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[172971_s_at]

Description C34620_rc /REP_DB=TREMBL Accession /FEA=EST Transcript /REVCOMP /GB=C34620 /DEF=C.elegans cDNA clone yk413a4 : 3prime end, single read.
Cluster 6grp_highest_10_10 > 91      6grp_high1_10_10 > 39      4grp_highest_8_8 > 62      4grp_high_8_8 > 18      6grp_highest_nonorm > 68      6grp_total > 29      4grp_total > 29      6grp_high1_sub > Cu      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 1615
1 2 3 4 range
A 2310.8
(3)
P 		1957
(1.5)
P 		904.2
(-3)
P 		1933.3
(1.4)
P 		1407
B 2360.5
(3)
P 		1690.4
(-0.5)
P 		1201.3
(-3)
P 		2261.3
(2.5)
P 		1159
C 2519.1
(3)
P 		1676.4
(-0.8)
P 		1192.3
(-3)
P 		2095.9
(1.1)
P 		1327
avr 2396.8
(3) 		1774.6
(0.1) 		1099.3
(-3) 		2096.8
(1.6) 		1298

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 1964
1 2 3 4 5 6 range
A 3242.9
(3)
P 		1956.2
(-1.1)
P 		1362.8
(-3)
P 		1469.7
(-2.7)
P 		2969
(2.1)
P 		2012.9
(-0.9)
P 		1880
B 2831.6
(3)
P 		1815.1
(-0.9)
P 		1279.4
(-3)
P 		1621.9
(-1.7)
P 		2840.8
(3)
P 		2121.2
(0.2)
P 		1561
C 2890.8
(2.5)
P 		1629.7
(-2.3)
P 		1452.2
(-3)
P 		1516.9
(-2.8)
P 		3013.9
(3)
P 		2130.6
(-0.4)
P 		1562
avr 2988.4
(3) 		1800.3
(-1.4) 		1364.8
(-3) 		1536.2
(-2.4) 		2941.2
(2.8) 		2088.2
(-0.3) 		1624
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 605
1 2 3 4 range
A 841.4
(3)
P 		424.8
(-1.1)
P 		236.4
(-3)
P 		283
(-2.5)
P 		605
B 752.8
(3)
P 		417.5
(-1.2)
P 		278.4
(-3)
P 		481.9
(-0.4)
P 		474
C 833.9
(3)
P 		482
(-1.4)
P 		415.5
(-2.2)
P 		353.4
(-3)
P 		481
avr 809.4
(3) 		441.4
(-1.4) 		310.1
(-3) 		372.8
(-2.2) 		499

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 857
1 2 3 4 5 6 range
A 597.8
(0)
P 		695.7
(1)
P 		296.8
(-3)
P 		372.8
(-2.2)
P 		895.9
(3)
P 		490.1
(-1.1)
P 		599
B 985.3
(1.8)
P 		604.2
(-0.9)
P 		310.7
(-3)
P 		429.6
(-2.2)
P 		1154.2
(3)
P 		791
(0.4)
P 		844
C 1071.5
(3)
P 		497.3
(-1.5)
P 		369.6
(-2.5)
P 		305.1
(-3)
P 		975.3
(2.2)
P 		713.2
(0.2)
P 		766
avr 884.9
(1.9) 		599.1
(-0.6) 		325.7
(-3) 		369.2
(-2.6) 		1008.5
(3) 		664.8
(-0) 		683
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 172971_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.26346
Sequence Type Exemplar sequence
Representative Public ID C34620 NCBI
Target Description C34620_rc /REP_DB=TREMBL Accession /FEA=EST Transcript /REVCOMP /GB=C34620 /DEF=C.elegans cDNA clone yk413a4 : 3prime end, single read.
Cluster Evidence This cluster is supported by a EST Transcript.
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_001028317(11), NM_001028318(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_001028317 NCBI Caenorhabditis elegans Y54G2A.11a (Y54G2A.11) mRNA, complete cds. 11/11 None
NM_001028318 NCBI Caenorhabditis elegans Y54G2A.11b (Y54G2A.11) mRNA, complete cds. 11/11 None
SNAP00000036470 ENSEMBL cdna:SNAP chromosome:CEL140:IV:2765975:2771732:-1 11/11 None
GENEFINDER00000036590 ENSEMBL cdna:GeneFinder chromosome:CEL140:IV:2765975:2771732:-1 11/11 None
Y54G2A.11a ENSEMBL cdna:known chromosome:CEL140:IV:2765610:2771787:-1 gene:Y54G2A.11 11/11 None
Y54G2A.11b ENSEMBL cdna:known chromosome:CEL140:IV:2765741:2766712:-1 gene:Y54G2A.11 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:2765951-2768194(-) 98.33 98.33
Public Domain and Genome References
Ensembl Y54G2A.11
Functional Annotations
Protein Similarities
Method ID Description E-Value
blast AAK68524 Hypothetical protein Y54G2A.11a [Caenorhabditis elegans] ref|NP_001023488.1| Y54G2A.11a [Caenorhabditis elegans] 0.0
blast CAE68229 Hypothetical protein CBG13902 [Caenorhabditis briggsae] 5.0E-60
blast AAP13740 Hypothetical protein Y54G2A.11b [Caenorhabditis elegans] ref|NP_001023489.1| Y54G2A.11b [Caenorhabditis elegans] 5.0E-29
blast AAK68524 Hypothetical protein Y54G2A.11a [Caenorhabditis elegans] ref|NP_001023488.1| Y54G2A.11a [Caenorhabditis elegans] 5.0E-29
Protein Domains
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_001023488.1 1 179-201
Y54G2A.11a 1 179-201
SNAP00000036470 1 179-201
GENEFINDER00000036590 1 179-201
Sequence
Target Sequence 
>C. ELEGANS:172971_S_AT
gagaaccgtctcaaaaccaactgatcaatgcgattntngtcanttttccaagttcacacc
ccgcagaaaacatattgcctataaaactccacttccatgcaaagtgcaaagttatcaacc
atngtcaccaaaaccaantcgcaagccatcgacaagcacaaaattcgacgattggcacca
caagcgtgggctccacagagcccatct

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
GAGAACCGTCTCAAAACCAACTGAT 608 391 57 Antisense
AACCGTCTCAAAACCAACTGATCAA 415 147 60 Antisense
AGTTCACACCCCGCAGAAAACATAT 371 63 107 Antisense
CACCCCGCAGAAAACATATTGCCTA 178 201 113 Antisense
TATTGCCTATAAAACTCCACTTCCA 473 665 129 Antisense
AACTCCACTTCCATGCAAAGTGCAA 545 141 141 Antisense
GCCATCGACAAGCACAAAATTCGAC 6 281 201 Antisense
AAAATTCGACGATTGGCACCACAAG 593 129 216 Antisense
TCGACGATTGGCACCACAAGCGTGG 576 599 221 Antisense
GATTGGCACCACAAGCGTGGGCTCC 582 435 226 Antisense
AGCGTGGGCTCCACAGAGCCCATCT 608 81 239 Antisense
Sequence Source Affymetrix Proprietary Database