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[172898_x_at] Probable RNA binding protein

Description EEED8.12 /REP_DB=WormBase Gene ID /WP=CE01885 /TR=SW:Q09301 /GB=AAC46772.1 /SUBMIT=ST.LOUIS /CHR=2 /FEA=Sanger Annotation /DEF=Probable RNA binding protein
Cluster 6grp_highest_10_10 > 76      6grp_high1_10_10 > 77      6grp_highest_nonorm > 91      6grp_total > 67      4grp_total > 29      6grp_highest_sub > Da      6grp_high1_sub > Da      6grp_total_sub > Increase      6grp_rule_based > S6      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 82
1 2 3 4 range
A 77.5
(3)
A 		73.8
(2)
A 		60.9
(-1.7)
A 		56.3
(-3)
P 		21
B 92.5
(3)
A 		61.2
(-0.4)
A 		64.2
(-0.1)
A 		37.9
(-3)
P 		55
C 44.4
(-2)
A 		74.1
(0.2)
A 		30.3
(-3)
A 		112
(3)
P 		82
avr 71.5
(3) 		69.7
(2.5) 		51.8
(-3) 		68.7
(2.1) 		20

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 355
1 2 3 4 5 6 range
A 93.9
(-2.6)
P 		96.5
(-2.5)
P 		106.2
(-2.3)
P 		103.4
(-2.3)
P 		77.8
(-3)
P 		310
(3)
P 		232
B 132.3
(-2)
P 		89.7
(-2.9)
P 		130.4
(-2)
P 		86.8
(-3)
P 		144.3
(-1.7)
P 		353.7
(3)
P 		267
C 106.2
(-2.7)
P 		91.1
(-3)
P 		129.6
(-2.3)
P 		140.4
(-2.1)
P 		112.1
(-2.6)
P 		432.4
(3)
P 		341
avr 110.8
(-2.6) 		92.4
(-3) 		122.1
(-2.3) 		110.2
(-2.6) 		111.4
(-2.6) 		365.4
(3) 		273
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 21
1 2 3 4 range
A 28.2
(3)
A 		16
(-0.7)
A 		15.9
(-0.7)
A 		8.2
(-3)
P 		20
B 29.5
(3)
A 		15.1
(-1)
A 		14.9
(-1.1)
A 		8.1
(-3)
P 		21
C 14.7
(-0.7)
A 		21.3
(3)
A 		10.6
(-3)
A 		18.9
(1.7)
P 		11
avr 24.1
(3) 		17.5
(-0.2) 		13.8
(-2) 		11.7
(-3) 		12

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 128
1 2 3 4 5 6 range
A 17.3
(-3)
P 		34.3
(-1.2)
P 		23.1
(-2.4)
P 		26.2
(-2.1)
P 		23.5
(-2.4)
P 		75.5
(3)
P 		58
B 46
(-1.7)
P 		29.9
(-2.6)
P 		31.7
(-2.5)
P 		23
(-3)
P 		58.6
(-1)
P 		131.9
(3)
P 		109
C 39.4
(-2.4)
P 		27.8
(-3)
P 		33
(-2.7)
P 		28.2
(-3)
P 		36.3
(-2.6)
P 		144.8
(3)
P 		117
avr 34.2
(-2.4) 		30.7
(-2.7) 		29.3
(-2.8) 		25.8
(-3) 		39.5
(-2.1) 		117.4
(3) 		92
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 172898_x_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.5857
Sequence Type Exemplar sequence
Representative Public ID EEED8.12 NCBI
Target Description EEED8.12 /REP_DB=WormBase Gene ID /WP=CE01885 /TR=SW:Q09301 /GB=AAC46772.1 /SUBMIT=ST.LOUIS /CHR=2 /FEA=Sanger Annotation /DEF=Probable 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_062620(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_062620 NCBI Caenorhabditis elegans EEED8.12 (EEED8.12) mRNA, complete cds. 11/11 A 
SNAP00000023172 ENSEMBL cdna:SNAP chromosome:CEL140:II:5408330:5408974:-1 11/11 None
GENEFINDER00000023188 ENSEMBL cdna:GeneFinder chromosome:CEL140:II:5408330:5408974:-1 11/11 None
EEED8.12 ENSEMBL cdna:known chromosome:CEL140:II:5408306:5408990:-1 gene:EEED8.12 11/11 A 
Annotation Notes
Cross Hybridizing mRNA Matched Probes Nature of Assignment Related Probesets by Grade
NM_062621 7/11 Cross Hyb Matching Probes A 
SNAP00000023173 7/11 Cross Hyb Matching Probes None
GENEFINDER00000023181 7/11 Cross Hyb Matching Probes None
EEED8.4 7/11 Cross Hyb Matching Probes A 
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrII:5410464-5411077(+) 91.25 91.25
chrII:5408327-5408972(-) 100.0 100.0
Public Domain and Genome References
Gene Title Probable RNA binding protein
Ensembl EEED8.12
Entrez Gene 173922 Entrez gene
SwissProt Q09301 EMBL-EBI
WormBase CE01885 Wormbase
Functional Annotations
Protein Similarities
Method ID Description E-Value
blast AAC46772 Hypothetical protein EEED8.12 [Caenorhabditis elegans] ref|NP_495021.1| EEED8.12 [Caenorhabditis elegans] sp|Q09301|YQOC_CAEEL Hypothetical RNA-binding protein EEED8.12 in chromosome II 1.0E-74
blast AAC46764 Hypothetical protein EEED8.4 [Caenorhabditis elegans] ref|NP_495022.1| EEED8.4 [Caenorhabditis elegans] sp|Q09295|YQO4_CAEEL Hypothetical RNA-binding protein EEED8.4 in chromosome II 7.0E-69
blast CAE61518 Hypothetical protein CBG05418 [Caenorhabditis briggsae] 4.0E-50
Protein Domains
Database ID Description E-Value
Pfam IPR000504 EMBL-EBI RNA-binding region RNP-1 (RNA recognition motif) 4.9E-21
Sequence
Target Sequence 
>C. ELEGANS:172898_X_AT
caactaccgttatcgctgacaacaactgcaatgaagaaagtagcaacagttttgaaatgg
aaattgaagcggaatctgcaattcttgagcagattcagaacaagatggcaaagaatctgg
aatctgcagcatatgttccaccaacagaagaagagcaaaaggcaattgatgccaagtctg
tattcattggaaatgtagattttaactctacaattgaagaagttgaagagcacttcaaag
gctgtggacacattgtgagaactacaattccaaaggacaaattcacgaaaaaacagaaaa
attttgcatacattgaattcgatgactcatccagcattgaaaatgcacttgtaatgaatg
gatcattgttcagaagcagaccaattgtggtcactgccaaaagaacaaatattcctggaa
tgggacatggtgtacgtggatcatcaagaggaaccttcggaagaggacgtggagctgctc
gcggagcaccaggaagacaacagacagtcgttgtcaagtatgtctatgta

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
CAACTACCGTTATCGCTGACAACAA 336 189 20 Antisense
GAAGCGGAATCTGCAATTCTTGAGC 494 343 85 Antisense
TCTGCAGCATATGTTCCACCAACAG 293 609 142 Antisense
GGCAATTGATGCCAAGTCTGTATTC 246 535 180 Antisense
GAGCACTTCAAAGGCTGTGGACACA 394 389 247 Antisense
GAATTCGATGACTCATCCAGCATTG 325 323 334 Antisense
GCAGACCAATTGTGGTCACTGCCAA 368 311 395 Antisense
GGGACATGGTGTACGTGGATCATCA 323 493 441 Antisense
GGAAGAGGACGTGGAGCTGCTCGCG 331 531 478 Antisense
GCTCGCGGAGCACCAGGAAGACAAC 452 299 496 Antisense
AGTCGTTGTCAAGTATGTCTATGTA 380 61 525 Antisense
Sequence Source Affymetrix Proprietary Database