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[172083_x_at]

Description Y41D4B.W /REP_DB=WormBase Gene ID /WP=CE21842 /CHR=4 /FEA=Sanger Annotation /DEF=(ST.LOUIS)
Cluster 6grp_highest_10_10 > 16      6grp_high1_10_10 > 40      4grp_highest_8_8 > 14      4grp_high_8_8 > 22      6grp_highest_nonorm > 09      6grp_total > 50      4grp_total > 16      6grp_highest_sub > 03_04      6grp_cgc > 93      6grp_high1_sub > 03      6grp_cgc_sub > 03      6grp_total_sub > Hat      6grp_rule_based > S3      4grp_rule_based > L4      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 14949
1 2 3 4 range
A 23904.4
(-3)
P 		29678.8
(-0.3)
P 		29592.9
(-0.3)
P 		36763.5
(3)
P 		12859
B 25320.9
(-3)
P 		26754.3
(-1.6)
P 		29359.7
(0.8)
P 		31676.3
(3)
P 		6355
C 22578.3
(-3)
P 		23851.7
(-2.5)
P 		23689.6
(-2.6)
P 		37527.3
(3)
P 		14949
avr 23934.5
(-3) 		26761.6
(-1.5) 		27547.4
(-1.1) 		35322.4
(3) 		11388

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 8376
1 2 3 4 5 6 range
A 25736
(2.7)
P 		21827
(-0.8)
P 		26062.7
(3)
P 		25678
(2.7)
P 		19421
(-3)
P 		21752.5
(-0.9)
P 		6642
B 19611.6
(-1.2)
P 		20428.9
(-0.4)
P 		23958.9
(3)
P 		22019.4
(1.1)
P 		18067
(-2.6)
P 		17686.4
(-3)
P 		6273
C 19696.6
(-3)
P 		22289.2
(-0.5)
P 		24686.2
(1.8)
P 		25970.3
(3)
P 		19811.9
(-2.9)
P 		20682.8
(-2.1)
P 		6274
avr 21681.4
(-0.3) 		21515
(-0.5) 		24902.6
(3) 		24555.9
(2.6) 		19100
(-3) 		20040.6
(-2) 		5803
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 3322
1 2 3 4 range
A 8703.6
(3)
P 		6442.5
(-1.1)
P 		7736.2
(1.3)
P 		5381.5
(-3)
P 		3322
B 8074.7
(3)
P 		6607.7
(-3)
P 		6803.3
(-2.2)
P 		6750.2
(-2.4)
P 		1467
C 7474
(0.6)
P 		6857.5
(-1.4)
P 		8256.5
(3)
P 		6327.7
(-3)
P 		1929
avr 8084.1
(3) 		6635.9
(-1.5) 		7598.7
(1.5) 		6153.1
(-3) 		1931

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 3019
1 2 3 4 5 6 range
A 4744.2
(-3)
P 		7762.8
(3)
P 		5675.9
(-1.1)
P 		6512.5
(0.5)
P 		5860.4
(-0.8)
P 		5296.1
(-1.9)
P 		3019
B 6823.9
(1)
P 		6799.9
(0.9)
P 		5817.9
(-3)
P 		5832.2
(-2.9)
P 		7340.4
(3)
P 		6595.2
(0.1)
P 		1523
C 7300.7
(3)
P 		6801.1
(1.6)
P 		6283
(0.1)
P 		5222.6
(-3)
P 		6410.8
(0.4)
P 		6923.7
(1.9)
P 		2078
avr 6289.6
(-0.9) 		7121.3
(3) 		5925.6
(-2.7) 		5855.8
(-3) 		6537.2
(0.2) 		6271.7
(-1) 		1266
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 172083_x_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.19377
Sequence Type Exemplar sequence
Representative Public ID Y41D4B.W NCBI
Target Description Y41D4B.W /REP_DB=WormBase Gene ID /WP=CE21842 /CHR=4 /FEA=Sanger Annotation /DEF=(ST.LOUIS)
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_067714(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_067714 NCBI Caenorhabditis elegans Ribosomal Protein, Small subunit family member (rps-28) (rps-28) mRNA, complete cds. 11/11 None
GENEFINDER00000005544 ENSEMBL cdna:GeneFinder chromosome:CEL140:IV:1659702:1659954:1 11/11 None
Y41D4B.5.2 ENSEMBL cdna:known chromosome:CEL140:IV:1659683:1660009:1 gene:Y41D4B.5 11/11 None
Y41D4B.5.1 ENSEMBL cdna:known chromosome:CEL140:IV:1659689:1660009:1 gene:Y41D4B.5 11/11 None
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
chrIV:1659707-1659960(+) 100.0 100.0
Public Domain and Genome References
Gene Title
Gene Symbol rps-28
Ensembl Y41D4B.5
Entrez Gene 176975 Entrez gene
SwissProt Q95Y04 EMBL-EBI
WormBase CE21842 Wormbase
Functional Annotations
Ortholog
ID Title Organism
CANINE:1588790_S_AT similar to 40S ribosomal protein S28 cfa
CANINE:1583354_AT similar to 40S ribosomal protein S28 cfa
CANINE_2:CFAAFFX.28295.1.S1_AT similar to 40S ribosomal protein S28 cfa
DROSOPHILA_2:1624792_AT Ribosomal protein S28b dm
DROSGENOME1:154190_AT Ribosomal protein S28b dm
HG-U133A:208904_S_AT ribosomal protein S28 hs
HG-U133_PLUS_2:208904_S_AT ribosomal protein S28 hs
HG-FOCUS:208904_S_AT ribosomal protein S28 hs
HG-U133A_2:208904_S_AT ribosomal protein S28 hs
HU35KSUBC:RC_D53139_F_AT ribosomal protein S28 hs
HU35KSUBD:RC_AA477463_F_AT ribosomal protein S28 hs
HU35KSUBD:RC_AA477463_I_AT ribosomal protein S28 hs
HUGENEFL:U58682_AT ribosomal protein S28 hs
U133_X3P:G12653172_3P_A_AT ribosomal protein S28 hs
HG-U95AV2:39798_AT ribosomal protein S28 hs
HG-U133A:208902_S_AT Ribosomal protein S28 hs
HG-U133A_2:208902_S_AT Ribosomal protein S28 hs
HG-U133_PLUS_2:208902_S_AT Ribosomal protein S28 hs
HU35KSUBA:AA095959_AT Ribosomal protein S28 hs
HU35KSUBC:RC_AA287067_AT Ribosomal protein S28 hs
U133_X3P:HS.153177.1.A2_3P_AT Ribosomal protein S28 hs
HG-U133A_2:208903_AT Ribosomal protein S28 hs
HG-U133_PLUS_2:208903_AT Ribosomal protein S28 hs
HG-U133A:208903_AT Ribosomal protein S28 hs
HG-U95B:48357_AT Ribosomal protein S28 hs
MU11KSUBA:U11248_F_AT ribosomal protein S28 mm
MG-U74AV2:100758_AT ribosomal protein S28 mm
MOE430A:1451101_A_AT ribosomal protein S28 mm
MOUSE430A_2:1451101_A_AT ribosomal protein S28 mm
MOUSE430_2:1451101_A_AT ribosomal protein S28 mm
MG-U74AV2:98086_R_AT ribosomal protein S28 mm
RAE230A:1388481_AT Ribosomal protein S28 rn
RAT230_2:1388481_AT Ribosomal protein S28 rn
YEAST_2:1776104_AT Protein component of the small (40S) ribosomal subunit; nearly identical to Rps28Bp and has similarity to rat S28 ribosomal protein 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
GO Molecular Function (view graph)
ID Description Evidence Links
3735 structural constituent of ribosome inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast AAK68479 Ribosomal protein, small subunit protein 28 [Caenorhabditis elegans] ref|NP_500115.1| Ribosomal Protein, Small subunit family member (rps-28) [Caenorhabditis elegans] sp|Q95Y04|RS28_CAEEL 40S ribosomal protein S28 emb|CAE67974.1| Hypothetical protein CBG13580 [Caenorhabditis briggsae] 1.0E-21
blast EAA07405 ENSANGP00000015156 [Anopheles gambiae str. PEST] ref|XP_311696.2| ENSANGP00000015156 [Anopheles gambiae str. PEST] 2.0E-15
blast AAP21778 ribosomal protein S28 [Branchiostoma belcheri tsingtaunese] 4.0E-15
Protein Domains
Database ID Description E-Value
Pfam IPR000289 EMBL-EBI Ribosomal protein S28e 1.1E-44
Sequence
Target Sequence 
>C. ELEGANS:172083_X_AT
atggacaagcttactcttgctcgtgtcaccaaggtcatcggacgtactggatcccaggga
caatgtacccaagtccgcgtcgaattcatcaacgaccagaacaaccgttccatcatcaga
aacgttaagggcccagtccgcgagggagacatccttaccct

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
ATGGACAAGCTTACTCTTGCTCGTG 294 53 13 Antisense
TACTCTTGCTCGTGTCACCAAGGTC 316 645 24 Antisense
GCTCGTGTCACCAAGGTCATCGGAC 538 299 31 Antisense
AAGGTCATCGGACGTACTGGATCCC 412 159 43 Antisense
GGACGTACTGGATCCCAGGGACAAT 539 515 52 Antisense
AGGGACAATGTACCCAAGTCCGCGT 175 57 68 Antisense
CCAAGTCCGCGTCGAATTCATCAAC 231 277 81 Antisense
AATTCATCAACGACCAGAACAACCG 597 175 95 Antisense
GAACAACCGTTCCATCATCAGAAAC 323 353 111 Antisense
TCAGAAACGTTAAGGGCCCAGTCCG 557 599 128 Antisense
TCCGCGAGGGAGACATCCTTACCCT 531 595 149 Antisense
Sequence Source Affymetrix Proprietary Database