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[172910_at] ribosomal protein L39

Description C26F1.9 /REP_DB=WormBase Gene ID /WP=CE06883 /GEN=rpl-39 /TR=SW:P52814 /GB=AAB37070.1 /SUBMIT=ST.LOUIS /CHR=5 /FEA=Sanger Annotation /DEF=ribosomal protein L39
Cluster 6grp_highest_10_10 > 14      6grp_high1_10_10 > 30      4grp_highest_8_8 > 06      4grp_high_8_8 > 22      6grp_highest_nonorm > 08      6grp_total > 43      4grp_total > 17      6grp_cgc > 81      6grp_high1_sub > 03      6grp_cgc_sub > 03      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 17087
1 2 3 4 range
A 20641.7
(-3)
P 		28335.5
(-0.3)
P 		25801.2
(-1.2)
P 		37728.8
(3)
P 		17087
B 21367.6
(-3)
P 		25379.8
(0.1)
P 		26982.7
(1.4)
P 		29042.1
(3)
P 		7675
C 21999
(-3)
P 		24870.1
(-1.7)
P 		22205.5
(-2.9)
P 		35063
(3)
P 		13064
avr 21336.1
(-3) 		26195.1
(-0.7) 		24996.5
(-1.3) 		33944.6
(3) 		12609

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 9871
1 2 3 4 5 6 range
A 19663.3
(-0.1)
P 		18420.1
(-0.9)
P 		24712
(3)
P 		18479.6
(-0.8)
P 		14914.8
(-3)
P 		16898
(-1.8)
P 		9797
B 18562.5
(0.3)
P 		18374.7
(0.1)
P 		21598
(3)
P 		14840.8
(-3)
P 		15291.4
(-2.6)
P 		15745.1
(-2.2)
P 		6757
C 18495.8
(2.4)
P 		18624.1
(3)
P 		18397.7
(2)
P 		17947.4
(0.1)
P 		17513.9
(-1.8)
P 		17228.8
(-3)
P 		1395
avr 18907.2
(0.2) 		18473
(-0.3) 		21569.2
(3) 		17089.3
(-1.7) 		15906.7
(-3) 		16624
(-2.2) 		5663
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 2217
1 2 3 4 range
A 7515.6
(3)
P 		6150.9
(-1.1)
P 		6744.9
(0.7)
P 		5522.8
(-3)
P 		1993
B 6814
(3)
P 		6268.2
(-2.2)
P 		6252.5
(-2.4)
P 		6188.9
(-3)
P 		625
C 7282.3
(1.5)
P 		7150.3
(1.1)
P 		7739.3
(3)
P 		5912.2
(-3)
P 		1827
avr 7204
(3) 		6523.1
(-0.1) 		6912.2
(1.7) 		5874.6
(-3) 		1329

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 3246
1 2 3 4 5 6 range
A 3624.8
(-3)
P 		6551.1
(3)
P 		5381.7
(0.6)
P 		4686.9
(-0.8)
P 		4500.6
(-1.2)
P 		4114.1
(-2)
P 		2926
B 6458.8
(3)
P 		6116.2
(2.2)
P 		5244.6
(0.1)
P 		3930.8
(-3)
P 		6212.7
(2.4)
P 		5871.3
(1.6)
P 		2528
C 6855.6
(3)
P 		5682.8
(0.8)
P 		4682.5
(-1)
P 		3609.2
(-3)
P 		5667.3
(0.8)
P 		5767.5
(1)
P 		3246
avr 5646.4
(1.6) 		6116.7
(3) 		5102.9
(0) 		4075.6
(-3) 		5460.2
(1.1) 		5251
(0.5) 		2041
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 172910_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.12361
Sequence Type Exemplar sequence
Representative Public ID C26F1.9 NCBI
Target Description C26F1.9 /REP_DB=WormBase Gene ID /WP=CE06883 /GEN=rpl-39 /TR=SW:P52814 /GB=AAB37070.1 /SUBMIT=ST.LOUIS /CHR=5 /FEA=Sanger Annotation /DEF=ribosomal protein L39
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_072605(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_072605 NCBI Caenorhabditis elegans Ribosomal Protein, Large subunit family member (rpl-39) (rpl-39) mRNA, complete cds. 11/11 None
SNAP00000018569 ENSEMBL cdna:SNAP chromosome:CEL140:V:7778411:7778668:-1 11/11 None
GENEFINDER00000018578 ENSEMBL cdna:GeneFinder chromosome:CEL140:V:7778411:7778668:-1 11/11 None
C26F1.9.1 ENSEMBL cdna:known chromosome:CEL140:V:7778330:7778671:-1 gene:C26F1.9 11/11 None
C26F1.9.2 ENSEMBL cdna:known chromosome:CEL140:V:7778346:7778673:-1 gene:C26F1.9 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
chrV:7778411-7778669(-) 100.0 100.0
Public Domain and Genome References
Gene Title ribosomal protein L39
Gene Symbol rpl-39
Ensembl C26F1.9
Entrez Gene 179153 Entrez gene
SwissProt P52814 EMBL-EBI
WormBase CE06883 Wormbase
Functional Annotations
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 AAB37070 Ribosomal protein, large subunit protein 39 [Caenorhabditis elegans] ref|NP_505006.1| Ribosomal Protein, Large subunit family member (rpl-39) [Caenorhabditis elegans] gb|AAG50229.1| ribosomal protein L39 [Caenorhabditis elegans] sp|P52814|RL39_CAEEL 60S ribosomal protein L39 emb|CAE73187.1| Hypothetical protein CBG20586 [Caenorhabditis briggsae] 4.0E-23
blast AAV34853 ribosomal protein L39 [Bombyx mori] emb|CAJ17439.1| ribosomal protein L39e [Cicindela litorea] emb|CAJ17438.1| ribosomal protein L39e [Biphyllus lunatus] gb|AAK92174.1| ribosomal protein L39 [Spodoptera frugiperda] dbj|BAD26652.1| Ribosomal protein L39 [Plutella xylostella] sp|Q962S4|RL39_SPOFR 60S ribosomal protein L39 sp|Q6F482|RL39_PLUXY 60S ribosomal protein L39 1.0E-17
Protein Domains
Database ID Description E-Value
Pfam IPR000077 EMBL-EBI Ribosomal protein L39e 6.1E-25
Sequence
Target Sequence 
>C. ELEGANS:172910_AT
atgtctgccttgaagaaatccttcatcaagcgcaagcttgctaagaagcaaaagcaaaat
cgtccaatgccacaatgggtccgcatgaagactggaaacaccatgaagtacaatgccaag
agacgc

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
ATGTCTGCCTTGAAGAAATCCTTCA 395 49 13 Antisense
GAAATCCTTCATCAAGCGCAAGCTT 436 361 27 Antisense
ATCCTTCATCAAGCGCAAGCTTGCT 693 37 30 Antisense
CAAGCGCAAGCTTGCTAAGAAGCAA 311 185 39 Antisense
AAAGCAAAATCGTCCAATGCCACAA 481 121 63 Antisense
TCGTCCAATGCCACAATGGGTCCGC 543 605 72 Antisense
CCAATGCCACAATGGGTCCGCATGA 256 273 76 Antisense
GCCACAATGGGTCCGCATGAAGACT 180 279 81 Antisense
GGTCCGCATGAAGACTGGAAACACC 457 501 90 Antisense
GGAAACACCATGAAGTACAATGCCA 73 529 106 Antisense
CATGAAGTACAATGCCAAGAGACGC 248 209 114 Antisense
Sequence Source Affymetrix Proprietary Database