[Home] | [Total List]

[173887_s_at]

Description CEC7444 /REP_DB=TREMBL Accession /5_PRIME_EXT_ID=Y43B11AR.B /5_PRIME_EXT_DB=WormBase Gene ID /GB=C11744 /WB_GENE_ID=Y43B11AR.B /WP=CE24278 /CHR=4 /FEA=Genomic Cluster /DEF=(ST.LOUIS) protein_id:AAF60569.1; C.elegans cDNA clone yk122f3 : 5prime end, single read.
Cluster 6grp_highest_10_10 > 05      6grp_high1_10_10 > 20      4grp_highest_8_8 > 06      4grp_high_8_8 > 22      6grp_highest_nonorm > 09      6grp_total > 41      4grp_total > 16      6grp_highest_sub > 03_04      6grp_cgc > 71      6grp_cgc_sub > 03      6grp_total_sub > Hat      4grp_rule_based > L4      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 17834
1 2 3 4 range
A 29085.1
(-3)
P 		36070.2
(-0.4)
P 		35777.2
(-0.5)
P 		45255.1
(3)
P 		16170
B 30221
(-3)
P 		33334
(-0.6)
P 		34803.4
(0.5)
P 		37984
(3)
P 		7763
C 27421.6
(-3)
P 		29557.9
(-2.2)
P 		28101.2
(-2.7)
P 		43298.1
(3)
P 		15877
avr 28909.2
(-3) 		32987.4
(-1.2) 		32893.9
(-1.2) 		42179.1
(3) 		13270

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 11251
1 2 3 4 5 6 range
A 32541
(3)
P 		27381.3
(-0.5)
P 		30472.2
(1.6)
P 		29782.2
(1.1)
P 		23796.9
(-3)
P 		27746.4
(-0.3)
P 		8744
B 25334.5
(0.7)
P 		25796.2
(1.2)
P 		27798.5
(3)
P 		25791.9
(1.2)
P 		22210.8
(-2.2)
P 		21289.6
(-3)
P 		6509
C 25799.7
(-0.9)
P 		27696.9
(0.4)
P 		31438.7
(3)
P 		30312.6
(2.2)
P 		26685.3
(-0.2)
P 		22662.6
(-3)
P 		8776
avr 27891.7
(1) 		26958.1
(0.1) 		29903.1
(3) 		28628.9
(1.7) 		24231
(-2.7) 		23899.5
(-3) 		6004
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 3965
1 2 3 4 range
A 10589.9
(3)
P 		7829.9
(-1.2)
P 		9352.9
(1.1)
P 		6624.5
(-3)
P 		3965
B 9637.2
(3)
P 		8232.7
(-2.4)
P 		8064.7
(-3)
P 		8094.4
(-2.9)
P 		1573
C 9077.3
(1.3)
P 		8498.1
(-0.1)
P 		9794.2
(3)
P 		7300.7
(-3)
P 		2494
avr 9768.1
(3) 		8186.9
(-0.9) 		9070.6
(1.3) 		7339.9
(-3) 		2428

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 3739
1 2 3 4 5 6 range
A 5998.7
(-3)
P 		9738.1
(3)
P 		6636.2
(-2)
P 		7553.5
(-0.5)
P 		7180.9
(-1.1)
P 		6755.4
(-1.8)
P 		3739
B 8815.2
(2.4)
P 		8586.5
(1.8)
P 		6750.3
(-3)
P 		6831.4
(-2.8)
P 		9024
(3)
P 		7938.8
(0.1)
P 		2274
C 9562.8
(3)
P 		8451.1
(1.1)
P 		8001.7
(0.3)
P 		6095.9
(-3)
P 		8635
(1.4)
P 		7586.5
(-0.4)
P 		3467
avr 8125.6
(0.7) 		8925.2
(3) 		7129.4
(-2.1) 		6826.9
(-3) 		8280
(1.2) 		7426.9
(-1.3) 		2098
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 173887_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.24628
Sequence Type Exemplar sequence
Representative Public ID CEC7444 NCBI
Target Description CEC7444 /REP_DB=TREMBL Accession /5_PRIME_EXT_ID=Y43B11AR.B /5_PRIME_EXT_DB=WormBase Gene ID /GB=C11744 /WB_GENE_ID=Y43B11AR.B /WP=CE24278 /CHR=4 /FEA=Genomic Cluster /DEF=(ST.LOUIS) protein_id:AAF60569.1; C.elegans cDNA clone yk122f3 : 5prime end, single read.
Cluster Evidence This cluster is supported by a Genomic Cluster.
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_068702(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_068702 NCBI Caenorhabditis elegans Ribosomal Protein, Small subunit family member (rps-4) (rps-4) mRNA, complete cds. 11/11 None
SNAP00000030381 ENSEMBL cdna:SNAP chromosome:CEL140:IV:7083719:7084645:-1 11/11 None
GENEFINDER00000030386 ENSEMBL cdna:GeneFinder chromosome:CEL140:IV:7083719:7084645:-1 11/11 None
Y43B11AR.4.1 ENSEMBL cdna:known chromosome:CEL140:IV:7083677:7084666:-1 gene:Y43B11AR.4 11/11 None
Y43B11AR.4.3 ENSEMBL cdna:known chromosome:CEL140:IV:7083677:7084668:-1 gene:Y43B11AR.4 11/11 None
Y43B11AR.4.2 ENSEMBL cdna:known chromosome:CEL140:IV:7083677:7084668:-1 gene:Y43B11AR.4 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:7083725-7084652(-) 100.0 100.0
Public Domain and Genome References
Gene Title
Gene Symbol rps-4
Ensembl Y43B11AR.4
Entrez Gene 177481 Entrez gene
SwissProt Q9N3X2 EMBL-EBI
WormBase CE24278 Wormbase
Functional Annotations
Ortholog
ID Title Organism
ATGENOME1:13074_AT 40S ribosomal protein S4 (RPS4A) at
ATH1-121501:264849_AT 40S ribosomal protein S4 (RPS4A) at
CANINE_2:CFAAFFX.19410.1.S1_AT similar to 40S ribosomal protein S4, X isoform cfa
CANINE_2:CFAAFFX.19410.1.S1_S_AT similar to 40S ribosomal protein S4, X isoform cfa
CANINE_2:CFAAFFX.21949.1.S1_X_AT similar to 40S ribosomal protein S4, X isoform cfa
DROSOPHILA_2:1639949_S_AT Ribosomal protein S4 dm
DROSGENOME1:143649_AT Ribosomal protein S4 dm
HG-U133_PLUS_2:200933_X_AT ribosomal protein S4, X-linked hs
HG-U133A_2:200933_X_AT ribosomal protein S4, X-linked hs
HG-U133A:200933_X_AT ribosomal protein S4, X-linked hs
HG-FOCUS:200933_X_AT ribosomal protein S4, X-linked hs
U133_X3P:G4506724_3P_A_AT ribosomal protein S4, X-linked hs
U133_X3P:HS.302114.0.S1_3P_X_AT ribosomal protein S4, X-linked hs
U133_X3P:HS.302114.0.S1_3P_AT ribosomal protein S4, X-linked hs
U133_X3P:HS.108124.5.A1_3P_X_AT ribosomal protein S4, X-linked hs
U133_X3P:HS.108124.5.A1_3P_A_AT ribosomal protein S4, X-linked hs
U133_X3P:216342_3P_X_AT ribosomal protein S4, X-linked hs
U133_X3P:213347_3P_X_AT ribosomal protein S4, X-linked hs
U133_X3P:217019_3P_AT ribosomal protein S4, X-linked hs
U133_X3P:200933_3P_X_AT ribosomal protein S4, X-linked hs
HG-U133A_2:213347_X_AT ribosomal protein S4, X-linked hs
HG-U133_PLUS_2:213347_X_AT ribosomal protein S4, X-linked hs
HG-U133A:213347_X_AT ribosomal protein S4, X-linked hs
HG-U133A_2:217019_AT ribosomal protein S4, X-linked hs
HG-U133_PLUS_2:217019_AT ribosomal protein S4, X-linked hs
HG-U133A:217019_AT ribosomal protein S4, X-linked hs
HG-U95AV2:34643_AT ribosomal protein S4, X-linked hs
HG-U95D:89818_AT Ribosomal protein S4, X-linked hs
MU11KSUBA:M73436_F_AT ribosomal protein S4, X-linked mm
MU11KSUBB:MSA.41517.0_S_AT ribosomal protein S4, X-linked mm
MU11KSUBB:MSA.32345.0_F_AT ribosomal protein S4, X-linked mm
MU11KSUBB:MSA.31676.0_F_AT ribosomal protein S4, X-linked mm
MU11KSUBB:MSA.30806.0_F_AT ribosomal protein S4, X-linked mm
MU11KSUBB:MSA.18706.0_S_AT ribosomal protein S4, X-linked mm
MG-U74AV2:100780_AT ribosomal protein S4, X-linked mm
MG-U74AV2:162244_R_AT ribosomal protein S4, X-linked mm
MOE430A:1416276_A_AT ribosomal protein S4, X-linked mm
MOUSE430A_2:1416276_A_AT ribosomal protein S4, X-linked mm
MOUSE430_2:1416276_A_AT ribosomal protein S4, X-linked mm
RG-U34A:RC_AA799501_AT ribosomal protein S4, X-linked rn
RG-U34A:X14210CDS_AT ribosomal protein S4, X-linked rn
RG-U34A:X14210CDS_G_AT ribosomal protein S4, X-linked rn
RAE230A:1371308_AT ribosomal protein S4, X-linked rn
RAT230_2:1371308_AT ribosomal protein S4, X-linked rn
YEAST_2:1779154_S_AT Protein component of the small (40S) ribosomal subunit; identical to Rps4Bp and has similarity to rat S4 ribosomal protein Sc
YEAST_2:1779154_S_AT Protein component of the small (40S) ribosomal subunit; mutation affects 20S pre-rRNA processing; identical to Rps4Bp and has similarity to rat S4 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 AAF60569 Ribosomal protein, small subunit protein 4 [Caenorhabditis elegans] ref|NP_501103.1| Ribosomal Protein, Small subunit family member (rps-4) [Caenorhabditis elegans] sp|Q9N3X2|RS4_CAEEL 40S ribosomal protein S4 1.0E-138
blast CAE61799 Hypothetical protein CBG05762 [Caenorhabditis briggsae] 1.0E-133
Protein Domains
Database ID Description E-Value
Pfam IPR000876 EMBL-EBI Ribosomal protein S4E 7.2E-32
Pfam IPR005824 EMBL-EBI KOW 7.9E-6
Sequence
Target Sequence 
>C. ELEGANS:173887_S_AT
tctgaagtacgctctcaactacaccgaggccaagaagattctcacccagagagttgtccg
cgtcgacggaaaggtcagaacctgccacaagttcccaaccggattcatggatgtcgttgc
catcgagcgtaccaacgagtatttccgtatgctctacgataccaagggaagatacgtcgt
ccacagaatccaagctgccgaggccgacttcaagctctgcaaggtcaagtctgtccgcac
cgtcaacaagggagttccagtcctcaccaccactgacggacgcaccatccgctacccaga
cccacatgtcaaggttaacgacaccattgttttcaacatcagcacccagaagatcaccga
ctccgtcaagttcgagccaggaaatttggcctacgtcactggaggacgtaacgttggtcg
tgtcggaattatcggacatcgtgagcgtctcccaggagcatctgacatcatccacatcaa
ggattctgctggacactccttcgccactcgtatctccaacgtcttcgtcattggaaaggg
aaacaaggctctcgtctccctcccaactggagctggaatccgtctctca

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
TCTGAAGTACGCTCTCAACTACACC 258 607 163 Antisense
GATTCTCACCCAGAGAGTTGTCCGC 689 431 199 Antisense
TGGATGTCGTTGCCATCGAGCGTAC 77 549 270 Antisense
TCGTCCACAGAATCCAAGCTGCCGA 47 605 339 Antisense
AGCTCTGCAAGGTCAAGTCTGTCCG 398 79 375 Antisense
CTACCCAGACCCACATGTCAAGGTT 497 225 454 Antisense
GACTCCGTCAAGTTCGAGCCAGGAA 372 373 521 Antisense
AATTTGGCCTACGTCACTGGAGGAC 20 173 545 Antisense
AGGAGCATCTGACATCATCCACATC 688 55 616 Antisense
AGGGAAACAAGGCTCTCGTCTCCCT 55 57 699 Antisense
AACTGGAGCTGGAATCCGTCTCTCA 426 143 727 Antisense
Sequence Source Affymetrix Proprietary Database