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[171817_x_at]

Description C37214_rc /REP_DB=TREMBL Accession /GB=C37214 /FEA=Transcript Cluster /DEF=C.elegans cDNA clone yk460g2 : 3prime end, single read.
Cluster 6grp_highest_10_10 > 31      6grp_high1_10_10 > 12      4grp_highest_8_8 > 09      4grp_high_8_8 > 62      6grp_highest_nonorm > 15      6grp_total > 22      4grp_total > 58      6grp_highest_sub > De      6grp_high1_sub > De      6grp_total_sub > Hat      4grp_rule_based > L3      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 10307
1 2 3 4 range
A 6275.2
(0.4)
P 		8895.2
(2.5)
P 		9445.5
(3)
P 		2209.3
(-3)
P 		7236
B 3568.3
(-2.3)
P 		9765.1
(1.5)
P 		12092.8
(3)
P 		2480.9
(-3)
P 		9612
C 5339.3
(-0.7)
P 		9132
(1.7)
P 		11247
(3)
P 		1786.1
(-3)
P 		9461
avr 5060.9
(-1) 		9264.1
(1.9) 		10928.4
(3) 		2158.8
(-3) 		8770

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 4162
1 2 3 4 5 6 range
A 4068.5
(-1.8)
P 		5855
(3)
P 		5714.2
(2.6)
P 		5506.3
(2.1)
P 		3627.3
(-3)
P 		3638.7
(-3)
P 		2228
B 6683.3
(3)
P 		5933.5
(1.8)
P 		5186.9
(0.5)
P 		3699.6
(-1.9)
P 		3711.1
(-1.9)
P 		3025.9
(-3)
P 		3657
C 7187.4
(3)
P 		5807.8
(0.5)
P 		6054.2
(1)
P 		4072.6
(-2.6)
P 		6128.2
(1.1)
P 		3865.3
(-3)
P 		3322
avr 5979.7
(3) 		5865.4
(2.7) 		5651.8
(2.2) 		4426.2
(-0.8) 		4488.9
(-0.6) 		3510
(-3) 		2470
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 3619
1 2 3 4 range
A 2284.8
(2.5)
P 		1930.9
(1.5)
P 		2469.2
(3)
P 		323.4
(-3)
P 		2146
B 1137.9
(-1.4)
P 		2411.7
(2)
P 		2802.2
(3)
P 		528.7
(-3)
P 		2274
C 1767.5
(-0.6)
P 		2625.5
(0.9)
P 		3919.9
(3)
P 		301.2
(-3)
P 		3619
avr 1730.1
(0) 		2322.7
(1.3) 		3063.8
(3) 		384.4
(-3) 		2679

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 1914
1 2 3 4 5 6 range
A 750
(-3)
P 		2082.3
(3)
P 		1244.4
(-0.8)
P 		1396.5
(-0.1)
P 		1094.6
(-1.4)
P 		885.9
(-2.4)
P 		1332
B 2325.5
(3)
P 		1975
(1.4)
P 		1259.5
(-1.8)
P 		979.9
(-3)
P 		1507.8
(-0.6)
P 		1128.3
(-2.3)
P 		1346
C 2664.1
(3)
P 		1772.1
(0.1)
P 		1540.9
(-0.7)
P 		819
(-3)
P 		1983
(0.8)
P 		1293.9
(-1.5)
P 		1845
avr 1913.2
(2.8) 		1943.1
(3) 		1348.3
(-1.1) 		1065.1
(-3) 		1528.5
(0.2) 		1102.7
(-2.7) 		878
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 171817_x_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.28042
Sequence Type Exemplar sequence
Representative Public ID C37214 NCBI
Target Description C37214_rc /REP_DB=TREMBL Accession /GB=C37214 /FEA=Transcript Cluster /DEF=C.elegans cDNA clone yk460g2 : 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 Genome Target Overlap based pipeline to a RefSeq identifier using 1 transcript(s).
Annotation Grade This is a grade B annotation.
Annotation Transcript Cluster (# of Matching Probes) NM_067796
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
SNAP00000033664 ENSEMBL cdna:SNAP chromosome:CEL140:IV:2388414:2388669:-1 None
GENEFINDER00000033679 ENSEMBL cdna:GeneFinder chromosome:CEL140:IV:2388368:2388669:-1 None
NM_067796 NCBI Caenorhabditis elegans Y38F2AR.9 (Y38F2AR.9) mRNA, complete cds. None
Y38F2AR.9.1 ENSEMBL cdna:known chromosome:CEL140:IV:2388192:2388675:-1 gene:Y38F2AR.9 None
Y38F2AR.9.2 ENSEMBL cdna:known chromosome:CEL140:IV:2388192:2388673:-1 gene:Y38F2AR.9 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:2388263-2388560(-) 90.88 90.88
Public Domain and Genome References
Gene Title
Ensembl Y38F2AR.9
Entrez Gene 177027 Entrez gene
SwissProt Q95XS2 EMBL-EBI
WormBase CE27617 Wormbase
Functional Annotations
Protein Similarities
Method ID Description E-Value
blast NP_500197 Y38F2AR.9 [Caenorhabditis elegans] gb|AAK68450.1| Hypothetical protein Y38F2AR.9 [Caenorhabditis elegans] 2.0E-28
blast CAE70295 Hypothetical protein CBG16816 [Caenorhabditis briggsae] 4.0E-26
blast NP_500197 Y38F2AR.9 [Caenorhabditis elegans] gb|AAK68450.1| Hypothetical protein Y38F2AR.9 [Caenorhabditis elegans] 2.0E-19
blast AAI06322 Unknown (protein for MGC:130844) [Xenopus laevis] gb|AAH41270.1| Sec61beta-prov protein [Xenopus laevis] 7.0E-18
Protein Domains
Database ID Description E-Value
Pfam IPR005609 EMBL-EBI Sec61beta 2.3E-27
Pfam IPR005609 EMBL-EBI Sec61beta 5.2E-19
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_500197.1 1 51-73
Y38F2AR.9.1 1 51-73
Y38F2AR.9.2 1 51-73
GENEFINDER00000033679 1 51-73
Sequence
Target Sequence 
>C. ELEGANS:171817_X_AT
gcgccggaggcaacaacggagggctttggcgctttnacaccgaggattngaccggcttga
agatcggaccagttccagtgcttgtcangtcgcttgttttcatcgnttccgtgttcgtgc
tccacatttggggnaaattcacgagaagccgcgcttaagccc

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
GCGCCGGAGGCAACAACGGAGGGCT 166 287 63 Antisense
GGAGGCAACAACGGAGGGCTTTGGC 497 515 68 Antisense
AGGCAACAACGGAGGGCTTTGGCGC 188 1 70 Antisense
CAACAACGGAGGGCTTTGGCGCTTT 342 189 73 Antisense
GACCGGCTTGAAGATCGGACCAGTT 445 381 112 Antisense
CGGCTTGAAGATCGGACCAGTTCCA 627 241 115 Antisense
GCTTGAAGATCGGACCAGTTCCAGT 395 307 117 Antisense
GAAGATCGGACCAGTTCCAGTGCTT 341 337 121 Antisense
AAGATCGGACCAGTTCCAGTGCTTG 686 153 122 Antisense
AAATTCACGAGAAGCCGCGCTTAAG 81 115 197 Antisense
TTCACGAGAAGCCGCGCTTAAGCCC 469 685 200 Antisense
Sequence Source Affymetrix Proprietary Database