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[187568_at]

Description F56D1.3 /REP_DB=WormBase Gene ID /WP=CE01971 /TR=SW:Q10129 /GB=AAA81099.1 /SUBMIT=ST.LOUIS /CHR=2 /FEA=Sanger Annotation
Cluster 6grp_highest_10_10 > 43      6grp_high1_10_10 > 33      4grp_highest_8_8 > 18      4grp_high_8_8 > 63      6grp_highest_nonorm > 61      6grp_total > 11      4grp_total > 56      6grp_highest_sub > 02      6grp_high1_sub > 02      6grp_total_sub > Hat      4grp_rule_based > L3      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 488
1 2 3 4 range
A 471.8
(-0.7)
P 		518.6
(-0)
P 		724.4
(3)
P 		313.7
(-3)
P 		411
B 344.2
(-1.6)
P 		422.8
(-0.6)
P 		705.2
(3)
P 		236.2
(-3)
P 		469
C 365.5
(-1.3)
P 		490.9
(0.5)
P 		662.1
(3)
P 		248.2
(-3)
P 		414
avr 393.8
(-1.2) 		477.4
(-0.1) 		697.2
(3) 		266
(-3) 		431

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 215
1 2 3 4 5 6 range
A 360.9
(-1.8)
P 		455.5
(2.1)
P 		478.3
(3)
P 		333
(-3)
P 		355.9
(-2.1)
P 		344.2
(-2.5)
P 		145
B 405.2
(0.9)
P 		426.7
(2)
P 		445.5
(3)
P 		332.3
(-3)
P 		418.4
(1.6)
P 		357.2
(-1.7)
P 		113
C 419.1
(1.1)
P 		487.3
(3)
P 		310.6
(-1.9)
P 		355.4
(-0.7)
P 		351
(-0.8)
P 		272.1
(-3)
P 		215
avr 395.1
(0.2) 		456.5
(3) 		411.5
(1) 		340.2
(-2.3) 		375.1
(-0.7) 		324.5
(-3) 		132
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 189
1 2 3 4 range
A 171.8
(2.3)
P 		112.6
(-0.2)
P 		189.4
(3)
P 		45.9
(-3)
P 		144
B 109.8
(0.2)
P 		104.4
(-0.1)
P 		163.4
(3)
P 		50.3
(-3)
P 		113
C 121
(-0.5)
P 		141.1
(0.2)
P 		230.7
(3)
P 		41.9
(-3)
P 		189
avr 134.2
(0.6) 		119.4
(-0) 		194.5
(3) 		46
(-3) 		149

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 104
1 2 3 4 5 6 range
A 66.5
(-3)
P 		162
(3)
P 		104.2
(-0.6)
P 		84.5
(-1.9)
P 		107.4
(-0.4)
P 		83.8
(-1.9)
P 		96
B 141
(0.9)
P 		142
(1)
P 		108.2
(-1.5)
P 		88
(-3)
P 		170
(3)
P 		133.2
(0.3)
P 		82
C 155.4
(3)
P 		148.7
(2.5)
P 		79.1
(-2.5)
P 		71.5
(-3)
P 		113.6
(0)
P 		91.1
(-1.6)
P 		84
avr 121
(0.4) 		150.9
(3) 		97.2
(-1.6) 		81.3
(-3) 		130.3
(1.2) 		102.7
(-1.2) 		70
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 187568_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.5161
Sequence Type Exemplar sequence
Representative Public ID F56D1.3 NCBI
Target Description F56D1.3 /REP_DB=WormBase Gene ID /WP=CE01971 /TR=SW:Q10129 /GB=AAA81099.1 /SUBMIT=ST.LOUIS /CHR=2 /FEA=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_001027036(9)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_001027036 NCBI Caenorhabditis elegans F56D1.3 (F56D1.3) mRNA, complete cds. 9/11 None
SNAP00000013100 ENSEMBL cdna:SNAP chromosome:CEL140:II:5474048:5475260:1 9/11 None
GENEFINDER00000013103 ENSEMBL cdna:GeneFinder chromosome:CEL140:II:5466444:5475260:1 11/11 None
F56D1.3.1 ENSEMBL cdna:known chromosome:CEL140:II:5474336:5476334:1 gene:F56D1.3 9/11 None
F56D1.3.2 ENSEMBL cdna:known chromosome:CEL140:II:5474343:5475445:1 gene:F56D1.3 9/11 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
chrII:5474375-5475258(+) 100.0 100.0
Public Domain and Genome References
Gene Title
Ensembl F56D1.3
Entrez Gene 3565469 Entrez gene
SwissProt Q10129 EMBL-EBI
WormBase CE29407 Wormbase
Functional Annotations
Ortholog
ID Title Organism
CANINE:1586347_AT similar to mitochondrial ribosomal protein S16 cfa
CANINE_2:CFA.4020.1.S1_A_AT similar to mitochondrial ribosomal protein S16 cfa
CANINE_2:CFA.4020.1.S1_AT similar to mitochondrial ribosomal protein S16 cfa
CANINE_2:CFA.4020.3.S1_S_AT similar to mitochondrial ribosomal protein S16 cfa
DROSOPHILA_2:1626433_AT mitochondrial ribosomal protein S16 dm
DROSGENOME1:147189_AT mitochondrial ribosomal protein S16 dm
HG-U133_PLUS_2:218046_S_AT mitochondrial ribosomal protein S16 hs
HG-U133A:218046_S_AT mitochondrial ribosomal protein S16 hs
HG-U133A_2:218046_S_AT mitochondrial ribosomal protein S16 hs
HU35KSUBA:RC_AA452894_AT mitochondrial ribosomal protein S16 hs
HU35KSUBA:RC_AA448627_F_AT mitochondrial ribosomal protein S16 hs
HU35KSUBD:RC_AA262559_AT mitochondrial ribosomal protein S16 hs
U133_X3P:G7705625_3P_S_AT mitochondrial ribosomal protein S16 hs
U133_X3P:HS.180312.0.A2_3P_AT mitochondrial ribosomal protein S16 hs
HG-U133_PLUS_2:222499_AT mitochondrial ribosomal protein S16 hs
HG-U133B:222499_AT mitochondrial ribosomal protein S16 hs
HG-U95B:48568_AT mitochondrial ribosomal protein S16 hs
HG-U95E:78404_R_AT mitochondrial ribosomal protein S16 hs
HU35KSUBD:RC_H29552_AT Mitochondrial ribosomal protein S16 hs
MOUSE430_2:1448869_A_AT mitochondrial ribosomal protein S16 mm
MOE430A:1448869_A_AT mitochondrial ribosomal protein S16 mm
MOUSE430A_2:1448869_A_AT mitochondrial ribosomal protein S16 mm
MU11KSUBB:W46035_S_AT mitochondrial ribosomal protein S16 mm
MG-U74AV2:94866_AT mitochondrial ribosomal protein S16 mm
MU19KSUBA:TC18600_AT Mitochondrial ribosomal protein S16, mRNA (cDNA clone MGC:30461 IMAGE:3986314) mm
MU19KSUBA:TC18600_G_AT Mitochondrial ribosomal protein S16, mRNA (cDNA clone MGC:30461 IMAGE:3986314) mm
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 AAN60516 Clear protein 1, isoform b [Caenorhabditis elegans] ref|NP_001022209.1| CLeaR family member (clr-1) [Caenorhabditis elegans] 0.0
blast AAN60515 Clear protein 1, isoform a [Caenorhabditis elegans] ref|NP_001022208.1| CLeaR family member (clr-1) [Caenorhabditis elegans] 0.0
blast AAC27551 CLR-1 [Caenorhabditis elegans] 0.0
blast AAA81099 Hypothetical protein F56D1.3 [Caenorhabditis elegans] ref|NP_001022207.1| F56D1.3 [Caenorhabditis elegans] sp|Q10129|RT16_CAEEL Probable mitochondrial 28S ribosomal protein S16 (MRP-S16) 2.0E-70
blast AAA81099 Hypothetical protein F56D1.3 [Caenorhabditis elegans] ref|NP_001022207.1| F56D1.3 [Caenorhabditis elegans] sp|Q10129|RT16_CAEEL Probable mitochondrial 28S ribosomal protein S16 (MRP-S16) 3.0E-70
blast T30112 hypothetical protein F56D1.3 - Caenorhabditis elegans 1.0E-68
Protein Domains
Database ID Description E-Value
Pfam IPR000242 EMBL-EBI Tyrosine specific protein phosphatase 6.6E-109
Pfam IPR000242 EMBL-EBI Tyrosine specific protein phosphatase 3.8E-81
Sequence
Target Sequence 
>C. ELEGANS:187568_AT
atattacggacgtccttcgatcggtttggctctttttggttgcacaaaccgaccgttcta
tcacgtttgtgtatttcctgatcgggctttaggtcgaagatacgagggtaacattcttga
acaggtgggaacttttgatccacttccaaatcagaagaacgagaagctagtggctctgaa
ttttggacgcctcaaatattggattggtgaacggaacgctcatatttccgttccagtgct
tgaacttctcggtgagcggagaaactgcctgtcg

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
ATATTACGGACGTCCTTCGATCGGT 196 17 36 Antisense
GATCGGTTTGGCTCTTTTTGGTTGC 503 415 54 Antisense
TTTGGTTGCACAAACCGACCGTTCT 169 631 70 Antisense
ACCGACCGTTCTATCACGTTTGTGT 527 89 83 Antisense
TGTGTATTTCCTGATCGGGCTTTAG 281 547 103 Antisense
GATACGAGGGTAACATTCTTGAACA 45 425 134 Antisense
GGTGGGAACTTTTGATCCACTTCCA 40 501 159 Antisense
TGGCTCTGAATTTTGGACGCCTCAA 447 545 206 Antisense
GGACGCCTCAAATATTGGATTGGTG 670 523 220 Antisense
GCTTGAACTTCTCGGTGAGCGGAGA 125 307 273 Antisense
CGGTGAGCGGAGAAACTGCCTGTCG 362 243 285 Antisense
Sequence Source Affymetrix Proprietary Database