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[173269_s_at] L13P family ribosomal protein /// lipoic acid synthase

Description CEC1772_rc /REP_DB=TREMBL Accession /GB=C10177 /FEA=Transcript Cluster /DEF=C.elegans cDNA clone yk122b2 : 3prime end, single read.
Cluster 6grp_highest_10_10 > 15      6grp_high1_10_10 > 40      4grp_highest_8_8 > 06      4grp_high_8_8 > 22      6grp_highest_nonorm > 19      6grp_total > 51      4grp_total > 17      6grp_highest_sub > 03      6grp_cgc > 82      6grp_high1_sub > 03      6grp_cgc_sub > 03      6grp_total_sub > Hat      6grp_rule_based > S3      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 13679
1 2 3 4 range
A 22294.1
(-3)
P 		32261.8
(1.8)
P 		28365.7
(-0.1)
P 		34811
(3)
P 		12517
B 25492.9
(-1.9)
P 		24127.8
(-3)
P 		26959.1
(-0.6)
P 		31277.7
(3)
P 		7150
C 21181.5
(-3)
P 		24435.3
(-1.6)
P 		23561
(-2)
P 		34860.6
(3)
P 		13679
avr 22989.5
(-3) 		26941.6
(-0.8) 		26295.3
(-1.1) 		33649.8
(3) 		10660

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 7348
1 2 3 4 5 6 range
A 22458
(1.1)
P 		20792.8
(-0.6)
P 		24239.5
(3)
P 		23126.7
(1.8)
P 		18560.1
(-3)
P 		22202.6
(0.8)
P 		5679
B 20484
(-0.1)
P 		20768.2
(0.2)
P 		24199.4
(3)
P 		19407.7
(-0.9)
P 		16997.1
(-2.9)
P 		16891.9
(-3)
P 		7308
C 19778.7
(-0.9)
P 		21794.6
(0.9)
P 		22316
(1.4)
P 		24118
(3)
P 		20143.8
(-0.6)
P 		17429.1
(-3)
P 		6689
avr 20906.9
(-0.2) 		21118.5
(0.1) 		23585
(3) 		22217.5
(1.4) 		18567
(-3) 		18841.2
(-2.7) 		5018
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 3116
1 2 3 4 range
A 8117.3
(3)
P 		7003.2
(0.8)
P 		7415.3
(1.6)
P 		5095.6
(-3)
P 		3022
B 8129.5
(3)
P 		5959
(-3)
P 		6247
(-2.2)
P 		6665.3
(-1)
P 		2171
C 7011.7
(-0.1)
P 		7025.3
(-0.1)
P 		8211.7
(3)
P 		5878
(-3)
P 		2334
avr 7752.8
(3) 		6662.5
(-0.5) 		7291.3
(1.5) 		5879.6
(-3) 		1873

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 3255
1 2 3 4 5 6 range
A 4139.9
(-3)
P 		7394.9
(3)
P 		5278.9
(-0.9)
P 		5865.5
(0.2)
P 		5600.6
(-0.3)
P 		5405.6
(-0.7)
P 		3255
B 7127.4
(3)
P 		6912.9
(2.4)
P 		5876.3
(-0.8)
P 		5140.4
(-3)
P 		6905.7
(2.3)
P 		6298.9
(0.5)
P 		1987
C 7331.1
(3)
P 		6650.2
(1.4)
P 		5679.8
(-1)
P 		4850.1
(-3)
P 		6518.2
(1)
P 		5834.5
(-0.6)
P 		2481
avr 6199.5
(0.2) 		6986
(3) 		5611.7
(-1.8) 		5285.3
(-3) 		6341.5
(0.7) 		5846.3
(-1) 		1701
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 173269_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.27890
Sequence Type Exemplar sequence
Representative Public ID CEC1772 NCBI
Target Description CEC1772_rc /REP_DB=TREMBL Accession /GB=C10177 /FEA=Transcript Cluster /DEF=C.elegans cDNA clone yk122b2 : 3prime end, single read.
Cluster Evidence This cluster is supported by a Transcript 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_065321(11), NM_065320(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_065321 NCBI Caenorhabditis elegans M01F1.3 (M01F1.3) mRNA, complete cds. 11/11 None
NM_065320 NCBI Caenorhabditis elegans Ribosomal Protein, Large subunit family member (rpl-16) (rpl-16) mRNA, complete cds. 11/11 A 
SNAP00000008226 ENSEMBL cdna:SNAP chromosome:CEL140:III:3502872:3503579:-1 11/11 None
GENEFINDER00000008231 ENSEMBL cdna:GeneFinder chromosome:CEL140:III:3502872:3503579:-1 11/11 None
M01F1.2.2 ENSEMBL cdna:known chromosome:CEL140:III:3502820:3503587:-1 gene:M01F1.2 11/11 None
M01F1.2.1 ENSEMBL cdna:known chromosome:CEL140:III:3502820:3503593:-1 gene:M01F1.2 11/11 None
M01F1.2.3 ENSEMBL cdna:known chromosome:CEL140:III:3502820:3503589:-1 gene:M01F1.2 11/11 None
M01F1.3.3 ENSEMBL cdna:known chromosome:CEL140:III:3502823:3505209:-1 gene:M01F1.3 11/11 None
M01F1.3.1 ENSEMBL cdna:known chromosome:CEL140:III:3502823:3505084:-1 gene:M01F1.3 11/11 A 
M01F1.3.2 ENSEMBL cdna:known chromosome:CEL140:III:3502823:3505020:-1 gene:M01F1.3 11/11 A 
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
chrIII:3502896-3503200(-) 79.17 79.17
Public Domain and Genome References
Gene Title L13P family ribosomal protein
lipoic acid synthase
Gene Symbol rpl-16
Ensembl M01F1.2
M01F1.3
Entrez Gene 175455 Entrez gene
3564813 Entrez gene
SwissProt Q27389 EMBL-EBI
Q21452 EMBL-EBI
WormBase CE01030 Wormbase
CE01031 Wormbase
Functional Annotations
Ortholog
ID Title Organism
ATH1-121501:258837_AT 60S ribosomal protein L13A (RPL13aA) at
ATH1-121501:246005_AT lipoic acid synthase family protein at
CANINE:1598572_AT similar to lipoic acid synthetase isoform 1 precursor cfa
CANINE_2:CFA.17585.1.S1_S_AT similar to lipoic acid synthetase isoform 1 precursor cfa
CANINE_2:CFA.9463.1.A1_AT similar to lipoic acid synthetase isoform 1 precursor cfa
DROSOPHILA_2:1631739_AT Ribosomal protein L13A dm
DROSGENOME1:153316_AT Ribosomal protein L13A dm
DROSOPHILA_2:1623470_AT Lipoic acid synthase dm
DROSGENOME1:149126_AT Lipoic acid synthase dm
DROSOPHILA_2:1632225_A_AT Lipoic acid synthase dm
CHICKEN:GGA.9006.1.S1_AT similar to Lipoic acid synthetase, mitochondrial precursor (Lip-syn) (Lipoate synthase) (HUSSY-01) gga
CHICKEN:GGAAFFX.23994.1.S1_AT similar to Lipoic acid synthetase, mitochondrial precursor (Lip-syn) (Lipoate synthase) (HUSSY-01) gga
HG-U133_PLUS_2:200715_X_AT ribosomal protein L13a hs
HG-U133A:200715_X_AT ribosomal protein L13a hs
HG-U133A_2:200715_X_AT ribosomal protein L13a hs
HG-U133_PLUS_2:210646_X_AT ribosomal protein L13a hs
HG-U133A:210646_X_AT ribosomal protein L13a hs
HG-U133A_2:210646_X_AT ribosomal protein L13a hs
HG-U133_PLUS_2:200716_X_AT ribosomal protein L13a hs
HG-U133A:200716_X_AT ribosomal protein L13a hs
HG-U133A_2:200716_X_AT ribosomal protein L13a hs
HG-FOCUS:200716_X_AT ribosomal protein L13a hs
HG-U133_PLUS_2:212790_X_AT ribosomal protein L13a hs
HG-U133A_2:212790_X_AT ribosomal protein L13a hs
HG-U133A:212790_X_AT ribosomal protein L13a hs
HU35KSUBD:RC_N68385_F_AT ribosomal protein L13a hs
HUGENEFL:X56932_AT ribosomal protein L13a hs
U133_X3P:G12804528_3P_X_AT ribosomal protein L13a hs
U133_X3P:G12653484_3P_S_AT ribosomal protein L13a hs
U133_X3P:211942_3P_X_AT ribosomal protein L13a hs
HG-U133A_2:211942_X_AT ribosomal protein L13a hs
HG-U133_PLUS_2:211942_X_AT ribosomal protein L13a hs
HG-U133A:211942_X_AT ribosomal protein L13a hs
HG-U95AV2:35119_AT ribosomal protein L13a hs
HG-U133_PLUS_2:214045_AT lipoic acid synthetase hs
HG-U133A_2:214045_AT lipoic acid synthetase hs
HG-U133A:214045_AT lipoic acid synthetase hs
HU35KSUBA:HUM_ALU_AT lipoic acid synthetase hs
HU35KSUBB:HUM_ALU_AT lipoic acid synthetase hs
HU35KSUBC:HUM_ALU_AT lipoic acid synthetase hs
HU35KSUBD:HUM_ALU_AT lipoic acid synthetase hs
HUGENEFL:HUM_ALU_AT lipoic acid synthetase hs
HC-G110:HUM_ALU_AT lipoic acid synthetase hs
HU35KSUBC:RC_N24865_AT lipoic acid synthetase hs
U133_X3P:HS.53531.0.A1_3P_AT lipoic acid synthetase hs
HG-U95AV2:36717_AT lipoic acid synthetase hs
HG-U95E:70808_R_AT lipoic acid synthetase hs
HG-U95E:72029_AT lipoic acid synthetase hs
HG-U95E:72031_G_AT lipoic acid synthetase hs
HG-U95E:72033_AT lipoic acid synthetase hs
HU35KSUBB:RC_T98603_S_AT Lipoic acid synthetase hs
HG-U95E:81756_AT Lipoic acid synthetase hs
MG-U74AV2:92834_AT ribosomal protein L13a mm
MOE430A:1455001_X_AT ribosomal protein L13a mm
MOUSE430A_2:1455001_X_AT ribosomal protein L13a mm
MOUSE430_2:1455001_X_AT ribosomal protein L13a mm
MOE430A:1455485_X_AT ribosomal protein L13a mm
MOUSE430A_2:1455485_X_AT ribosomal protein L13a mm
MOUSE430_2:1455485_X_AT ribosomal protein L13a mm
MU11KSUBA:AA408475_RC_S_AT ribosomal protein L13a mm
MU11KSUBB:MSA.3380.0_F_AT ribosomal protein L13a mm
MU11KSUBB:X51528_F_AT ribosomal protein L13a mm
MOE430A:1433928_A_AT ribosomal protein L13a mm
MOUSE430A_2:1433928_A_AT ribosomal protein L13a mm
MOUSE430_2:1433928_A_AT ribosomal protein L13a mm
MOE430A:1435873_A_AT ribosomal protein L13a mm
MOUSE430A_2:1435873_A_AT ribosomal protein L13a mm
MOUSE430_2:1435873_A_AT ribosomal protein L13a mm
MOE430A:1417608_A_AT ribosomal protein L13a mm
MOUSE430A_2:1417608_A_AT ribosomal protein L13a mm
MOUSE430_2:1417608_A_AT ribosomal protein L13a mm
MOE430A:1418700_AT lipoic acid synthetase mm
MOUSE430A_2:1418700_AT lipoic acid synthetase mm
MOUSE430_2:1418700_AT lipoic acid synthetase mm
MG-U74AV2:98909_AT lipoic acid synthetase mm
MOE430B:1431935_AT lipoic acid synthetase mm
MOUSE430_2:1431935_AT lipoic acid synthetase mm
MOE430B:1447027_S_AT lipoic acid synthetase mm
MOUSE430_2:1447027_S_AT lipoic acid synthetase mm
MU19KSUBA:TC23577_AT MLIP1 mRNA for lipoic acid synthase mm
MU19KSUBC:TC38659_AT MLIP1 mRNA for lipoic acid synthase mm
RG-U34A:RC_AI012805_AT ribosomal protein L13A rn
RG-U34A:RC_AA891713_AT ribosomal protein L13A rn
RAE230A:1367588_A_AT ribosomal protein L13A rn
RAT230_2:1367588_A_AT ribosomal protein L13A rn
RG-U34C:RC_AI237159_AT lipoic acid synthetase (predicted) rn
RAE230A:1389154_AT lipoic acid synthetase (predicted) rn
RAT230_2:1389154_AT lipoic acid synthetase (predicted) rn
YEAST_2:1777458_AT N-terminally acetylated protein component of the large (60S) ribosomal subunit, binds to 5.8 S rRNA; has similarity to Rpl16Ap, E. coli L13 and rat L13a ribosomal proteins; transcriptionally regulated by Rap1p Sc
YEAST_2:1777168_AT Protein involved in biosynthesis of the coenzyme lipoic acid, has similarity to E. coli lipoic acid synthase Sc
Gene Ontology
GO Biological Process (view graph)
ID Description Evidence Links
6412 protein biosynthesis inferred from electronic annotation QuickGO AmiGO
9107 lipoate 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
15934 large ribosomal subunit 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
16992 lipoate synthase activity inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast CAA86516 Hypothetical protein M01F1.3 [Caenorhabditis elegans] ref|NP_497722.3| M01F1.3 [Caenorhabditis elegans] 0.0
blast CAE64948 Hypothetical protein CBG09779 [Caenorhabditis briggsae] 0.0
blast EAA09970 ENSANGP00000016313 [Anopheles gambiae str. PEST] ref|XP_314540.2| ENSANGP00000016313 [Anopheles gambiae str. PEST] 1.0E-115
Protein Domains
Database ID Description E-Value
Pfam IPR007197 EMBL-EBI Radical SAM 1.2E-20
Pfam IPR005822 EMBL-EBI Ribosomal protein L13 3.7E-41
Sequence
Target Sequence 
>C. ELEGANS:173269_S_AT
ccagccaaataccagaagaccaagtctctccatgccccatcagccagcagattccgactt
caaccaagaagaaagttctccgtcgttggacgcttatcgcacgaggtcggatggcaattc
caggatgttgttgccaagctcgaggctaagagaaaggtgaagggagccgcctactt

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
CCAGCCAAATACCAGAAGACCAAGT 251 273 55 Antisense
CCAGAAGACCAAGTCTCTCCATGCC 201 273 66 Antisense
AGCAGATTCCGACTTCAACCAAGAA 514 77 100 Antisense
ACGCTTATCGCACGAGGTCGGATGG 384 91 144 Antisense
GCACGAGGTCGGATGGCAATTCCAG 554 315 153 Antisense
AGGTCGGATGGCAATTCCAGGATGT 692 57 158 Antisense
TCCAGGATGTTGTTGCCAAGCTCGA 688 587 173 Antisense
GGATGTTGTTGCCAAGCTCGAGGCT 364 513 177 Antisense
GTTGTTGCCAAGCTCGAGGCTAAGA 98 439 181 Antisense
GCCAAGCTCGAGGCTAAGAGAAAGG 229 277 187 Antisense
GAAAGGTGAAGGGAGCCGCCTACTT 428 351 206 Antisense
Sequence Source Affymetrix Proprietary Database