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[193839_s_at] RNA recognition motif. (aka RRM, RBD, or RNP domain)

Description Y106G6D.7 /REP_DB=WormBase Gene ID /WP=CE24110 /TR=Q9U304 /GB=CAA20980.2 /SUBMIT=HINXTON /CHR=1 /FEA=Sanger Annotation /DEF=RNA recognition motif. (aka RRM, RBD, or RNP domain)
Cluster 6grp_highest_10_10 > 23      6grp_high1_10_10 > 12      4grp_high_8_8 > 12      6grp_highest_nonorm > 80      6grp_total > 22      4grp_total > 12      6grp_highest_sub > 01_02_03      6grp_high1_sub > De      6grp_total_sub > Hat      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 134
1 2 3 4 range
A 203.9
(2.2)
P 		210.4
(2.8)
P 		141.6
(-3)
P 		212.9
(3)
P 		71
B 209.4
(-2.5)
P 		203.3
(-3)
P 		217.3
(-1.8)
P 		275.9
(3)
P 		73
C 213.7
(0.4)
A 		176.2
(-3)
P 		178.1
(-2.8)
P 		243.2
(3)
P 		67
avr 209
(-0.2) 		196.6
(-1.4) 		179
(-3) 		244
(3) 		65

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 98
1 2 3 4 5 6 range
A 208.8
(0.6)
P 		239.8
(3)
P 		193.5
(-0.6)
P 		163.9
(-2.9)
P 		162.2
(-3)
P 		190.9
(-0.8)
P 		78
B 229.1
(0.7)
P 		233.1
(1)
P 		260.3
(3)
P 		194.9
(-1.8)
P 		212.1
(-0.5)
P 		177.9
(-3)
P 		82
C 255.6
(3)
P 		221.5
(0.8)
P 		243.9
(2.2)
P 		236.3
(1.7)
P 		215.6
(0.4)
P 		164.6
(-3)
P 		91
avr 231.2
(2.8) 		231.5
(2.9) 		232.6
(3) 		198.4
(-0.7) 		196.6
(-0.9) 		177.8
(-3) 		55
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 43
1 2 3 4 range
A 74.2
(3)
P 		45.7
(-1)
P 		37
(-2.2)
P 		31.2
(-3)
P 		43
B 66.8
(3)
P 		50.2
(-3)
P 		50.3
(-3)
P 		58.8
(0.1)
P 		17
C 70.7
(3)
A 		50.7
(-1)
P 		62.1
(1.3)
P 		41
(-3)
P 		30
avr 70.6
(3) 		48.9
(-1.8) 		49.8
(-1.6) 		43.7
(-3) 		27

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 56
1 2 3 4 5 6 range
A 38.5
(-3)
P 		85.3
(3)
P 		42.2
(-2.5)
P 		41.6
(-2.6)
P 		48.9
(-1.7)
P 		46.5
(-2)
P 		47
B 79.7
(1.9)
P 		77.6
(1.5)
P 		63.2
(-1)
P 		51.6
(-3)
P 		86.2
(3)
P 		66.3
(-0.5)
P 		35
C 94.7
(3)
P 		67.6
(-0.4)
P 		62.1
(-1.1)
P 		47.5
(-3)
P 		69.8
(-0.2)
P 		55.1
(-2)
P 		47
avr 71
(1.8) 		76.8
(3) 		55.8
(-1.2) 		46.9
(-3) 		68.3
(1.3) 		56
(-1.2) 		30
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 193839_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.806
Sequence Type Exemplar sequence
Representative Public ID Y106G6D.7 NCBI
Target Description Y106G6D.7 /REP_DB=WormBase Gene ID /WP=CE24110 /TR=Q9U304 /GB=CAA20980.2 /SUBMIT=HINXTON /CHR=1 /FEA=Sanger Annotation /DEF=RNA recognition motif. (aka RRM, RBD, or RNP domain)
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_060270(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_060270 NCBI Caenorhabditis elegans Y106G6D.7 (Y106G6D.7) mRNA, complete cds. 11/11 None
GENEFINDER00000020362 ENSEMBL cdna:GeneFinder chromosome:CEL140:I:10130673:10137991:1 11/11 None
SNAP00000020355 ENSEMBL cdna:SNAP chromosome:CEL140:I:10133445:10137991:1 11/11 None
Y106G6D.7 ENSEMBL cdna:known chromosome:CEL140:I:10130592:10138310:1 gene:Y106G6D.7 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:10130570-10137922(+) 100.0 100.0
Public Domain and Genome References
Gene Title RNA recognition motif. (aka RRM, RBD, or RNP domain)
Ensembl Y106G6D.7
Entrez Gene 172878 Entrez gene
SwissProt Q9U304 EMBL-EBI
WormBase CE24110 Wormbase
Functional Annotations
Protein Similarities
Method ID Description E-Value
blast CAA20980 Hypothetical protein Y106G6D.7 [Caenorhabditis elegans] ref|NP_492671.1| Y106G6D.7 [Caenorhabditis elegans] 0.0
blast CAE66839 Hypothetical protein CBG12209 [Caenorhabditis briggsae] 1.0E-178
blast CAE66839 Hypothetical protein CBG12209 [Caenorhabditis briggsae] 1.0E-172
blast CAE66839 Hypothetical protein CBG12209 [Caenorhabditis briggsae] 1.0E-143
blast AAX25744 SJCHGC00921 protein [Schistosoma japonicum] 1.0E-23
Protein Domains
Database ID Description E-Value
Pfam IPR000504 EMBL-EBI RNA-binding region RNP-1 (RNA recognition motif) 5.2E-8
Pfam IPR000504 EMBL-EBI RNA-binding region RNP-1 (RNA recognition motif) 5.2E-8
Pfam IPR000504 EMBL-EBI RNA-binding region RNP-1 (RNA recognition motif) 5.2E-8
Sequence
Target Sequence 
>C. ELEGANS:193839_S_AT
acctcttccatcaggccaacaaaatggaatgaatgtacctccaccaaatggattcaatgg
agctccgatgcgaggtggatttgtgccacgtggaggaaataatttctcacaatcgagagg
tggaatgatgggaagaggaggtcatggaggaggaggaggacctcaaaatttctatcaaaa
tggtcccaacaactttaacaatggtccgccagagcaacaagggcaattcagaggaaatca
gggaaatgatggtggattccgtggaggatttagaggaggatatcgtggacgcggtggagg
tcgaggtggattccaaggaggttcacgtggtgatgattctcaaccatcacaatctgaact
tatggaactgatcaaatcaattggtccacgtggaactgtattatcgtgtaatgggttccc
gaaagatgttacgttagaagatgtggttgagtttttcaatgattatgaaccggatcgtaa
ttccattcggatacgacgaggagatgatggtgtaatgactggagaatgtatgctggcgtg
tcaaaatcaggagaacgctcgccgtgcctcaatggatctcgatggtc

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
ACCTCTTCCATCAGGCCAACAAAAT 624 87 2232 Antisense
GAATGAATGTACCTCCACCAAATGG 184 331 2258 Antisense
ATGGAGCTCCGATGCGAGGTGGATT 682 51 2288 Antisense
GAGGAGGACCTCAAAATTTCTATCA 682 403 2384 Antisense
AATGGTCCCAACAACTTTAACAATG 234 163 2410 Antisense
AACAATGGTCCGCCAGAGCAACAAG 149 135 2428 Antisense
GGACGCGGTGGAGGTCGAGGTGGAT 449 517 2518 Antisense
GATGATTCTCAACCATCACAATCTG 176 411 2563 Antisense
AACCGGATCGTAATTCCATTCGGAT 481 69 2699 Antisense
ACTGGAGAATGTATGCTGGCGTGTC 435 97 2749 Antisense
CGTGCCTCAATGGATCTCGATGGTC 419 245 2794 Antisense
Sequence Source Affymetrix Proprietary Database