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[179863_at]

Description F54C4.1 /REP_DB=WormBase Gene ID /WP=CE19890 /TR=Q9TZ90 /GB=AAC68778.1 /SUBMIT=ST.LOUIS /CHR=3 /FEA=Sanger Annotation
Cluster 6grp_highest_10_10 > 49      6grp_high1_10_10 > 82      4grp_high_8_8 > 46      6grp_highest_nonorm > 64      6grp_total > 80      4grp_total > 41      6grp_highest_sub > 04_05_06      6grp_cgc > 65      6grp_high1_sub > 04      6grp_total_sub > Hat      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 659
1 2 3 4 range
A 632.4
(-3)
P 		954.9
(1.8)
P 		846.2
(0.2)
P 		1038.3
(3)
A 		406
B 682
(-0.6)
P 		795.8
(0.5)
P 		1075.1
(3)
P 		416.6
(-3)
P 		659
C 670.1
(-3)
P 		907.3
(1.3)
P 		861.4
(0.5)
P 		1000.6
(3)
P 		331
avr 661.5
(-3) 		886
(2.1) 		927.6
(3) 		818.5
(0.5) 		266

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 493
1 2 3 4 5 6 range
A 718.1
(-3)
P 		730.4
(-2.8)
P 		801.7
(-1.5)
P 		1044.8
(3)
P 		845.2
(-0.7)
P 		981.4
(1.8)
P 		327
B 551.9
(-3)
P 		995.1
(3)
P 		725.5
(-0.6)
P 		853.4
(1.1)
P 		885.6
(1.5)
P 		706.4
(-0.9)
P 		443
C 714.9
(-3)
P 		918.4
(1.7)
P 		876
(0.7)
P 		975.9
(3)
P 		805.6
(-0.9)
P 		937.3
(2.1)
P 		261
avr 661.6
(-3) 		881.3
(1.4) 		801.1
(-0.2) 		958
(3) 		845.5
(0.7) 		875
(1.3) 		296
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 211
1 2 3 4 range
A 230.2
(3)
P 		207.3
(1.2)
P 		221.2
(2.3)
P 		152
(-3)
A 		78
B 217.5
(1.8)
P 		196.6
(1)
P 		249.1
(3)
P 		88.8
(-3)
P 		160
C 221.8
(-0.6)
P 		260.9
(1.2)
P 		300.2
(3)
P 		168.7
(-3)
P 		132
avr 223.2
(1.3) 		221.6
(1.2) 		256.8
(3) 		136.5
(-3) 		120

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 227
1 2 3 4 5 6 range
A 132.4
(-3)
P 		259.8
(2.8)
P 		174.6
(-1.1)
P 		265
(3)
P 		255
(2.5)
P 		238.9
(1.8)
P 		133
B 192
(-2.5)
P 		331.2
(2.1)
P 		176.2
(-3)
P 		226
(-1.4)
P 		359.8
(3)
P 		263.4
(-0.2)
P 		184
C 265
(0.5)
P 		280.2
(1.3)
P 		223
(-1.6)
P 		196.3
(-3)
P 		260.7
(0.3)
P 		313.8
(3)
P 		118
avr 196.5
(-2.7) 		290.4
(2.9) 		191.3
(-3) 		229.1
(-0.7) 		291.8
(3) 		272
(1.8) 		101
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 179863_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.8202
Sequence Type Exemplar sequence
Representative Public ID F54C4.1 NCBI
Target Description F54C4.1 /REP_DB=WormBase Gene ID /WP=CE19890 /TR=Q9TZ90 /GB=AAC68778.1 /SUBMIT=ST.LOUIS /CHR=3 /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_064737(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_064737 NCBI Caenorhabditis elegans F54C4.1 (F54C4.1) mRNA, complete cds. 11/11 None
SNAP00000020630 ENSEMBL cdna:SNAP chromosome:CEL140:III:87563:89151:1 11/11 None
GENEFINDER00000020631 ENSEMBL cdna:GeneFinder chromosome:CEL140:III:87563:88283:1 9/11 None
F54C4.1 ENSEMBL cdna:known chromosome:CEL140:III:87560:89229:1 gene:F54C4.1 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
chrIII:87562-89151(+) 100.0 100.0
Public Domain and Genome References
Gene Title
Ensembl F54C4.1
Entrez Gene 175174 Entrez gene
SwissProt Q9TZ90 EMBL-EBI
WormBase CE19890 Wormbase
Functional Annotations
Ortholog
ID Title Organism
CANINE:1604293_AT similar to 39S ribosomal protein L40, mitochondrial precursor (L40mt) (MRP-40) (Nuclear localization signal containing protein deleted in velocardiofacial syndrome) (Up-regulated in metastasis) cfa
CANINE_2:CFA.17004.1.S1_AT similar to 39S ribosomal protein L40, mitochondrial precursor (L40mt) (MRP-40) (Nuclear localization signal containing protein deleted in velocardiofacial syndrome) (Up-regulated in metastasis) cfa
CANINE_2:CFAAFFX.22522.1.S1_S_AT similar to 39S ribosomal protein L40, mitochondrial precursor (L40mt) (MRP-40) (Nuclear localization signal containing protein deleted in velocardiofacial syndrome) (Up-regulated in metastasis) cfa
DROSOPHILA_2:1641549_AT mitochondrial ribosomal protein L40 dm
DROSGENOME1:149682_AT mitochondrial ribosomal protein L40 dm
CHICKEN:GGA.2600.2.S1_A_AT similar to nuclear localization signal containing protein deleted in Velo-Cardio-Facial syndrome gga
HG-U133_PLUS_2:203152_AT mitochondrial ribosomal protein L40 hs
HG-U133A:203152_AT mitochondrial ribosomal protein L40 hs
HG-FOCUS:203152_AT mitochondrial ribosomal protein L40 hs
HG-U133A_2:203152_AT mitochondrial ribosomal protein L40 hs
HU35KSUBA:RC_AA461057_AT mitochondrial ribosomal protein L40 hs
HU35KSUBA:AA307896_AT mitochondrial ribosomal protein L40 hs
U133_X3P:G4505402_3P_AT mitochondrial ribosomal protein L40 hs
HG-U95AV2:32745_AT mitochondrial ribosomal protein L40 hs
MG-U74AV2:93603_AT mitochondrial ribosomal protein L40 mm
MOE430A:1448849_AT mitochondrial ribosomal protein L40 mm
MOUSE430A_2:1448849_AT mitochondrial ribosomal protein L40 mm
MOUSE430_2:1448849_AT mitochondrial ribosomal protein L40 mm
MU19KSUBB:TC33201_AT Mitochondrial ribosomal protein L40, mRNA (cDNA clone MGC:41161 IMAGE:1246513) mm
RG-U34A:RC_AA799888_AT mitochondrial ribosomal protein L40 rn
RG-U34B:RC_AA943496_AT mitochondrial ribosomal protein L40 rn
RG-U34B:RC_AA900993_S_AT mitochondrial ribosomal protein L40 rn
RAE230A:1374931_AT mitochondrial ribosomal protein L40 rn
RAT230_2:1374931_AT mitochondrial ribosomal protein L40 rn
RAE230A:1388517_AT mitochondrial ribosomal protein L40 rn
RAT230_2:1388517_AT mitochondrial ribosomal protein L40 rn
Protein Similarities
Method ID Description E-Value
blast AAC68778 Hypothetical protein F54C4.1 [Caenorhabditis elegans] ref|NP_497138.1| F54C4.1 [Caenorhabditis elegans] 1.0E-85
blast CAE57494 Hypothetical protein CBG00465 [Caenorhabditis briggsae] 4.0E-71
blast AAC68778 Hypothetical protein F54C4.1 [Caenorhabditis elegans] ref|NP_497138.1| F54C4.1 [Caenorhabditis elegans] 7.0E-68
blast CAE57494 Hypothetical protein CBG00465 [Caenorhabditis briggsae] 6.0E-55
blast EAA06344 ENSANGP00000019899 [Anopheles gambiae str. PEST] ref|XP_311037.2| ENSANGP00000019899 [Anopheles gambiae str. PEST] 2.0E-27
Sequence
Target Sequence 
>C. ELEGANS:179863_AT
ttcaaacccgccaaattcatcaaacaattcccgccggctcctcggtttttatgaaaagac
agaagaaaattgatccggaggtagcaaagcagcgagagacccgacgcagaaaacggctgg
aaaaggatattcgtcagatgcaaaagcactcgaaaaagccgaaaccagtggatgagctca
ctttggacgtgaaatccgcgaaaaatatcggagaacgccgccgcccacgcaccgagctca
ccttggagcaaattgacgaacgagccatcgctctgaaggattatacacgctcccggttgg
ctttgcagcaggaggatgacgcgtggattcgtggagccatcgaatcgcagagaaaagctc
taaatgagctgaaaatgctcaaattggagctctacgaggcggctgtacagccagcagcca
aggatttaccgcttattgttcagggaccctcactgactccgcccattcgaaactacgagg
c

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
TTCAAACCCGCCAAATTCATCAAAC 83 687 56 Antisense
AAAGCAGCGAGAGACCCGACGCAGA 586 123 141 Antisense
GCACCGAGCTCACCTTGGAGCAAAT 354 311 284 Antisense
GACGAACGAGCCATCGCTCTGAAGG 399 379 310 Antisense
TGAAGGATTATACACGCTCCCGGTT 501 573 329 Antisense
CTCCCGGTTGGCTTTGCAGCAGGAG 37 235 345 Antisense
TGACGCGTGGATTCGTGGAGCCATC 323 569 372 Antisense
AGCTCTACGAGGCGGCTGTACAGCC 311 75 443 Antisense
CAGCCAGCAGCCAAGGATTTACCGC 229 203 463 Antisense
ATTGTTCAGGGACCCTCACTGACTC 147 5 490 Antisense
CTCCGCCCATTCGAAACTACGAGGC 18 235 512 Antisense
Sequence Source Affymetrix Proprietary Database