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[192887_at] 60S ribosomal protein

Description F52B5.6 /REP_DB=WormBase Gene ID /WP=CE05721 /GEN=rpl-25.2 /TR=SW:Q20647 /GB=CAA99858.1 /SUBMIT=HINXTON /CHR=1 /FEA=Sanger Annotation /DEF=60S ribosomal protein
Cluster 6grp_highest_10_10 > 36      6grp_high1_10_10 > 40      4grp_highest_8_8 > 14      4grp_high_8_8 > 22      6grp_highest_nonorm > 19      6grp_total > 53      4grp_total > 16      6grp_highest_sub > 03      6grp_cgc > 91      6grp_high1_sub > 03      6grp_cgc_sub > 03      6grp_total_sub > Hat      4grp_rule_based > L4      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 19205
1 2 3 4 range
A 20593.6
(-3)
P 		28584.9
(-0.2)
P 		26471.8
(-0.9)
P 		37609.5
(3)
P 		17016
B 21604.9
(-3)
P 		21969.1
(-2.7)
P 		25142.1
(-0.2)
P 		29259.2
(3)
P 		7654
C 18404.4
(-3)
P 		20931
(-2)
P 		20981.2
(-1.9)
P 		33025.5
(3)
P 		14621
avr 20201
(-3) 		23828.3
(-1.3) 		24198.4
(-1.2) 		33298.1
(3) 		13097

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 5134
1 2 3 4 5 6 range
A 21904.7
(3)
P 		17201.1
(-3)
P 		21398.4
(2.4)
P 		20321
(1)
P 		18545.2
(-1.3)
P 		20625
(1.4)
P 		4704
B 17824.7
(-0.9)
P 		18270.7
(0.1)
P 		19684.1
(3)
P 		18572.8
(0.7)
P 		17161.7
(-2.2)
P 		16792.8
(-3)
P 		2891
C 16770.7
(-3)
P 		18486.3
(-0.7)
P 		21179.3
(3)
P 		18177.2
(-1.1)
P 		18568
(-0.6)
P 		17240
(-2.4)
P 		4409
avr 18833.4
(-1.2) 		17986
(-3) 		20753.9
(3) 		19023.7
(-0.8) 		18091.6
(-2.8) 		18219.3
(-2.5) 		2768
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 2072
1 2 3 4 range
A 7498.1
(3)
P 		6205
(-0.9)
P 		6920.2
(1.3)
P 		5505.3
(-3)
P 		1993
B 6889.6
(3)
P 		5425.9
(-3)
P 		5826
(-1.4)
P 		6235.2
(0.3)
P 		1464
C 6092.4
(-1.2)
P 		6017.8
(-1.5)
P 		7312.6
(3)
P 		5568.6
(-3)
P 		1744
avr 6826.7
(3) 		5882.9
(-2.4) 		6686.3
(2.2) 		5769.7
(-3) 		1057

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 3317
1 2 3 4 5 6 range
A 4038
(-3)
P 		6117.6
(3)
P 		4660.1
(-1.2)
P 		5153.9
(0.2)
P 		5596.1
(1.5)
P 		5021.5
(-0.2)
P 		2080
B 6202.1
(0.9)
P 		6081.6
(0.6)
P 		4779.9
(-3)
P 		4919.3
(-2.6)
P 		6972.6
(3)
P 		6262
(1.1)
P 		2193
C 6216.2
(3)
P 		5640.7
(1.7)
P 		5390.5
(1.1)
P 		3655.5
(-3)
P 		6008.3
(2.5)
P 		5771.2
(2)
P 		2561
avr 5485.4
(0.4) 		5946.6
(2.1) 		4943.5
(-1.6) 		4576.2
(-3) 		6192.3
(3) 		5684.9
(1.1) 		1616
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 192887_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.2534
Sequence Type Exemplar sequence
Representative Public ID F52B5.6 NCBI
Target Description F52B5.6 /REP_DB=WormBase Gene ID /WP=CE05721 /GEN=rpl-25.2 /TR=SW:Q20647 /GB=CAA99858.1 /SUBMIT=HINXTON /CHR=1 /FEA=Sanger Annotation /DEF=60S 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_059862(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_059862 NCBI Caenorhabditis elegans Ribosomal Protein, Large subunit family member (rpl-25.2) (rpl-25.2) mRNA, complete cds. 11/11 None
SNAP00000039363 ENSEMBL cdna:SNAP chromosome:CEL140:I:8337238:8337769:-1 11/11 None
GENEFINDER00000039367 ENSEMBL cdna:GeneFinder chromosome:CEL140:I:8337238:8337769:-1 11/11 None
F52B5.6.1 ENSEMBL cdna:known chromosome:CEL140:I:8337185:8337773:-1 gene:F52B5.6 11/11 None
F52B5.6.2 ENSEMBL cdna:known chromosome:CEL140:I:8337186:8337771:-1 gene:F52B5.6 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:8337168-8337700(-) 100.0 100.0
Public Domain and Genome References
Gene Title 60S ribosomal protein
Gene Symbol rpl-25.2
Ensembl F52B5.6
Entrez Gene 172617 Entrez gene
SwissProt Q20647 EMBL-EBI
WormBase CE05721 Wormbase
Functional Annotations
Ortholog
ID Title Organism
CANINE_2:CFA.394.1.A1_X_AT similar to 60S ribosomal protein L23a cfa
CANINE_2:CFAAFFX.10089.1.S1_X_AT similar to 60S ribosomal protein L23a cfa
CANINE_2:CFAAFFX.11362.1.S1_AT similar to 60S ribosomal protein L23a cfa
CANINE_2:CFAAFFX.17447.1.S1_X_AT similar to 60S ribosomal protein L23a cfa
CANINE_2:CFAAFFX.20956.1.S1_AT similar to 60S ribosomal protein L23a cfa
CANINE_2:CFAAFFX.20956.1.S1_X_AT similar to 60S ribosomal protein L23a cfa
CANINE_2:CFAAFFX.20985.1.S1_X_AT similar to 60S ribosomal protein L23a cfa
CANINE_2:CFAAFFX.21051.1.S1_X_AT similar to 60S ribosomal protein L23a cfa
CANINE_2:CFAAFFX.24940.1.S1_S_AT similar to 60S ribosomal protein L23a cfa
CANINE_2:CFAAFFX.25045.1.S1_X_AT similar to 60S ribosomal protein L23a cfa
CANINE_2:CFAAFFX.26692.1.S1_X_AT similar to 60S ribosomal protein L23a cfa
CANINE_2:CFAAFFX.2686.1.S1_AT similar to 60S ribosomal protein L23a cfa
CANINE_2:CFAAFFX.2686.1.S1_X_AT similar to 60S ribosomal protein L23a cfa
CANINE_2:CFAAFFX.27054.1.S1_AT similar to 60S ribosomal protein L23a cfa
CANINE_2:CFAAFFX.4101.1.S1_X_AT similar to 60S ribosomal protein L23a cfa
CANINE_2:CFAAFFX.4692.1.S1_X_AT similar to 60S ribosomal protein L23a cfa
CANINE_2:CFAAFFX.5912.1.S1_AT similar to 60S ribosomal protein L23a cfa
CANINE_2:CFAAFFX.5912.1.S1_X_AT similar to 60S ribosomal protein L23a cfa
CANINE_2:CFAAFFX.725.1.S1_AT similar to 60S ribosomal protein L23a cfa
CANINE_2:CFAAFFX.727.1.S1_X_AT similar to 60S ribosomal protein L23a cfa
CANINE_2:CFAAFFX.7478.1.S1_X_AT similar to 60S ribosomal protein L23a cfa
CANINE_2:CFAAFFX.8146.1.S1_X_AT similar to 60S ribosomal protein L23a cfa
HUGENEFL:U06155_AT similar to 60S ribosomal protein L23a hs
HUGENEFL:U06155_S_AT similar to 60S ribosomal protein L23a hs
RG-U34A:X65228CDS_S_AT similar to 60S ribosomal protein L23a rn
RG-U34C:RC_AI231140_G_AT similar to 60S ribosomal protein L23a rn
RG-U34C:RC_AI235452_AT Similar to 60S ribosomal protein L23a rn
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
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 CAA99858 Hypothetical protein F52B5.6 [Caenorhabditis elegans] ref|NP_492263.1| Ribosomal Protein, Large subunit family member (rpl-25.2) [Caenorhabditis elegans] sp|Q20647|R23A2_CAEEL 60S ribosomal protein L23a 1.0E-76
blast CAE60469 Hypothetical protein CBG04080 [Caenorhabditis briggsae] 5.0E-67
Protein Domains
Database ID Description E-Value
Pfam IPR005633 EMBL-EBI Ribosomal protein L23, N-terminal domain 1.2E-18
Pfam IPR001014 EMBL-EBI Ribosomal L23 protein 6.6E-31
Sequence
Target Sequence 
>C. ELEGANS:192887_AT
gttcgtacatcagtccacttcagacgcccaaagacccttgtgactgccagagctccaaga
tatgcccgcaagtctgctccagccagagacaagctcgatagcttcgctgtcatcaaggct
ccacacaccaccgagagctccatgaagaagatcgaagaccacaacacccttgtcttcatt
gttgacgagaaggccaacaagcatcacatcaagagagccgtccatgccctttacaacgtc
aaggctgttaaggtcaacaccctgattactccactccaacagaagaaagcttacgttcga
ttggcttcggactacgatgctct

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GTTCGTACATCAGTCCACTTCAGAC 336 443 100 Antisense
GTGACTGCCAGAGCTCCAAGATATG 240 483 139 Antisense
CCAAGATATGCCCGCAAGTCTGCTC 327 277 154 Antisense
GTCTGCTCCAGCCAGAGACAAGCTC 280 471 171 Antisense
GACAAGCTCGATAGCTTCGCTGTCA 530 365 187 Antisense
AGAAGATCGAAGACCACAACACCCT 301 75 245 Antisense
CACCCTTGTCTTCATTGTTGACGAG 385 199 264 Antisense
GTCCATGCCCTTTACAACGTCAAGG 395 477 319 Antisense
TAAGGTCAACACCCTGATTACTCCA 318 637 348 Antisense
TGATTACTCCACTCCAACAGAAGAA 227 563 362 Antisense
GATTGGCTTCGGACTACGATGCTCT 140 435 398 Antisense
Sequence Source Affymetrix Proprietary Database