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[187764_at]

Description Y55F3AM.1 /REP_DB=WormBase Gene ID /WP=CE22547 /TR=SW:Q9N361 /GB=AAF60793.1 /SUBMIT=ST.LOUIS /CHR=4 /FEA=Sanger Annotation
Cluster 6grp_highest_10_10 > 15      6grp_high1_10_10 > 40      4grp_highest_8_8 > 08      4grp_high_8_8 > 52      6grp_highest_nonorm > 52      6grp_total > 51      4grp_total > 51      6grp_highest_sub > 03      6grp_high1_sub > 03      6grp_total_sub > Hat      4grp_rule_based > L2      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 502
1 2 3 4 range
A 751.4
(-0.5)
P 		1018.5
(3)
P 		881.8
(1.2)
P 		560.2
(-3)
P 		458
B 795.3
(0.8)
P 		949.1
(3)
P 		921.9
(2.6)
P 		524.6
(-3)
P 		425
C 799.1
(1.4)
P 		901.2
(3)
P 		794
(1.3)
P 		516.9
(-3)
P 		384
avr 781.9
(0.5) 		956.3
(3) 		865.9
(1.7) 		533.9
(-3) 		422

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 748
1 2 3 4 5 6 range
A 666.6
(1.1)
P 		636.5
(0.5)
P 		759.5
(3)
P 		655
(0.9)
P 		580.6
(-0.6)
P 		461.9
(-3)
P 		298
B 595.6
(-2.5)
P 		732.6
(-1.3)
P 		1209.6
(3)
P 		724.4
(-1.4)
P 		689.1
(-1.7)
P 		542
(-3)
P 		668
C 728
(0.2)
P 		763.8
(0.7)
P 		721.8
(0.1)
P 		930.6
(3)
P 		496.3
(-3)
P 		585.4
(-1.8)
P 		434
avr 663.4
(-0.8) 		711
(-0) 		897
(3) 		770
(0.9) 		588.7
(-2) 		529.8
(-3) 		367
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 195
1 2 3 4 range
A 273.6
(3)
P 		221.1
(1.4)
P 		230.5
(1.7)
P 		82
(-3)
P 		192
B 253.6
(3)
P 		234.4
(2.2)
P 		213.6
(1.3)
P 		111.8
(-3)
P 		142
C 264.5
(2.6)
P 		259.1
(2.4)
P 		276.7
(3)
P 		87.2
(-3)
P 		190
avr 263.9
(3) 		238.2
(2.1) 		240.3
(2.2) 		93.7
(-3) 		170

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 181
1 2 3 4 5 6 range
A 122.9
(-2.5)
P 		226.4
(3)
P 		165.4
(-0.2)
P 		166.1
(-0.2)
P 		175.2
(0.3)
P 		112.5
(-3)
P 		114
B 207.2
(-2.1)
P 		243.8
(0.1)
P 		293.7
(3)
P 		191.9
(-3)
P 		280
(2.2)
P 		202.1
(-2.4)
P 		102
C 269.8
(3)
P 		233.1
(1)
P 		183.7
(-1.7)
P 		187.2
(-1.5)
P 		160.6
(-3)
P 		196
(-1.1)
P 		109
avr 200
(-0.2) 		234.4
(3) 		214.3
(1.1) 		181.7
(-1.9) 		205.3
(0.3) 		170.2
(-3) 		64
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 187764_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.11107
Sequence Type Exemplar sequence
Representative Public ID Y55F3AM.1 NCBI
Target Description Y55F3AM.1 /REP_DB=WormBase Gene ID /WP=CE22547 /TR=SW:Q9N361 /GB=AAF60793.1 /SUBMIT=ST.LOUIS /CHR=4 /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_067631(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_067631 NCBI Caenorhabditis elegans Y55F3AM.1 (Y55F3AM.1) mRNA, complete cds. 11/11 None
SNAP00000030057 ENSEMBL cdna:SNAP chromosome:CEL140:IV:1052758:1057514:1 11/11 None
GENEFINDER00000030077 ENSEMBL cdna:GeneFinder chromosome:CEL140:IV:1056443:1057514:1 11/11 None
Y55F3AM.1.1 ENSEMBL cdna:known chromosome:CEL140:IV:1056890:1057611:1 gene:Y55F3AM.1 11/11 None
Y55F3AM.1.2 ENSEMBL cdna:known chromosome:CEL140:IV:1056890:1057620:1 gene:Y55F3AM.1 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
chrIV:1056910-1057520(+) 100.0 100.0
Public Domain and Genome References
Gene Title
Ensembl Y55F3AM.1
Entrez Gene 176926 Entrez gene
SwissProt Q9N361 EMBL-EBI
WormBase CE22547 Wormbase
Functional Annotations
Ortholog
ID Title Organism
CANINE:1586851_AT similar to Mitochondrial 28S ribosomal protein S25 (S25mt) (MRP-S25) cfa
CANINE:1586432_AT similar to Mitochondrial 28S ribosomal protein S25 (S25mt) (MRP-S25) cfa
CANINE_2:CFA.10309.1.A1_S_AT similar to Mitochondrial 28S ribosomal protein S25 (S25mt) (MRP-S25) cfa
CANINE_2:CFA.10309.2.S1_A_AT similar to Mitochondrial 28S ribosomal protein S25 (S25mt) (MRP-S25) cfa
DROSOPHILA_2:1634823_AT mitochondrial ribosomal protein S25 dm
DROSGENOME1:145071_AT mitochondrial ribosomal protein S25 dm
CHICKEN:GGA.6989.1.S1_AT mitochondrial ribosomal protein S25 gga
HG-U133_PLUS_2:224015_S_AT mitochondrial ribosomal protein S25 hs
HG-U133B:224015_S_AT mitochondrial ribosomal protein S25 hs
HU35KSUBB:RC_Z40223_AT mitochondrial ribosomal protein S25 hs
HU35KSUBC:RC_N93665_AT mitochondrial ribosomal protein S25 hs
HU35KSUBD:RC_N33024_AT mitochondrial ribosomal protein S25 hs
U133_X3P:G13097791_3P_A_AT mitochondrial ribosomal protein S25 hs
U133_X3P:HS.23450.1.A3_3P_AT mitochondrial ribosomal protein S25 hs
U133_X3P:HS.23450.1.A1_3P_A_AT mitochondrial ribosomal protein S25 hs
HG-U133_PLUS_2:224869_S_AT mitochondrial ribosomal protein S25 hs
HG-U133B:224869_S_AT mitochondrial ribosomal protein S25 hs
HG-U133_PLUS_2:224873_S_AT mitochondrial ribosomal protein S25 hs
HG-U133B:224873_S_AT mitochondrial ribosomal protein S25 hs
HG-U95B:50219_AT mitochondrial ribosomal protein S25 hs
HG-U95B:57938_AT mitochondrial ribosomal protein S25 hs
HG-U95C:64627_AT mitochondrial ribosomal protein S25 hs
HG-U95D:81586_AT mitochondrial ribosomal protein S25 hs
HU35KSUBB:RC_R62456_AT Mitochondrial ribosomal protein S25 hs
U133_X3P:HS.23450.2.A1_3P_AT Mitochondrial ribosomal protein S25 hs
HG-U133_PLUS_2:225477_S_AT Mitochondrial ribosomal protein S25 hs
HG-U133B:225477_S_AT Mitochondrial ribosomal protein S25 hs
HG-U95C:49655_S_AT Mitochondrial ribosomal protein S25 hs
MOUSE430_2:1449194_AT mitochondrial ribosomal protein S25 mm
MOE430A:1449194_AT mitochondrial ribosomal protein S25 mm
MOUSE430A_2:1449194_AT mitochondrial ribosomal protein S25 mm
MOUSE430A_2:1418717_AT mitochondrial ribosomal protein S25 mm
MOE430A:1418717_AT mitochondrial ribosomal protein S25 mm
MOUSE430_2:1418717_AT mitochondrial ribosomal protein S25 mm
MU11KSUBA:C77199_RC_AT mitochondrial ribosomal protein S25 mm
MG-U74AV2:104234_AT mitochondrial ribosomal protein S25 mm
MG-U74AV2:102128_F_AT mitochondrial ribosomal protein S25 mm
MG-U74BV2:163978_AT mitochondrial ribosomal protein S25 mm
MOE430A:1418716_AT mitochondrial ribosomal protein S25 mm
MOUSE430A_2:1418716_AT mitochondrial ribosomal protein S25 mm
MOUSE430_2:1418716_AT mitochondrial ribosomal protein S25 mm
MOE430B:1445613_AT Mitochondrial ribosomal protein S25, mRNA (cDNA clone MGC:30559 IMAGE:5126320) mm
MOUSE430_2:1445613_AT Mitochondrial ribosomal protein S25, mRNA (cDNA clone MGC:30559 IMAGE:5126320) mm
MOE430B:1446955_AT Mitochondrial ribosomal protein S25, mRNA (cDNA clone MGC:30559 IMAGE:5126320) mm
MOUSE430_2:1446955_AT Mitochondrial ribosomal protein S25, mRNA (cDNA clone MGC:30559 IMAGE:5126320) mm
MU19KSUBA:TC17461_AT Mitochondrial ribosomal protein S25, mRNA (cDNA clone MGC:30559 IMAGE:5126320) mm
MU19KSUBA:TC19283_AT Mitochondrial ribosomal protein S25, mRNA (cDNA clone MGC:30559 IMAGE:5126320) mm
MU19KSUBB:TC29184_AT Mitochondrial ribosomal protein S25, mRNA (cDNA clone MGC:30559 IMAGE:5126320) mm
MU19KSUBB:TC34485_AT Mitochondrial ribosomal protein S25, mRNA (cDNA clone MGC:30559 IMAGE:5126320) mm
MU19KSUBC:TC41429_AT Mitochondrial ribosomal protein S25, mRNA (cDNA clone MGC:30559 IMAGE:5126320) mm
RG-U34C:RC_AI169648_AT mitochondrial ribosomal protein S25 (predicted) rn
RAE230A:1371548_AT mitochondrial ribosomal protein S25 (predicted) rn
RAT230_2:1371548_AT mitochondrial ribosomal protein S25 (predicted) rn
Protein Similarities
Method ID Description E-Value
blast AAF60793 Hypothetical protein Y55F3AM.1 [Caenorhabditis elegans] ref|NP_500032.1| Y55F3AM.1 [Caenorhabditis elegans] sp|Q9N361|RT25_CAEEL Probable mitochondrial 28S ribosomal protein S25 (S25mt) (MRP-S25) 1.0E-98
blast CAE63854 Hypothetical protein CBG08414 [Caenorhabditis briggsae] 7.0E-92
blast CAE63854 Hypothetical protein CBG08414 [Caenorhabditis briggsae] 9.0E-92
blast CAE63854 Hypothetical protein CBG08414 [Caenorhabditis briggsae] 1.0E-91
Protein Domains
Database ID Description E-Value
Pfam IPR007741 EMBL-EBI Mitochondrial ribosome 1.3E-40
Pfam IPR007741 EMBL-EBI Mitochondrial ribosome 1.3E-40
Pfam IPR007741 EMBL-EBI Mitochondrial ribosome 1.3E-40
Sequence
Target Sequence 
>C. ELEGANS:187764_AT
gtgaagcttcgcgacaacgtcaacgtgttctcgatgggttttcataaaaatccgacgccc
gagcagtctggagcacgagatttcgtctactggaactgggcgcagcttcaatatcacaat
ccaaaagttcagctcgttaagcatgccgataaagttgtgacgccctttgccagagcatat
ctgaacgacggccgggaagtgctattcgacttggacggcatgaagcgcgaggaaatcgag
aaattattggcgaaaacgctaggaaaaacggaattagtggagcgaagagagcatttggag
agtattgccaagcttaatcccgccgatttcggatccaaaaatgagcgacagtgtatgtgc
gaagttcaaggccaacatccgtgcacgggactcctgcgagcaccgcaatgtgtcaccg

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GTGAAGCTTCGCGACAACGTCAACG 499 481 76 Antisense
AACGTCAACGTGTTCTCGATGGGTT 209 145 91 Antisense
GATTTCGTCTACTGGAACTGGGCGC 501 427 154 Antisense
GGGCGCAGCTTCAATATCACAATCC 123 493 173 Antisense
AGTTCAGCTCGTTAAGCATGCCGAT 24 65 201 Antisense
ACGCCCTTTGCCAGAGCATATCTGA 360 91 235 Antisense
GAACGACGGCCGGGAAGTGCTATTC 436 345 258 Antisense
AGAGTATTGCCAAGCTTAATCCCGC 400 67 374 Antisense
TAATCCCGCCGATTTCGGATCCAAA 489 635 390 Antisense
CGAAGTTCAAGGCCAACATCCGTGC 516 253 435 Antisense
CTGCGAGCACCGCAATGTGTCACCG 352 237 469 Antisense
Sequence Source Affymetrix Proprietary Database