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[173337_s_at] RNA recognition motif. (aka RRM, RBD, or RNP domain)

Description AV203959 /REP_DB=TREMBL Accession /GB=AV203959 /FEA=Transcript Cluster /DEF=Caenorhabditis elegans cDNA clone:yk584c1 : 5prime end, single read.
Cluster 6grp_highest_10_10 > 68      6grp_high1_10_10 > 96      4grp_highest_8_8 > 14      4grp_high_8_8 > 22      6grp_highest_nonorm > 39      6grp_total > 87      4grp_total > 16      6grp_highest_sub > In      6grp_high1_sub > In      6grp_total_sub > Increase      4grp_rule_based > L4      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 9827
1 2 3 4 range
A 9340.9
(-3)
P 		11822.4
(-1.5)
P 		13375
(-0.5)
P 		19167.6
(3)
P 		9827
B 9754.6
(-3)
P 		11518.3
(-1.7)
P 		13046.8
(-0.6)
P 		17900.4
(3)
P 		8146
C 9434.3
(-3)
P 		12136.4
(-1.3)
P 		11838.5
(-1.5)
P 		18984.6
(3)
P 		9550
avr 9509.9
(-3) 		11825.7
(-1.5) 		12753.4
(-0.9) 		18684.2
(3) 		9174

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 6937
1 2 3 4 5 6 range
A 5357.8
(-3)
P 		5669.3
(-2.6)
P 		7926.5
(0.2)
P 		7443.3
(-0.4)
P 		8406.9
(0.8)
P 		10227.3
(3)
P 		4870
B 6002.9
(-3)
P 		7559.2
(-1.4)
P 		9837.5
(1)
P 		7100.1
(-1.9)
P 		9485.3
(0.6)
P 		11808.8
(3)
P 		5806
C 5279.7
(-3)
P 		6898.2
(-1.6)
P 		6179.4
(-2.2)
P 		7323.6
(-1.2)
P 		9095.5
(0.3)
P 		12217.1
(3)
P 		6937
avr 5546.8
(-3) 		6708.9
(-1.8) 		7981.1
(-0.5) 		7289
(-1.2) 		8995.9
(0.5) 		11417.7
(3) 		5871
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 1560
1 2 3 4 range
A 3401
(2.4)
P 		2566.3
(-3)
P 		3496.5
(3)
P 		2805.8
(-1.5)
P 		930
B 3110.7
(-1.4)
P 		2844.8
(-3)
P 		3023.3
(-1.9)
P 		3814.6
(3)
P 		970
C 3123
(-3)
P 		3489.3
(-0.8)
P 		4126.1
(3)
P 		3201.1
(-2.5)
P 		1003
avr 3211.6
(-0.5) 		2966.8
(-3) 		3548.6
(3) 		3273.8
(0.2) 		582

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 3416
1 2 3 4 5 6 range
A 987.7
(-3)
P 		2016.3
(1)
P 		1726.2
(-0.1)
P 		1887.8
(0.5)
P 		2536.8
(3)
P 		2490
(2.8)
P 		1549
B 2088.7
(-2.5)
P 		2516.1
(-1.5)
P 		2388.8
(-1.8)
P 		1880.6
(-3)
P 		3853.7
(1.7)
P 		4403.5
(3)
P 		2523
C 1957
(-1.9)
P 		2104.8
(-1.6)
P 		1572.8
(-2.8)
P 		1472.8
(-3)
P 		2943.2
(0.4)
P 		4089.8
(3)
P 		2617
avr 1677.8
(-3) 		2212.4
(-1.4) 		1895.9
(-2.3) 		1747.1
(-2.8) 		3111.2
(1.3) 		3661.1
(3) 		1983
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 173337_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.27788
Sequence Type Exemplar sequence
Representative Public ID AV203959 NCBI
Target Description AV203959 /REP_DB=TREMBL Accession /GB=AV203959 /FEA=Transcript Cluster /DEF=Caenorhabditis elegans cDNA clone:yk584c1 : 5prime 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_060622(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_060622 NCBI Caenorhabditis elegans R09B3.3 (R09B3.3) mRNA, complete cds. 11/11 None
SNAP00000010421 ENSEMBL cdna:SNAP chromosome:CEL140:I:11918543:11919078:-1 11/11 None
GENEFINDER00000010427 ENSEMBL cdna:GeneFinder chromosome:CEL140:I:11918543:11919078:-1 11/11 None
R09B3.3.3 ENSEMBL cdna:known chromosome:CEL140:I:11918242:11919095:-1 gene:R09B3.3 11/11 None
R09B3.3.1 ENSEMBL cdna:known chromosome:CEL140:I:11918443:11919133:-1 gene:R09B3.3 11/11 None
R09B3.3.2 ENSEMBL cdna:known chromosome:CEL140:I:11918443:11919145:-1 gene:R09B3.3 11/11 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
chrI:11918385-11919041(-) 87.24 87.24
Public Domain and Genome References
Gene Title RNA recognition motif. (aka RRM, RBD, or RNP domain)
Ensembl R09B3.3
Entrez Gene 173071 Entrez gene
SwissProt O45713 EMBL-EBI
WormBase CE16308 Wormbase
Functional Annotations
Gene Ontology
GO Molecular Function (view graph)
ID Description Evidence Links
3676 nucleic acid binding inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast CAB03237 Hypothetical protein R09B3.3 [Caenorhabditis elegans] ref|NP_493023.1| R09B3.3 [Caenorhabditis elegans] 2.0E-35
blast CAB03237 Hypothetical protein R09B3.3 [Caenorhabditis elegans] ref|NP_493023.1| R09B3.3 [Caenorhabditis elegans] 4.0E-33
blast CAB03236 Hypothetical protein R09B3.2 [Caenorhabditis elegans] ref|NP_493022.1| R09B3.2 [Caenorhabditis elegans] 2.0E-24
blast CAE71715 Hypothetical protein CBG18692 [Caenorhabditis briggsae] 2.0E-24
Protein Domains
Database ID Description E-Value
Pfam IPR000504 EMBL-EBI RNA-binding region RNP-1 (RNA recognition motif) 3.1E-29
Pfam IPR000504 EMBL-EBI RNA-binding region RNP-1 (RNA recognition motif) 8.5E-27
Sequence
Target Sequence 
>C. ELEGANS:173337_S_AT
tctggattctctgtttacgtcggaaacgctccattccaaactaccgaggacgaccttggc
aactacttcagccaggctggaaacgtcagcaacgtcagaatcgtttgcgaccgcgagacc
ggacgtccacgtggattcgccttcgtcgagttcaccgaggaggccactgnnnagagaacc
gtcgaccaattcaacggagtcgatttcaacggaagagctctacgcgtcaacttggctcaa
aacag

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
TCTGGATTCTCTGTTTACGTCGGAA 568 603 62 Antisense
GCTCCATTCCAAACTACCGAGGACG 299 299 89 Antisense
TACCGAGGACGACCTTGGCAACTAC 167 635 103 Antisense
AGCCAGGCTGGAAACGTCAGCAACG 364 83 131 Antisense
GTCAGCAACGTCAGAATCGTTTGCG 312 465 146 Antisense
CAGAATCGTTTGCGACCGCGAGACC 237 203 157 Antisense
CCTTCGTCGAGTTCACCGAGGAGGC 548 267 201 Antisense
GACCAATTCAACGGAGTCGATTTCA 672 383 245 Antisense
GTCGATTTCAACGGAAGAGCTCTAC 371 473 260 Antisense
AGAGCTCTACGCGTCAACTTGGCTC 116 69 275 Antisense
TACGCGTCAACTTGGCTCAAAACAG 114 649 282 Antisense
Sequence Source Affymetrix Proprietary Database