[Home] | [Total List]

[190108_at] ribosomal protein

Description C48B6.2 /REP_DB=WormBase Gene ID /WP=CE08804 /TR=SW:O01513 /GB=AAC48162.1 /SUBMIT=ST.LOUIS /CHR=1 /FEA=Sanger Annotation /DEF=ribosomal protein
Cluster 6grp_highest_10_10 > 65      6grp_high1_10_10 > 76      4grp_highest_8_8 > 07      4grp_high_8_8 > 21      6grp_highest_nonorm > 75      6grp_total > 66      4grp_total > 18      6grp_high1_sub > Da      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 385
1 2 3 4 range
A 936.2
(-0.8)
P 		876.2
(-3)
P 		886.5
(-2.6)
P 		1036.3
(3)
P 		160
B 792.4
(-3)
P 		1043.5
(0.9)
P 		834.1
(-2.3)
P 		1177
(3)
P 		385
C 968.7
(-3)
P 		1095
(0.8)
P 		973.5
(-2.9)
P 		1167.7
(3)
P 		199
avr 899.1
(-3) 		1004.9
(-0.2) 		898
(-3) 		1127
(3) 		229

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 533
1 2 3 4 5 6 range
A 644.1
(-3)
P 		742.2
(-1.2)
P 		824.6
(0.3)
P 		782
(-0.5)
P 		672.7
(-2.5)
P 		970.6
(3)
P 		327
B 960.7
(0.2)
P 		913.5
(-0.5)
P 		1038.7
(1.4)
P 		820.5
(-1.9)
P 		745.6
(-3)
P 		1143.7
(3)
P 		398
C 722.9
(-3)
P 		978.9
(0.4)
P 		723.2
(-3)
P 		857.1
(-1.2)
P 		738.9
(-2.8)
P 		1176.7
(3)
P 		454
avr 775.9
(-2.1) 		878.2
(-0.5) 		862.2
(-0.7) 		819.9
(-1.4) 		719.1
(-3) 		1097
(3) 		378
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 189
1 2 3 4 range
A 340.9
(3)
P 		190.2
(-1.8)
P 		231.7
(-0.5)
P 		151.7
(-3)
P 		189
B 252.7
(2.5)
P 		257.7
(3)
P 		193.3
(-3)
P 		250.8
(2.4)
P 		64
C 320.7
(2.2)
P 		314.8
(2)
P 		339.3
(3)
P 		196.9
(-3)
P 		142
avr 304.8
(3) 		254.2
(0.1) 		254.8
(0.1) 		199.8
(-3) 		105

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 308
1 2 3 4 5 6 range
A 118.7
(-3)
P 		264
(3)
P 		179.6
(-0.5)
P 		198.3
(0.3)
P 		203
(0.5)
P 		236.3
(1.9)
P 		145
B 334.3
(0.4)
P 		304.1
(-0.5)
P 		252.2
(-2)
P 		217.3
(-3)
P 		302.9
(-0.5)
P 		426.5
(3)
P 		209
C 267.9
(-0.4)
P 		298.7
(0.4)
P 		184.1
(-2.7)
P 		172.4
(-3)
P 		239.1
(-1.2)
P 		393.9
(3)
P 		222
avr 240.3
(-1.3) 		288.9
(0.6) 		205.3
(-2.6) 		196
(-3) 		248.3
(-1) 		352.2
(3) 		156
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 190108_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.1455
Sequence Type Exemplar sequence
Representative Public ID C48B6.2 NCBI
Target Description C48B6.2 /REP_DB=WormBase Gene ID /WP=CE08804 /TR=SW:O01513 /GB=AAC48162.1 /SUBMIT=ST.LOUIS /CHR=1 /FEA=Sanger Annotation /DEF=ribosomal 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_059571(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_059571 NCBI Caenorhabditis elegans C48B6.2 (C48B6.2) mRNA, complete cds. 11/11 None
SNAP00000029807 ENSEMBL cdna:SNAP chromosome:CEL140:I:6924916:6925618:1 11/11 None
GENEFINDER00000029816 ENSEMBL cdna:GeneFinder chromosome:CEL140:I:6924916:6925618:1 11/11 None
C48B6.2.1 ENSEMBL cdna:known chromosome:CEL140:I:6924896:6925683:1 gene:C48B6.2 11/11 None
C48B6.2.2 ENSEMBL cdna:known chromosome:CEL140:I:6924898:6925665:1 gene:C48B6.2 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
chrI:6924846-6925549(+) 100.0 100.0
Public Domain and Genome References
Gene Title ribosomal protein
Ensembl C48B6.2
Entrez Gene 172420 Entrez gene
SwissProt O01513 EMBL-EBI
WormBase CE08804 Wormbase
Functional Annotations
Ortholog
ID Title Organism
ATH1-121501:246527_AT RNA-binding S4 domain-containing protein at
CANINE_2:CFAAFFX.27630.1.S1_S_AT similar to U3 small nucleolar ribonucleoprotein protein IMP3 (U3 snoRNP protein IMP3) (BRMS2) cfa
DROSGENOME1:147369_AT dm
DROSOPHILA_2:1640069_AT dm
HG-U133A_2:221688_S_AT IMP3, U3 small nucleolar ribonucleoprotein, homolog (yeast) hs
HG-U133A:221688_S_AT IMP3, U3 small nucleolar ribonucleoprotein, homolog (yeast) hs
HG-U133_PLUS_2:221688_S_AT IMP3, U3 small nucleolar ribonucleoprotein, homolog (yeast) hs
HU35KSUBA:RC_AA423991_AT IMP3, U3 small nucleolar ribonucleoprotein, homolog (yeast) hs
U133_X3P:G12053320_3P_S_AT IMP3, U3 small nucleolar ribonucleoprotein, homolog (yeast) hs
HG-U95B:57201_AT IMP3, U3 small nucleolar ribonucleoprotein, homolog (yeast) hs
MG-U74AV2:92817_AT IMP3, U3 small nucleolar ribonucleoprotein, homolog (yeast) mm
MG-U74CV2:171039_AT IMP3, U3 small nucleolar ribonucleoprotein, homolog (yeast) mm
MOE430A:1416210_AT IMP3, U3 small nucleolar ribonucleoprotein, homolog (yeast) mm
MOUSE430A_2:1416210_AT IMP3, U3 small nucleolar ribonucleoprotein, homolog (yeast) mm
MOUSE430_2:1416210_AT IMP3, U3 small nucleolar ribonucleoprotein, homolog (yeast) mm
MU11KSUBA:AA138773_AT IMP3, U3 small nucleolar ribonucleoprotein, homolog (yeast) (Imp3), mRNA mm
MU19KSUBA:TC18823_AT IMP3, U3 small nucleolar ribonucleoprotein, homolog (yeast) (Imp3), mRNA mm
RG-U34A:RC_AA799369_AT similar to RIKEN cDNA 1190002L16 (predicted) rn
RG-U34B:RC_AA964500_AT similar to RIKEN cDNA 1190002L16 (predicted) rn
RAE230A:1388321_AT similar to RIKEN cDNA 1190002L16 (predicted) rn
RAT230_2:1388321_AT similar to RIKEN cDNA 1190002L16 (predicted) rn
YEAST_2:1777403_AT Component of the SSU processome, which is required for pre-18S rRNA processing, essential protein that interacts with Mpp10p and mediates interactions of Imp4p and Mpp10p with U3 snoRNA Sc
Gene Ontology
GO Molecular Function (view graph)
ID Description Evidence Links
3723 RNA binding inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast NP_491972 C48B6.2 [Caenorhabditis elegans] gb|AAC48162.1| Hypothetical protein C48B6.2 [Caenorhabditis elegans] sp|O01513|YS4L_CAEEL Putative 40S ribosomal protein S4-like 1.0E-100
blast CAE67285 Hypothetical protein CBG12733 [Caenorhabditis briggsae] 3.0E-92
Protein Domains
Database ID Description E-Value
Pfam IPR002942 EMBL-EBI RNA-binding S4 8.3E-11
Sequence
Target Sequence 
>C. ELEGANS:190108_AT
gagcactacgctttgtacaacactttggctgcaaagagtcgtgaagtagctgatcttatc
aaaaacctatcagaatcggatcccttccgatcaaaatgcacagaggatatgctcaccaaa
ttttacgcagctggacttgtgcccactagtgatacgttggaaagaattggaaaggtgact
ggagcatcattcgctcgtcgtcgtcttccagtcgtgatgagaaatattggaatgtgtgaa
tcagtcaaaactgcgtcagatctcgtggagcagggacacgttcgaatcggaacgaaactg
gttaccgatccagcatttatggttacacgatcgtctg

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GAGCACTACGCTTTGTACAACACTT 114 391 136 Antisense
AACCTATCAGAATCGGATCCCTTCC 601 147 199 Antisense
ATCCCTTCCGATCAAAATGCACAGA 603 37 215 Antisense
ATTTTACGCAGCTGGACTTGTGCCC 329 15 255 Antisense
GGACTTGTGCCCACTAGTGATACGT 149 525 268 Antisense
GACTGGAGCATCATTCGCTCGTCGT 440 375 312 Antisense
CGTCGTCTTCCAGTCGTGATGAGAA 688 245 334 Antisense
AAACTGCGTCAGATCTCGTGGAGCA 106 121 383 Antisense
GGAGCAGGGACACGTTCGAATCGGA 210 521 402 Antisense
GAAACTGGTTACCGATCCAGCATTT 703 357 429 Antisense
GCATTTATGGTTACACGATCGTCTG 157 309 448 Antisense
Sequence Source Affymetrix Proprietary Database