
P 		902.3
(-0.2)
P 		268
B 1125
(3)
P 		921.4
(0.5)
P 		751.3
(-1.7)
P 		644.4
(-3)
P 		766.3
(-1.5)
P 		836.1
(-0.6)
P 		481
C 1425.9
(3)
P 		745.2
(-1.6)
P 		731.9
(-1.7)
P 		542
(-3)
P 		1009
(0.2)
P 		752.1
(-1.6)
P 		884
avr 1198.5
(3) 		848
(-0.9) 		765.5
(-1.9) 		663.5
(-3) 		850.6
(-0.9) 		830.2
(-1.1) 		535
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 322
1 2 3 4 range
A 445
(3)
P 		225.8
(-1.1)
P 		240.5
(-0.8)
P 		123.1
(-3)
P 		322
B 315.3
(3)
P 		253.8
(-2.4)
P 		247.3
(-3)
P 		256.3
(-2.2)
P 		68
C 396
(3)
P 		338.3
(1.5)
P 		393.2
(2.9)
P 		165.6
(-3)
P 		230
avr 385.4
(3) 		272.6
(-0.3) 		293.7
(0.3) 		181.7
(-3) 		204

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 420
1 2 3 4 5 6 range
A 192.5
(-2.3)
P 		312.1
(3)
P 		177.2
(-3)
P 		203.9
(-1.8)
P 		234.3
(-0.5)
P 		219.7
(-1.1)
P 		135
B 391.4
(3)
P 		306.7
(0.7)
P 		182.4
(-2.7)
P 		170.7
(-3)
P 		311.3
(0.8)
P 		311.8
(0.8)
P 		221
C 528.5
(3)
P 		227.4
(-1.3)
P 		186.3
(-1.9)
P 		109
(-3)
P 		326.5
(0.1)
P 		251.8
(-1)
P 		420
avr 370.8
(3) 		282.1
(0.5) 		182
(-2.4) 		161.2
(-3) 		290.7
(0.7) 		261.1
(-0.1) 		210
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 173352_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.27844
Sequence Type Exemplar sequence
Representative Public ID AV184592 NCBI
Target Description AV184592_rc /REP_DB=TREMBL Accession /GB=AV184592 /FEA=Transcript Cluster /DEF=Caenorhabditis elegans cDNA clone:yk666g3 : 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 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_067132(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_067132 NCBI Caenorhabditis elegans SR Protein (splicing factor) family member (rsp-8) (rsp-8) mRNA, complete cds. 11/11 A 
GENEFINDER00000031605 ENSEMBL cdna:GeneFinder chromosome:CEL140:III:11824983:11830604:1 11/11 None
SNAP00000031598 ENSEMBL cdna:SNAP chromosome:CEL140:III:11826673:11830604:1 11/11 None
C18D11.4 ENSEMBL cdna:known chromosome:CEL140:III:11826091:11830827:1 gene:C18D11.4 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:11830481-11830715(+) 76.97 76.97
Public Domain and Genome References
Gene Title RNA recognition motif. (aka RRM, RBD, or RNP domain)
Gene Symbol rsp-8
Ensembl C18D11.4
Entrez Gene 176613 Entrez gene
SwissProt Q9XTZ2 EMBL-EBI
WormBase CE18515 Wormbase
Functional Annotations
Ortholog
ID Title Organism
CANINE_2:CFAAFFX.5098.1.S1_AT similar to RIKEN cDNA G430041M01 cfa
DROSOPHILA_2:1639205_S_AT transformer 2 dm
DROSGENOME1:141588_AT transformer 2 dm
CHICKEN:GGAAFFX.11701.1.S1_AT similar to RIKEN cDNA G430041M01 gga
HG-FOCUS:204658_AT transformer-2 alpha hs
HG-U133A:204658_AT transformer-2 alpha hs
HG-U133_PLUS_2:204658_AT transformer-2 alpha hs
HG-U133A_2:204658_AT transformer-2 alpha hs
HU35KSUBA:R32266_AT transformer-2 alpha hs
HUGENEFL:U53209_AT transformer-2 alpha hs
U133_X3P:G9558732_3P_AT transformer-2 alpha hs
HG-U95AV2:39344_AT transformer-2 alpha hs
HG-U133_PLUS_2:213575_AT Transformer-2 alpha hs
HG-U133A_2:213575_AT Transformer-2 alpha hs
HG-U133A:213575_AT Transformer-2 alpha hs
HG-U95AV2:39343_AT Transformer-2 alpha hs
U133_X3P:HS.24937.1.S2_3P_AT Transformer-2 alpha hs
U133_X3P:HS.24937.1.S1_3P_AT Transformer-2 alpha hs
U133_X3P:HS.130829.0.A1_3P_AT Transformer-2 alpha hs
HG-U133A_2:213593_S_AT Transformer-2 alpha hs
HG-U133_PLUS_2:213593_S_AT Transformer-2 alpha hs
HG-U133A:213593_S_AT Transformer-2 alpha hs
HG-U133_PLUS_2:229574_AT Transformer-2 alpha hs
HG-U133B:229574_AT Transformer-2 alpha hs
HG-U95E:90181_AT Transformer-2 alpha hs
HG-U133_PLUS_2:227939_S_AT Transformer-2 alpha hs
HG-U133B:227939_S_AT Transformer-2 alpha hs
HG-U133_PLUS_2:235716_AT Transformer-2 alpha hs
HG-U133B:235716_AT Transformer-2 alpha hs
HG-U95B:43377_S_AT Transformer-2 alpha hs
HG-U95B:50403_AT Transformer-2 alpha hs
HG-U95D:67944_AT Transformer-2 alpha hs
HG-U95D:67946_G_AT Transformer-2 alpha hs
HG-U95E:77744_R_AT Transformer-2 alpha hs
HU35KSUBA:AA455812_AT Transformer-2 alpha hs
HU35KSUBA:RC_AA256380_AT Transformer-2 alpha hs
HU35KSUBC:RC_AA278594_AT Transformer-2 alpha hs
U133_X3P:HS.194258.0.A1_3P_AT Transformer-2 alpha hs
U133_X3P:HS.24937.2.A1_3P_A_AT Transformer-2 alpha hs
MG-U74BV2:109169_AT RIKEN cDNA G430041M01 gene mm
MOE430A:1454725_AT RIKEN cDNA G430041M01 gene mm
MOUSE430A_2:1454725_AT RIKEN cDNA G430041M01 gene mm
MOUSE430_2:1454725_AT RIKEN cDNA G430041M01 gene mm
MU19KSUBA:TC25756_AT RIKEN cDNA G430041M01 gene (G430041M01Rik), mRNA mm
MU19KSUBC:TC35937_AT RIKEN cDNA G430041M01 gene (G430041M01Rik), mRNA mm
Protein Similarities
Method ID Description E-Value
blast CAB07322 Hypothetical protein C18D11.4 [Caenorhabditis elegans] ref|NP_499533.1| SR Protein (splicing factor) family member (rsp-8) [Caenorhabditis elegans] 1.0E-60
blast CAB07322 Hypothetical protein C18D11.4 [Caenorhabditis elegans] ref|NP_499533.1| SR Protein (splicing factor) family member (rsp-8) [Caenorhabditis elegans] 1.0E-57
blast CAE67724 Hypothetical protein CBG13299 [Caenorhabditis briggsae] 1.0E-50
blast CAE67724 Hypothetical protein CBG13299 [Caenorhabditis briggsae] 9.0E-48
blast CAB07322 Hypothetical protein C18D11.4 [Caenorhabditis elegans] ref|NP_499533.1| SR Protein (splicing factor) family member (rsp-8) [Caenorhabditis elegans] 3.0E-47
blast CAE67724 Hypothetical protein CBG13299 [Caenorhabditis briggsae] 8.0E-39
blast XP_796831 PREDICTED: similar to splicing factor, arginine/serine-rich 10 (transformer 2 homolog, Drosophila), partial [Strongylocentrotus purpuratus] 2.0E-27
blast XP_796831 PREDICTED: similar to splicing factor, arginine/serine-rich 10 (transformer 2 homolog, Drosophila), partial [Strongylocentrotus purpuratus] 4.0E-27
Protein Domains
Database ID Description E-Value
Pfam IPR000504 EMBL-EBI RNA-binding region RNP-1 (RNA recognition motif) 2.3E-22
Pfam IPR000504 EMBL-EBI RNA-binding region RNP-1 (RNA recognition motif) 1.9E-19
Pfam IPR000504 EMBL-EBI RNA-binding region RNP-1 (RNA recognition motif) 2.3E-22
Sequence
Target Sequence 
>C. ELEGANS:173352_S_AT
tggaggtggtggacaccgtccgtatgatccatcgttcagacgtcgcgtcgaatcgtacgg
atctggaaatagcggtggtggcggcggacgtcgtgatagatat

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
TGGAGGTGGTGGACACCGTCCGTAT 62 551 26 Antisense
TGGTGGACACCGTCCGTATGATCCA 496 553 32 Antisense
GTCCGTATGATCCATCGTTCAGACG 119 477 43 Antisense
TATGATCCATCGTTCAGACGTCGCG 53 655 48 Antisense
TCCATCGTTCAGACGTCGCGTCGAA 586 587 53 Antisense
ATCGTTCAGACGTCGCGTCGAATCG 377 35 56 Antisense
TCAGACGTCGCGTCGAATCGTACGG 502 613 61 Antisense
GTCGAATCGTACGGATCTGGAAATA 380 473 72 Antisense
GTACGGATCTGGAAATAGCGGTGGT 639 457 80 Antisense
GATCTGGAAATAGCGGTGGTGGCGG 414 413 85 Antisense
TGGCGGCGGACGTCGTGATAGATAT 138 545 104 Antisense
Sequence Source Affymetrix Proprietary Database