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[192011_s_at] Probable RNA binding protein

Description K02F3.11 /REP_DB=WormBase Gene ID /WP=CE26938 /TR=Q21155 /GB=AAK21429.1 /SUBMIT=ST.LOUIS /CHR=3 /FEA=Sanger Annotation /DEF=Probable RNA binding protein
Cluster 6grp_highest_10_10 > 96      6grp_high1_10_10 > 79      4grp_highest_8_8 > 09      4grp_high_8_8 > 53      6grp_highest_nonorm > 95      6grp_total > 69      4grp_total > 58      6grp_highest_sub > Cu      6grp_cgc > 29      6grp_high1_sub > Cu      6grp_cgc_sub > Cu      6grp_total_sub > Cup      4grp_rule_based > L3      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 846
1 2 3 4 range
A 718
(-1.9)
P 		1360.5
(3)
P 		986.2
(0.2)
P 		569.8
(-3)
P 		791
B 779.6
(-1.2)
P 		898
(-0.2)
P 		1269.7
(3)
P 		569.5
(-3)
P 		700
C 724
(-0.7)
P 		926.5
(1.5)
P 		1067.4
(3)
P 		514.9
(-3)
P 		553
avr 740.5
(-1) 		1061.7
(2.5) 		1107.8
(3) 		551.4
(-3) 		556

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 592
1 2 3 4 5 6 range
A 777.3
(1.2)
P 		610.7
(-0.8)
P 		518.1
(-1.9)
P 		431.8
(-3)
P 		698.7
(0.3)
P 		920.3
(3)
P 		489
B 654.5
(-1.1)
P 		598.6
(-1.9)
P 		659.9
(-1.1)
P 		515.1
(-3)
P 		703.6
(-0.5)
P 		964.2
(3)
P 		449
C 735.3
(0.5)
P 		470.2
(-2.1)
P 		447.2
(-2.4)
P 		386.3
(-3)
P 		818
(1.4)
P 		977.8
(3)
P 		592
avr 722.4
(0.3) 		559.8
(-1.6) 		541.7
(-1.9) 		444.4
(-3) 		740.1
(0.5) 		954.1
(3) 		510
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 289
1 2 3 4 range
A 261.4
(2)
P 		295.3
(3)
P 		257.8
(1.9)
P 		83.4
(-3)
P 		212
B 248.6
(1.4)
P 		221.8
(0.5)
P 		294.2
(3)
P 		121.4
(-3)
P 		173
C 239.7
(0.2)
P 		266.4
(0.8)
P 		372
(3)
P 		86.8
(-3)
P 		285
avr 249.9
(1.3) 		261.2
(1.7) 		308
(3) 		97.2
(-3) 		211

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 282
1 2 3 4 5 6 range
A 143.3
(-1.2)
P 		217.2
(2.6)
P 		112.8
(-2.8)
P 		109.5
(-3)
P 		210.8
(2.3)
P 		224.1
(3)
P 		115
B 227.7
(-0.5)
P 		199.3
(-1.3)
P 		160.2
(-2.4)
P 		136.4
(-3)
P 		285.8
(1)
P 		359.5
(3)
P 		223
C 272.5
(1.7)
P 		143.5
(-1.4)
P 		113.8
(-2.1)
P 		77.7
(-3)
P 		264.7
(1.5)
P 		327.3
(3)
P 		250
avr 214.5
(0.3) 		186.7
(-0.6) 		128.9
(-2.4) 		107.9
(-3) 		253.8
(1.5) 		303.6
(3) 		196
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 192011_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.8173
Sequence Type Exemplar sequence
Representative Public ID K02F3.11 NCBI
Target Description K02F3.11 /REP_DB=WormBase Gene ID /WP=CE26938 /TR=Q21155 /GB=AAK21429.1 /SUBMIT=ST.LOUIS /CHR=3 /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_064875(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_064875 NCBI Caenorhabditis elegans RNP (RRM RNA binding domain) containing family member (rnp-5) (rnp-5) mRNA, complete cds. 11/11 A 
SNAP00000008342 ENSEMBL cdna:SNAP chromosome:CEL140:III:852928:853897:-1 11/11 None
GENEFINDER00000008345 ENSEMBL cdna:GeneFinder chromosome:CEL140:III:852928:853896:-1 11/11 None
K02F3.11 ENSEMBL cdna:known chromosome:CEL140:III:852674:853897:-1 gene:K02F3.11 11/11 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:852927-853896(-) 94.54 100.0
Public Domain and Genome References
Gene Title Probable RNA binding protein
Gene Symbol rnp-5
Ensembl K02F3.11
Entrez Gene 175244 Entrez gene
SwissProt Q21155 EMBL-EBI
WormBase CE29981 Wormbase
Functional Annotations
Ortholog
ID Title Organism
CANINE:1599234_AT similar to RNA-binding protein S1, serine-rich domain cfa
CANINE_2:CFAAFFX.29652.1.S1_AT similar to RNA-binding protein S1, serine-rich domain cfa
DROSOPHILA_2:1633915_AT RNA-binding protein S1 dm
DROSGENOME1:154209_AT RNA-binding protein S1 dm
CHICKEN:GGAAFFX.5848.1.S1_AT similar to Rnps1 protein gga
CHICKEN:GGAAFFX.5852.1.S1_AT similar to Rnps1 protein gga
PLASMODIUM_ANOPHELES:200060_S_AT RNA binding protein S1, serine-rich domain hs
HG-U133_PLUS_2:200060_S_AT RNA binding protein S1, serine-rich domain hs
HG-U133A:200060_S_AT RNA binding protein S1, serine-rich domain hs
HG-U133B:200060_S_AT RNA binding protein S1, serine-rich domain hs
HG-FOCUS:200060_S_AT RNA binding protein S1, serine-rich domain hs
HG-U133A_2:200060_S_AT RNA binding protein S1, serine-rich domain hs
U133_X3P:200060_S_AT RNA binding protein S1, serine-rich domain hs
HG-U133_PLUS_2:207939_X_AT RNA binding protein S1, serine-rich domain hs
HG-U133A:207939_X_AT RNA binding protein S1, serine-rich domain hs
HG-U133A_2:207939_X_AT RNA binding protein S1, serine-rich domain hs
HU35KSUBA:HUM_ALU_AT RNA binding protein S1, serine-rich domain hs
HU35KSUBB:HUM_ALU_AT RNA binding protein S1, serine-rich domain hs
HU35KSUBC:HUM_ALU_AT RNA binding protein S1, serine-rich domain hs
HU35KSUBD:HUM_ALU_AT RNA binding protein S1, serine-rich domain hs
HUGENEFL:HUM_ALU_AT RNA binding protein S1, serine-rich domain hs
HC-G110:HUM_ALU_AT RNA binding protein S1, serine-rich domain hs
HU35KSUBD:RC_T33593_S_AT RNA binding protein S1, serine-rich domain hs
HUGENEFL:L37368_AT RNA binding protein S1, serine-rich domain hs
U133_X3P:G6857825_3P_X_AT RNA binding protein S1, serine-rich domain hs
U133_X3P:G12804496_3P_A_AT RNA binding protein S1, serine-rich domain hs
HG-U95AV2:36186_AT RNA binding protein S1, serine-rich domain hs
RG-U34B:RC_AI008971_AT ribonucleic acid binding protein S1 (predicted) rn
RAE230A:1371596_AT ribonucleic acid binding protein S1 (predicted) rn
RAT230_2:1371596_AT ribonucleic acid binding protein S1 (predicted) rn
RAE230B:1382287_AT ribonucleic acid binding protein S1 (predicted) rn
RAT230_2:1382287_AT ribonucleic acid binding protein S1 (predicted) rn
RAE230B:1384984_AT Ribonucleic acid binding protein S1 (predicted) rn
RAT230_2:1384984_AT Ribonucleic acid binding protein S1 (predicted) rn
Protein Similarities
Method ID Description E-Value
blast AAK21429 Rnp (rrm rna binding domain) containing protein 5 [Caenorhabditis elegans] ref|NP_497276.2| RNP (RRM RNA binding domain) containing family member (rnp-5) [Caenorhabditis elegans] 6.0E-46
blast T16535 hypothetical protein K02F3.11 - Caenorhabditis elegans 6.0E-46
blast CAE56475 Hypothetical protein CBG24189 [Caenorhabditis briggsae] 1.0E-31
Protein Domains
Database ID Description E-Value
Pfam IPR000504 EMBL-EBI RNA-binding region RNP-1 (RNA recognition motif) 3.4E-19
Pfam IPR000504 EMBL-EBI RNA-binding region RNP-1 (RNA recognition motif) 3.4E-19
Sequence
Target Sequence 
>C. ELEGANS:192011_S_AT
gatcgtcgtgacagaagcgggagccgtcagaggagacgcgcttctccgaggagaagccca
gcagcaagatcagccagtccggccaagcgtgtagtgatcaaaaatttgagcagaaatgtt
ctgaaaacgcacctcgaggagattttctcgatctacggagccatcaagaatgtcgatctt
ccaccagatcgcttccataaccatgttcatcgtggatatggatacgttgaatatgacaat
ttggaagacgccgaaaagtcgatcaagcacatggatggaggacaaatcgatggaatggct
gttcacgtcgaaatgactatcggacgacaatctgtcccattcc

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GATCGTCGTGACAGAAGCGGGAGCC 410 417 370 Antisense
GAGCCGTCAGAGGAGACGCGCTTCT 575 385 390 Antisense
GAGAAGCCCAGCAGCAAGATCAGCC 44 393 420 Antisense
CAGTCCGGCCAAGCGTGTAGTGATC 363 205 444 Antisense
GAAATGTTCTGAAAACGCACCTCGA 437 361 482 Antisense
AAACGCACCTCGAGGAGATTTTCTC 451 125 494 Antisense
TCTCGATCTACGGAGCCATCAAGAA 608 609 515 Antisense
TGTCGATCTTCCACCAGATCGCTTC 513 557 540 Antisense
AGATCGCTTCCATAACCATGTTCAT 248 67 555 Antisense
GATGGAATGGCTGTTCACGTCGAAA 417 407 658 Antisense
ATCGGACGACAATCTGTCCCATTCC 218 35 688 Antisense
Sequence Source Affymetrix Proprietary Database