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[173112_s_at] ribosomal protein S9

Description AV182341_rc /REP_DB=TREMBL Accession /FEA=EST Transcript /REVCOMP /GB=AV182341 /DEF=Caenorhabditis elegans cDNA clone:yk636e1 : 3prime end, single read.
Cluster 6grp_highest_10_10 > 07      6grp_high1_10_10 > 52      4grp_highest_8_8 > 21      4grp_high_8_8 > 23      6grp_highest_nonorm > 18      6grp_total > 61      4grp_total > 16      6grp_highest_sub > 04      6grp_cgc > 73      6grp_high1_sub > 03      6grp_cgc_sub > 02_03      6grp_total_sub > Hat      6grp_rule_based > S4      4grp_rule_based > L4      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 9855
1 2 3 4 range
A 20219
(-3)
P 		23025.7
(-0.7)
P 		24954.9
(0.9)
P 		27523.6
(3)
P 		7305
B 19190.1
(-3)
P 		21120.6
(-1.5)
P 		24126.6
(0.9)
P 		26700.9
(3)
P 		7511
C 18721.8
(-3)
P 		19351.5
(-2.6)
P 		19057.9
(-2.8)
P 		28576.5
(3)
P 		9855
avr 19377
(-3) 		21165.9
(-1.7) 		22713.1
(-0.6) 		27600.3
(3) 		8223

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 5568
1 2 3 4 5 6 range
A 15739.5
(-3)
P 		18267.9
(2.4)
P 		18075
(2)
P 		18556.3
(3)
P 		16656.6
(-1)
P 		18364.1
(2.6)
P 		2817
B 14723.7
(-1.9)
P 		17744.4
(1.7)
P 		18842.1
(3)
P 		17816
(1.8)
P 		15481.1
(-1)
P 		13776.1
(-3)
P 		5066
C 16186.4
(-0.7)
P 		19109.3
(2.7)
P 		18288.6
(1.7)
P 		19344.5
(3)
P 		16806.3
(-0)
P 		14281
(-3)
P 		5064
avr 15549.9
(-2.9) 		18373.9
(2.6) 		18401.9
(2.7) 		18572.3
(3) 		16314.7
(-1.4) 		15473.7
(-3) 		3099
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 3333
1 2 3 4 range
A 7361.8
(3)
P 		4998.3
(-1.3)
P 		6523.7
(1.5)
P 		4028.9
(-3)
P 		3333
B 6119.6
(3)
P 		5216.3
(-3)
P 		5590.7
(-0.5)
P 		5690
(0.1)
P 		903
C 6197.4
(1.5)
P 		5563.7
(-0.5)
P 		6642.3
(3)
P 		4818.5
(-3)
P 		1824
avr 6559.6
(3) 		5259.4
(-1.6) 		6252.2
(1.9) 		4845.8
(-3) 		1714

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 3596
1 2 3 4 5 6 range
A 2901.5
(-3)
P 		6497
(3)
P 		3936.3
(-1.3)
P 		4706.3
(0)
P 		5026.2
(0.5)
P 		4471.1
(-0.4)
P 		3596
B 5123.1
(-1.1)
P 		5906.4
(1.7)
P 		4575.4
(-3)
P 		4718.8
(-2.5)
P 		6289.8
(3)
P 		5137
(-1)
P 		1714
C 5999.6
(3)
P 		5830.8
(2.5)
P 		4654.8
(-0.8)
P 		3890.2
(-3)
P 		5438.3
(1.4)
P 		4780.7
(-0.5)
P 		2109
avr 4674.7
(-2) 		6078.1
(3) 		4388.8
(-3) 		4438.4
(-2.8) 		5584.8
(1.2) 		4796.3
(-1.6) 		1689
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 173112_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.26792
Sequence Type Exemplar sequence
Representative Public ID AV182341 NCBI
Target Description AV182341_rc /REP_DB=TREMBL Accession /FEA=EST Transcript /REVCOMP /GB=AV182341 /DEF=Caenorhabditis elegans cDNA clone:yk636e1 : 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_063983(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_063983 NCBI Caenorhabditis elegans Ribosomal Protein, Small subunit family member (rps-9) (rps-9) mRNA, complete cds. 11/11 A 
SNAP00000001348 ENSEMBL cdna:SNAP chromosome:CEL140:II:11125374:11126266:-1 11/11 None
GENEFINDER00000001360 ENSEMBL cdna:GeneFinder chromosome:CEL140:II:11125374:11126266:-1 11/11 None
F40F8.10.3 ENSEMBL cdna:known chromosome:CEL140:II:11125063:11126281:-1 gene:F40F8.10 11/11 None
F40F8.10.1 ENSEMBL cdna:known chromosome:CEL140:II:11125317:11126281:-1 gene:F40F8.10 11/11 A 
F40F8.10.2 ENSEMBL cdna:known chromosome:CEL140:II:11125317:11126275:-1 gene:F40F8.10 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
chrII:11125507-11125978(-) 79.58 79.58
Public Domain and Genome References
Gene Title ribosomal protein S9
Gene Symbol rps-9
Ensembl F40F8.10
Entrez Gene 174699 Entrez gene
SwissProt Q20228 EMBL-EBI
WormBase CE05849 Wormbase
Functional Annotations
Ortholog
ID Title Organism
ATH1-121501:249427_AT 40S ribosomal protein S9 (RPS9C) at
CANINE:1583957_S_AT similar to 40S ribosomal protein S9 cfa
CANINE:1592244_X_AT similar to 40S ribosomal protein S9 cfa
CANINE:1589592_AT similar to 40S ribosomal protein S9 cfa
CANINE_2:CFA.297.2.A1_S_AT similar to 40S ribosomal protein S9 cfa
DROSOPHILA_2:1624070_AT Ribosomal protein S9 dm
DROSOPHILA_2:1635388_S_AT Ribosomal protein S9 dm
DROSGENOME1:142798_AT Ribosomal protein S9 dm
HG-U95AV2:31511_AT ribosomal protein S9 hs
HG-U133A:217747_S_AT ribosomal protein S9 hs
HG-U133_PLUS_2:217747_S_AT ribosomal protein S9 hs
HG-FOCUS:217747_S_AT ribosomal protein S9 hs
HG-U133A_2:217747_S_AT ribosomal protein S9 hs
HUGENEFL:U14971_AT ribosomal protein S9 hs
U133_X3P:G4506744_3P_X_AT ribosomal protein S9 hs
U133_X3P:G4506744_3P_AT ribosomal protein S9 hs
U133_X3P:217747_3P_S_AT ribosomal protein S9 hs
U133_X3P:HS2.425881.1.S1_3P_X_AT Ribosomal protein S9 hs
U133_X3P:HS2.425881.1.S1_3P_AT Ribosomal protein S9 hs
U133_X3P:HS.180920.1.S1_3P_X_AT Ribosomal protein S9 hs
U133_X3P:HS.180920.1.S1_3P_AT Ribosomal protein S9 hs
U133_X3P:214317_3P_X_AT Ribosomal protein S9 hs
U133_X3P:1557981_3P_AT Ribosomal protein S9 hs
HG-U133_PLUS_2:1557981_AT Ribosomal protein S9 hs
HG-U133A_2:214317_X_AT Ribosomal protein S9 hs
HG-U133_PLUS_2:214317_X_AT Ribosomal protein S9 hs
HG-U133A:214317_X_AT Ribosomal protein S9 hs
RG-U34A:X66370_AT ribosomal protein S9 rn
RAE230A:1387888_AT ribosomal protein S9 rn
RAT230_2:1387888_AT ribosomal protein S9 rn
YEAST_2:1770298_AT Protein component of the small (40S) ribosomal subunit; nearly identical to Rps9Ap and has similarity to E. coli S4 and rat S9 ribosomal proteins Sc
Gene Ontology
GO Biological Process (view graph)
ID Description Evidence Links
6412 protein biosynthesis inferred from electronic annotation QuickGO AmiGO
GO Cellular Component (view graph)
ID Description Evidence Links
5622 intracellular inferred from electronic annotation QuickGO AmiGO
5840 ribosome inferred from electronic annotation QuickGO AmiGO
15935 small ribosomal subunit inferred from electronic annotation QuickGO AmiGO
GO Molecular Function (view graph)
ID Description Evidence Links
3723 RNA binding inferred from electronic annotation QuickGO AmiGO
3735 structural constituent of ribosome inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast CAA93262 Hypothetical protein F40F8.10 [Caenorhabditis elegans] ref|NP_496384.1| Ribosomal Protein, Small subunit family member (rps-9) [Caenorhabditis elegans] sp|Q20228|RS9_CAEEL 40S ribosomal protein S9 1.0E-102
blast CAE59565 Hypothetical protein CBG02962 [Caenorhabditis briggsae] 1.0E-101
Protein Domains
Database ID Description E-Value
Pfam IPR001912 EMBL-EBI Ribosomal protein S4 1.5E-38
Pfam IPR002942 EMBL-EBI RNA-binding S4 3.0E-8
Sequence
Target Sequence 
>C. ELEGANS:173112_S_AT
cttgtcaagatcggtgtcctcgacgagaccaagatgaagctcgattacgttctcggtctt
aaggtcgaggacttccttgagcgcaggctccaaacccaggtcttcaagctcggacttgcc
aagtctatccaccacgcccgtatcttgatcaagcagcaccacatcc

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
CTTGTCAAGATCGGTGTCCTCGACG 647 215 13 Antisense
ATCGGTGTCCTCGACGAGACCAAGA 398 35 22 Antisense
TCCTCGACGAGACCAAGATGAAGCT 337 593 29 Antisense
GATGAAGCTCGATTACGTTCTCGGT 397 411 45 Antisense
TCGATTACGTTCTCGGTCTTAAGGT 601 581 53 Antisense
TCGGTCTTAAGGTCGAGGACTTCCT 506 597 65 Antisense
AAGGTCGAGGACTTCCTTGAGCGCA 72 159 73 Antisense
GGTCTTCAAGCTCGGACTTGCCAAG 541 499 111 Antisense
TCGGACTTGCCAAGTCTATCCACCA 326 607 122 Antisense
CACGCCCGTATCTTGATCAAGCAGC 65 201 145 Antisense
ATCTTGATCAAGCAGCACCACATCC 258 31 154 Antisense
Sequence Source Affymetrix Proprietary Database