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[173179_s_at] Probable RNA binding protein

Description AV184918_rc /REP_DB=TREMBL Accession /FEA=EST Transcript /REVCOMP /GB=AV184918 /DEF=Caenorhabditis elegans cDNA clone:yk671b7 : 3prime end, single read.
Cluster 6grp_highest_10_10 > 98      6grp_high1_10_10 > 89      4grp_highest_8_8 > 10      4grp_high_8_8 > 54      6grp_highest_nonorm > 95      6grp_total > 89      4grp_total > 56      6grp_highest_sub > Cu      6grp_cgc > 69      6grp_high1_sub > Cu      6grp_cgc_sub > Da      4grp_rule_based > L3      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 710
1 2 3 4 range
A 585.7
(-2.7)
P 		1011.2
(1.2)
P 		1211.8
(3)
P 		553.3
(-3)
P 		659
B 520.9
(-3)
P 		980
(2.5)
P 		1017.8
(3)
P 		613.5
(-1.9)
P 		497
C 611.3
(-1.1)
P 		818.8
(2.5)
P 		850.3
(3)
P 		501.6
(-3)
P 		349
avr 572.6
(-2.8) 		936.7
(1.9) 		1026.6
(3) 		556.1
(-3) 		471

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 621
1 2 3 4 5 6 range
A 574.5
(-1.5)
P 		664.2
(-0.5)
P 		436.4
(-3)
P 		522
(-2.1)
P 		858.6
(1.6)
P 		984.7
(3)
P 		548
B 549.4
(-1.9)
P 		436.8
(-3)
P 		505.6
(-2.3)
P 		625.3
(-1.2)
P 		662.5
(-0.8)
P 		1057.3
(3)
P 		621
C 920.6
(2.9)
P 		610
(-1.6)
P 		510.7
(-3)
P 		713.5
(-0.1)
P 		928.9
(3)
P 		794.4
(1.1)
P 		418
avr 681.5
(-0.4) 		570.3
(-1.9) 		484.2
(-3) 		620.3
(-1.2) 		816.7
(1.3) 		945.5
(3) 		461
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 236
1 2 3 4 range
A 213.3
(0.4)
P 		219.5
(0.5)
P 		316.8
(3)
P 		81
(-3)
P 		236
B 166.1
(-1.1)
P 		242
(3)
P 		235.8
(2.7)
P 		130.7
(-3)
P 		111
C 202.4
(0.3)
P 		235.4
(1.3)
P 		296.3
(3)
P 		84.6
(-3)
P 		212
avr 193.9
(0.1) 		232.3
(1.3) 		283
(3) 		98.8
(-3) 		184

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 299
1 2 3 4 5 6 range
A 105.9
(-2.6)
P 		236.2
(2.2)
P 		95
(-3)
P 		132.4
(-1.6)
P 		259.1
(3)
P 		239.7
(2.3)
P 		164
B 191.1
(-1.5)
P 		145.4
(-2.5)
P 		122.8
(-3)
P 		165.6
(-2.1)
P 		269.2
(0.2)
P 		394.3
(3)
P 		272
C 341.2
(3)
P 		186.1
(-1.4)
P 		130
(-3)
P 		143.5
(-2.6)
P 		300.6
(1.8)
P 		265.9
(0.9)
P 		211
avr 212.7
(0.2) 		189.2
(-0.6) 		115.9
(-3) 		147.2
(-2) 		276.3
(2.2) 		300
(3) 		184
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 173179_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.26902
Sequence Type Exemplar sequence
Representative Public ID AV184918 NCBI
Target Description AV184918_rc /REP_DB=TREMBL Accession /FEA=EST Transcript /REVCOMP /GB=AV184918 /DEF=Caenorhabditis elegans cDNA clone:yk671b7 : 3prime end, single read.
Cluster Evidence This cluster is supported by a EST Transcript.
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:852891-853207(-) 87.67 87.67
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:173179_S_AT
tctgtcccattccagcgtagaagttctccatttagaagacgctcgccgccaccaagagac
agaatgtcaccaatgagaagaggaggccgcagtccaccaccacatcgcagacgttctcca
atgggcggccgtggctcaggagccaacaatatgccacttggagggcccaacagattccgc

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
TCTGTCCCATTCCAGCGTAGAAGTT 602 605 13 Antisense
ATTCCAGCGTAGAAGTTCTCCATTT 572 7 21 Antisense
TTCTCCATTTAGAAGACGCTCGCCG 566 693 36 Antisense
TCGCCGCCACCAAGAGACAGAATGT 319 599 55 Antisense
GACAGAATGTCACCAATGAGAAGAG 148 367 70 Antisense
TGAGAAGAGGAGGCCGCAGTCCACC 356 569 86 Antisense
ATCGCAGACGTTCTCCAATGGGCGG 1 35 116 Antisense
CGGCCGTGGCTCAGGAGCCAACAAT 421 241 138 Antisense
GCTCAGGAGCCAACAATATGCCACT 338 301 146 Antisense
AATATGCCACTTGGAGGGCCCAACA 470 169 160 Antisense
ACTTGGAGGGCCCAACAGATTCCGC 486 103 168 Antisense
Sequence Source Affymetrix Proprietary Database