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[171888_x_at] RNA recognition motif. (aka RRM, RBD, or RNP domain)

Description CEK051H3R_rc /REP_DB=TREMBL Accession /GB=D70958 /FEA=Transcript Cluster /DEF=C.elegans cDNA clone yk51h3 : 3prime end, single read.
Cluster 6grp_highest_10_10 > 76      6grp_high1_10_10 > 67      4grp_highest_8_8 > 61      4grp_high_8_8 > 26      6grp_highest_nonorm > 90      6grp_total > 68      4grp_total > 30      6grp_highest_sub > Da      6grp_high1_sub > Da      6grp_total_sub > Increase      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 70
1 2 3 4 range
A 135.3
(3)
P 		89.2
(-1)
P 		66.7
(-3)
P 		92.2
(-0.8)
P 		69
B 136.3
(3)
P 		109.4
(-0.2)
P 		85.6
(-3)
P 		122.1
(1.3)
P 		51
C 123.8
(3)
P 		99.6
(-0.3)
P 		79.9
(-3)
P 		116.3
(2)
P 		44
avr 131.8
(3) 		99.4
(-0.6) 		77.4
(-3) 		110.2
(0.6) 		54

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 162
1 2 3 4 5 6 range
A 158.3
(2.2)
P 		91.8
(-2.5)
P 		113.1
(-1)
P 		119
(-0.6)
P 		84.7
(-3)
P 		169.2
(3)
P 		85
B 129.1
(-0.3)
P 		62.7
(-3)
P 		105.9
(-1.2)
P 		93
(-1.8)
P 		124.7
(-0.5)
P 		209
(3)
P 		146
C 91
(-2.6)
P 		84.6
(-2.9)
P 		81.3
(-3)
P 		89.4
(-2.7)
P 		81.7
(-3)
P 		224.3
(3)
P 		143
avr 126.1
(-0.7) 		79.7
(-3) 		100.1
(-2) 		100.5
(-2) 		97
(-2.1) 		200.8
(3) 		121
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 36
1 2 3 4 range
A 49.2
(3)
P 		19.4
(-2)
P 		17.4
(-2.3)
P 		13.5
(-3)
P 		36
B 43.5
(3)
P 		27
(-1.2)
P 		19.8
(-3)
P 		26
(-1.4)
P 		24
C 41
(3)
P 		28.6
(-0.5)
P 		27.9
(-0.7)
P 		19.6
(-3)
P 		21
avr 44.6
(3) 		25
(-1.7) 		21.7
(-2.5) 		19.7
(-3) 		25

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 60
1 2 3 4 5 6 range
A 29.2
(-1.3)
P 		32.7
(-0.1)
P 		24.6
(-3)
P 		30.2
(-1)
P 		25.6
(-2.6)
P 		41.2
(3)
P 		17
B 44.9
(-0.5)
P 		20.9
(-3)
P 		25.7
(-2.5)
P 		24.6
(-2.6)
P 		50.6
(0.1)
P 		77.9
(3)
P 		57
C 33.7
(-1.4)
P 		25.8
(-2.2)
P 		20.7
(-2.7)
P 		18
(-3)
P 		26.4
(-2.1)
P 		75.1
(3)
P 		57
avr 35.9
(-1.2) 		26.5
(-2.6) 		23.7
(-3) 		24.3
(-2.9) 		34.2
(-1.5) 		64.7
(3) 		41
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 171888_x_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.27897
Sequence Type Exemplar sequence
Representative Public ID CEK051H3R NCBI
Target Description CEK051H3R_rc /REP_DB=TREMBL Accession /GB=D70958 /FEA=Transcript Cluster /DEF=C.elegans cDNA clone yk51h3 : 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_067285
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_067285 NCBI Caenorhabditis elegans Y37D8A.21 (Y37D8A.21) mRNA, complete cds. A 
SNAP00000028786 ENSEMBL cdna:SNAP chromosome:CEL140:III:12927990:12931377:-1 None
GENEFINDER00000028806 ENSEMBL cdna:GeneFinder chromosome:CEL140:III:12927990:12928169:-1 None
Y37D8A.21 ENSEMBL cdna:known chromosome:CEL140:III:12927573:12931383:-1 gene:Y37D8A.21 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:12927900-12928189(-) 77.29 77.29
Public Domain and Genome References
Gene Title RNA recognition motif. (aka RRM, RBD, or RNP domain)
Ensembl Y37D8A.21
Entrez Gene 176710 Entrez gene
SwissProt Q9XWV4 EMBL-EBI
WormBase CE20224 Wormbase
Functional Annotations
Protein Similarities
Method ID Description E-Value
blast CAA21536 Hypothetical protein Y37D8A.21 [Caenorhabditis elegans] ref|NP_499686.1| Y37D8A.21 [Caenorhabditis elegans] 1.0E-102
blast CAA21536 Hypothetical protein Y37D8A.21 [Caenorhabditis elegans] ref|NP_499686.1| Y37D8A.21 [Caenorhabditis elegans] 4.0E-78
blast CAE69545 Hypothetical protein CBG15757 [Caenorhabditis briggsae] 4.0E-28
blast CAE69545 Hypothetical protein CBG15757 [Caenorhabditis briggsae] 5.0E-28
blast CAA21536 Hypothetical protein Y37D8A.21 [Caenorhabditis elegans] ref|NP_499686.1| Y37D8A.21 [Caenorhabditis elegans] 1.0E-19
Protein Domains
Database ID Description E-Value
Pfam IPR000504 EMBL-EBI RNA-binding region RNP-1 (RNA recognition motif) 1.0E-14
Sequence
Target Sequence 
>C. ELEGANS:171888_X_AT
atgcttcctcatcaacattttgtaaatcanatgatgcagcaacanattaatagatccgct
cctccgtacaatggacgtcatcagaattccacgccacaccgtcatcacngatcgtcatgg
atatgaccgaagctcgagccggcatcatcgcaatgatgacagaagacgtgnacgttattg
atcgatgattcgggcgggaaatcataattattttga

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
ATGCTTCCTCATCAACATTTTGTAA 409 43 76 Antisense
TTCCTCATCAACATTTTGTAAATCA 59 701 80 Antisense
CTCCTCCGTACAATGGACGTCATCA 469 235 134 Antisense
TGGACGTCATCAGAATTCCACGCCA 259 549 147 Antisense
TCATGGATATGACCGAAGCTCGAGC 496 621 190 Antisense
TATGACCGAAGCTCGAGCCGGCATC 73 655 197 Antisense
GAGCCGGCATCATCGCAATGATGAC 180 385 211 Antisense
CATCGCAATGATGACAGAAGACGTG 356 211 221 Antisense
GTTATTGATCGATGATTCGGGCGGG 222 447 249 Antisense
TGATCGATGATTCGGGCGGGAAATC 389 563 254 Antisense
GGGCGGGAAATCATAATTATTTTGA 637 491 267 Antisense
Sequence Source Affymetrix Proprietary Database