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[190513_at]

Description Y47G6A.20B /REP_DB=WormBase Gene ID /WP=CE24366 /TR=Q9N3S4 /GB=AAF60666.1 /SUBMIT=ST.LOUIS /CHR=1 /FEA=Sanger Annotation /DEF=RNA-binding protein
Cluster 6grp_highest_10_10 > 94      6grp_high1_10_10 > 58      6grp_highest_nonorm > 91      6grp_total > 59      4grp_total > 47      6grp_highest_sub > Cu      6grp_cgc > 18      6grp_high1_sub > Cu      6grp_cgc_sub > Cu      6grp_total_sub > Cup      4grp_rule_based > L1      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 163
1 2 3 4 range
A 314.6
(3)
P 		151.5
(-3)
A 		187.5
(-1.7)
A 		223.9
(-0.3)
A 		163
B 285.4
(3)
P 		206.6
(-1.6)
A 		209.9
(-1.4)
M 		182.3
(-3)
P 		103
C 299
(3)
P 		227.2
(-0.9)
M 		202.8
(-2.3)
P 		189.1
(-3)
A 		110
avr 299.7
(3) 		195.1
(-3) 		200.1
(-2.7) 		198.4
(-2.8) 		105

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 172
1 2 3 4 5 6 range
A 202.5
(1.3)
P 		204.5
(1.4)
P 		167.2
(-2)
P 		156.4
(-3)
P 		200.8
(1.1)
P 		221.4
(3)
P 		65
B 323.9
(3)
P 		218.8
(-2.8)
P 		252.3
(-1)
P 		215.5
(-3)
P 		254
(-0.9)
P 		307.7
(2.1)
P 		108
C 228
(-0.6)
P 		241.3
(-0.2)
P 		163.2
(-3)
P 		194.3
(-1.9)
P 		246.3
(0)
P 		328.1
(3)
P 		165
avr 251.5
(0.9) 		221.5
(-1) 		194.2
(-2.7) 		188.7
(-3) 		233.7
(-0.2) 		285.7
(3) 		97
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 83
1 2 3 4 range
A 114.5
(3)
P 		32.9
(-3)
A 		49
(-1.8)
A 		32.8
(-3)
A 		82
B 91
(3)
P 		51
(-1.6)
A 		48.6
(-1.9)
M 		38.8
(-3)
P 		52
C 99
(3)
P 		65.3
(-0)
M 		70.7
(0.5)
P 		31.9
(-3)
A 		67
avr 101.5
(3) 		49.7
(-1.6) 		56.1
(-1.1) 		34.5
(-3) 		67

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 78
1 2 3 4 5 6 range
A 37.3
(-2.9)
P 		72.7
(3)
P 		36.4
(-3)
P 		39.7
(-2.5)
P 		60.6
(1)
P 		53.9
(-0.1)
P 		36
B 112.7
(2.8)
P 		72.8
(-1.4)
P 		61.3
(-2.6)
P 		57.1
(-3)
P 		103.2
(1.8)
P 		114.7
(3)
P 		58
C 84.5
(0.9)
P 		73.6
(-0.1)
P 		41.5
(-2.8)
P 		39.1
(-3)
P 		79.7
(0.4)
P 		109.8
(3)
P 		71
avr 78.2
(1.2) 		73
(0.5) 		46.4
(-2.9) 		45.3
(-3) 		81.2
(1.5) 		92.8
(3) 		48
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 190513_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.99
Sequence Type Exemplar sequence
Representative Public ID Y47G6A.20B NCBI
Target Description Y47G6A.20B /REP_DB=WormBase Gene ID /WP=CE24366 /TR=Q9N3S4 /GB=AAF60666.1 /SUBMIT=ST.LOUIS /CHR=1 /FEA=Sanger Annotation /DEF=RNA-binding protein
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_058775(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_058775 NCBI Caenorhabditis elegans RNP (RRM RNA binding domain) containing family member (rnp-6) (rnp-6) mRNA, complete cds. 11/11 A 
GENEFINDER00000034097 ENSEMBL cdna:GeneFinder chromosome:CEL140:I:3539327:3546896:-1 11/11 None
SNAP00000033987 ENSEMBL cdna:SNAP chromosome:CEL140:I:3539649:3551248:-1 11/11 None
Y47G6A.20b ENSEMBL cdna:known chromosome:CEL140:I:3539570:3546896:-1 gene:Y47G6A.20 11/11 A 
Annotation Notes
There are no noteworthy cross hybridizing mRNAs found for this probe set.
Splice Variants
Entrez Total Refseq Isoforms Total Detected By This Probeset Refseq Probesets
171922 3 1 NM_058775 190513_at (11)
NM_058776 171942_x_at (9)
NM_170843 171942_x_at (9)
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrI:3539648-3546896(-) 99.82 100.0
Public Domain and Genome References
Ensembl Y47G6A.20
Functional Annotations
Protein Similarities
Method ID Description E-Value
blast NP_491176 RNP (RRM RNA binding domain) containing family member (rnp-6) [Caenorhabditis elegans] gb|AAF60666.1| Rnp (rrm rna binding domain) containing protein 6, isoform b [Caenorhabditis elegans] 0.0
blast CAE68956 Hypothetical protein CBG14936 [Caenorhabditis briggsae] 0.0
blast NP_491177 RNP (RRM RNA binding domain) containing family member (rnp-6) [Caenorhabditis elegans] gb|AAF60676.1| Rnp (rrm rna binding domain) containing protein 6, isoform a [Caenorhabditis elegans] 1.0E-159
Protein Domains
Database ID Description E-Value
Pfam IPR000504 EMBL-EBI RNA-binding region RNP-1 (RNA recognition motif) 1.5E-24
Pfam IPR000504 EMBL-EBI RNA-binding region RNP-1 (RNA recognition motif) 2.5E-14
Pfam IPR000504 EMBL-EBI RNA-binding region RNP-1 (RNA recognition motif) 7.0E-7
Pfam IPR000504 EMBL-EBI RNA-binding region RNP-1 (RNA recognition motif) 1.5E-24
Pfam IPR000504 EMBL-EBI RNA-binding region RNP-1 (RNA recognition motif) 2.5E-14
Pfam IPR000504 EMBL-EBI RNA-binding region RNP-1 (RNA recognition motif) 7.0E-7
Sequence
Target Sequence 
>C. ELEGANS:190513_AT
ggtggaagttctctgatgcttgctaataatgcaaaggcaaaagaagcagctgcagcgttg
gcgctggaaccgaagaagaagaagaaagttaaggaagggaagaagattcagcccaagctc
aacacggctcaagctttagctgccgccgcaaaagccggtgaaatgtcggatgctttgaag
aatgaggttatgaatagtgaagatgcttcccttgcctcacaggaaggtctcgaaattcgt
ggaaacgatgctcgtcatcttttaatgacaaaactgatgagaactaatcgatcaaatgtg
attgttcttcgaaatatggtgactccacaggatatcgatgaattccttgagggcgagatt
cgtgaagaatgtggaaaatatggaaatgtcattgatgtggtaatcgcgaattttgcatcc
agcggacttgtcaagatttttgtgaaatactcggattcgatgcaggtggatcgggcaaaa
gcggcactggat

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GGTGGAAGTTCTCTGATGCTTGCTA 326 499 1690 Antisense
AGAAGCAGCTGCAGCGTTGGCGCTG 111 73 1731 Antisense
AGAAGATTCAGCCCAAGCTCAACAC 260 75 1790 Antisense
CACGGCTCAAGCTTTAGCTGCCGCC 525 197 1812 Antisense
CTGCCGCCGCAAAAGCCGGTGAAAT 54 237 1829 Antisense
ATAGTGAAGATGCTTCCCTTGCCTC 300 21 1883 Antisense
TCCCTTGCCTCACAGGAAGGTCTCG 384 593 1897 Antisense
GAAACGATGCTCGTCATCTTTTAAT 63 359 1931 Antisense
GGTAATCGCGAATTTTGCATCCAGC 553 503 2088 Antisense
TTTGCATCCAGCGGACTTGTCAAGA 20 669 2101 Antisense
GGATCGGGCAAAAGCGGCACTGGAT 361 511 2157 Antisense
Sequence Source Affymetrix Proprietary Database