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[173229_s_at]

Description C60047_rc /REP_DB=TREMBL Accession /GB=C60047 /FEA=Transcript Cluster /DEF=C.elegans cDNA clone yk446f5 : 3prime end, single read.
Cluster 6grp_highest_10_10 > 84      6grp_high1_10_10 > 57      4grp_highest_8_8 > 23      4grp_high_8_8 > 06      6grp_highest_nonorm > 58      6grp_total > 58      4grp_total > 02      6grp_highest_sub > Cu      6grp_high1_sub > Cu      6grp_total_sub > Cup      4grp_rule_based > L4      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 18747
1 2 3 4 range
A 2543.1
(-2.6)
P 		1402
(-3)
P 		1711.8
(-2.9)
P 		20149.4
(3)
P 		18747
B 2895.2
(-2.7)
P 		2540.1
(-2.8)
P 		1953.9
(-3)
P 		18781.9
(3)
P 		16828
C 2503.4
(-2.7)
P 		2096
(-2.9)
P 		1804.6
(-3)
P 		17472.9
(3)
P 		15668
avr 2647.2
(-2.7) 		2012.7
(-2.9) 		1823.4
(-3) 		18801.4
(3) 		16978

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 1570
1 2 3 4 5 6 range
A 3655.2
(3)
P 		2388.7
(-2.5)
P 		2674
(-1.3)
P 		2285.3
(-3)
P 		2779.4
(-0.8)
P 		2842.3
(-0.6)
P 		1370
B 2837
(1.4)
P 		2805.7
(1)
P 		2466.6
(-3)
P 		2532.1
(-2.2)
P 		2602.4
(-1.4)
P 		2971.5
(3)
P 		505
C 2237
(-2.4)
P 		2481.9
(-1.4)
P 		2169.8
(-2.7)
P 		2999
(0.6)
P 		2085.4
(-3)
P 		3612.8
(3)
P 		1527
avr 2909.7
(1) 		2558.8
(-2) 		2436.8
(-3) 		2605.5
(-1.6) 		2489.1
(-2.6) 		3142.2
(3) 		705
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 3698
1 2 3 4 range
A 926
(-1.6)
P 		304.3
(-3)
P 		447.5
(-2.7)
P 		2949.5
(3)
P 		2645
B 923.2
(-2.2)
P 		627.4
(-2.7)
P 		452.8
(-3)
P 		4002.4
(3)
P 		3550
C 828.7
(-2.4)
P 		602.6
(-3)
P 		628.9
(-2.9)
P 		2946.2
(3)
P 		2344
avr 892.6
(-2.2) 		511.4
(-3) 		509.7
(-3) 		3299.4
(3) 		2790

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 657
1 2 3 4 5 6 range
A 673.8
(-0.9)
P 		849.5
(3)
P 		582.3
(-2.9)
P 		579.6
(-3)
P 		838.7
(2.8)
P 		692
(-0.5)
P 		270
B 987.1
(1.6)
P 		933.9
(0.9)
P 		599
(-3)
P 		670.7
(-2.2)
P 		1057.3
(2.4)
P 		1108.1
(3)
P 		509
C 829.2
(-0.5)
P 		757.3
(-1.1)
P 		552.3
(-3)
P 		603.1
(-2.5)
P 		674.8
(-1.9)
P 		1209.4
(3)
P 		657
avr 830
(0.6) 		846.9
(0.8) 		577.9
(-3) 		617.8
(-2.4) 		856.9
(0.9) 		1003.2
(3) 		425
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 173229_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.27654
Sequence Type Exemplar sequence
Representative Public ID C60047 NCBI
Target Description C60047_rc /REP_DB=TREMBL Accession /GB=C60047 /FEA=Transcript Cluster /DEF=C.elegans cDNA clone yk446f5 : 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_058689(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_058689 NCBI Caenorhabditis elegans Y54E10BR.4 (Y54E10BR.4) mRNA, complete cds. 11/11 A 
SNAP00000038968 ENSEMBL cdna:SNAP chromosome:CEL140:I:3015746:3021423:1 11/11 None
GENEFINDER00000038975 ENSEMBL cdna:GeneFinder chromosome:CEL140:I:3015746:3021423:1 11/11 None
Y54E10BR.4 ENSEMBL cdna:known chromosome:CEL140:I:3015743:3021520:1 gene:Y54E10BR.4 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
chrI:3018567-3021415(+) 83.12 83.12
Public Domain and Genome References
Gene Title
Ensembl Y54E10BR.4
Entrez Gene 171874 Entrez gene
SwissProt Q9N3D3 EMBL-EBI
WormBase CE27481 Wormbase
Functional Annotations
Ortholog
ID Title Organism
ATH1-121501:249315_AT expressed protein at
CANINE_2:CFAAFFX.31016.1.S1_S_AT similar to nin one binding protein cfa
DROSOPHILA_2:1633322_AT dm
DROSGENOME1:153909_AT dm
CHICKEN:GGA.9918.1.S1_S_AT similar to nin one binding protein; adenocarcinoma antigen recognized by T lymphocytes 4 gga
CHICKEN:GGAAFFX.26721.1.S1_S_AT similar to nin one binding protein; adenocarcinoma antigen recognized by T lymphocytes 4 gga
HG-U133_PLUS_2:223018_AT nin one binding protein hs
HG-U133B:223018_AT nin one binding protein hs
HU35KSUBA:AA093998_AT nin one binding protein hs
HU35KSUBA:RC_AA489080_AT nin one binding protein hs
U133_X3P:G12652610_3P_AT nin one binding protein hs
HG-U95B:45763_AT nin one binding protein hs
HG-U95E:71687_AT Nin one binding protein hs
HG-U95E:71688_AT Nin one binding protein hs
MG-U74BV2:108040_AT RIKEN cDNA 1700021I09 gene mm
MOE430B:1454957_AT RIKEN cDNA 1700021I09 gene mm
MOUSE430_2:1454957_AT RIKEN cDNA 1700021I09 gene mm
MU19KSUBB:TC29981_AT RIKEN cDNA 1700021I09 gene, mRNA (cDNA clone IMAGE:6396144) mm
MU19KSUBB:TC31547_AT RIKEN cDNA 1700021I09 gene, mRNA (cDNA clone IMAGE:6396144) mm
RG-U34B:RC_AA956531_AT nin one binding protein rn
RG-U34B:RC_AA851261_AT nin one binding protein rn
RG-U34B:RC_AA851261_G_AT nin one binding protein rn
RAE230A:1388878_AT nin one binding protein rn
RAT230_2:1388878_AT nin one binding protein rn
YEAST_2:1772781_AT Essential nuclear protein involved in proteasome maturation and synthesis of 40S ribosomal subunits; required for cleavage of the 20S pre-rRNA to generate the mature 18S rRNA Sc
Protein Similarities
Method ID Description E-Value
blast AAF59552 Hypothetical protein Y54E10BR.4 [Caenorhabditis elegans] ref|NP_491090.1| Y54E10BR.4 [Caenorhabditis elegans] 0.0
blast CAE60563 Hypothetical protein CBG04192 [Caenorhabditis briggsae] 1.0E-160
blast AAF59552 Hypothetical protein Y54E10BR.4 [Caenorhabditis elegans] ref|NP_491090.1| Y54E10BR.4 [Caenorhabditis elegans] 1.0E-119
blast CAE60563 Hypothetical protein CBG04192 [Caenorhabditis briggsae] 1.0E-100
blast XP_781262 PREDICTED: similar to nin one binding protein [Strongylocentrotus purpuratus] 1.0E-41
Sequence
Target Sequence 
>C. ELEGANS:173229_S_AT
gaatggcaaatcgacgtggcctagtttacacattggccaatcccaaaggtggnaaacacg
caacaaatgagcgccttttcgaagatcaaccaatgcctcacatgagaatggnnnnnnnnn
nnnnnnnnnnnnttgcggatggcccattttatgtgcangangtcacttttaggtagacat
tgagtcggagttcggacaaatcaaataatcgtgccaagcagaaccgcaatccgaatgagt
cgaaacgtggcggaaga

BLASTn GenBank NR
Note: "n"'s represent regions that are not probed by the probe sequences.
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GAATGGCAAATCGACGTGGCCTAGT 556 331 101 Antisense
AAACACGCAACAAATGAGCGCCTTT 586 127 154 Antisense
GCAACAAATGAGCGCCTTTTCGAAG 410 315 160 Antisense
TGAGCGCCTTTTCGAAGATCAACCA 649 567 168 Antisense
CGAAGATCAACCAATGCCTCACATG 162 253 180 Antisense
GATCAACCAATGCCTCACATGAGAA 650 421 184 Antisense
AATAATCGTGCCAAGCAGAACCGCA 3 171 304 Antisense
ATCGTGCCAAGCAGAACCGCAATCC 639 33 308 Antisense
GCCAAGCAGAACCGCAATCCGAATG 538 277 313 Antisense
GCAGAACCGCAATCCGAATGAGTCG 260 313 318 Antisense
GAATGAGTCGAAACGTGGCGGAAGA 632 329 333 Antisense
Sequence Source Affymetrix Proprietary Database