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[173406_at]

Description AU115990_rc /REP_DB=TREMBL Accession /GB=AU115990 /FEA=Transcript Cluster /DEF=Caenorhabditis elegans cDNA clone:yk739c4 : 3prime end, single read.
Cluster 6grp_highest_10_10 > 92      6grp_high1_10_10 > 39      4grp_highest_8_8 > 32      4grp_high_8_8 > 51      6grp_highest_nonorm > 85      6grp_total > 49      4grp_total > 61      6grp_highest_sub > Cu      6grp_high1_sub > Cu      6grp_total_sub > Cup      4grp_rule_based > L1      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 471
1 2 3 4 range
A 955.2
(2.7)
P 		972.6
(3)
P 		900.9
(1.9)
P 		573.3
(-3)
P 		399
B 971.6
(2.8)
P 		977.4
(3)
P 		953.4
(2.3)
P 		759
(-3)
P 		218
C 1043.8
(3)
P 		951.1
(1.4)
P 		912.1
(0.7)
P 		701
(-3)
P 		343
avr 990.2
(3) 		967
(2.6) 		922.1
(1.7) 		677.8
(-3) 		312

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 614
1 2 3 4 5 6 range
A 859.8
(3)
P 		537.8
(-1.4)
P 		561.8
(-1.1)
P 		419
(-3)
P 		604.6
(-0.5)
P 		804
(2.2)
P 		441
B 927.9
(3)
P 		616.5
(-0.9)
P 		675.8
(-0.1)
P 		445.6
(-3)
P 		754
(0.8)
P 		883.4
(2.4)
P 		482
C 1033.2
(3)
P 		556.6
(-1.8)
P 		548.8
(-1.9)
P 		437.9
(-3)
P 		871.1
(1.4)
P 		883.5
(1.5)
P 		595
avr 940.3
(3) 		570.3
(-1.4) 		595.5
(-1.1) 		434.2
(-3) 		743.2
(0.7) 		857
(2) 		506
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 264
1 2 3 4 range
A 347.8
(3)
P 		211.1
(-0.1)
P 		235.5
(0.4)
P 		83.9
(-3)
P 		264
B 309.8
(3)
P 		241.4
(0.2)
P 		220.9
(-0.6)
P 		161.7
(-3)
P 		148
C 345.5
(3)
P 		273.5
(1.1)
P 		317.9
(2.3)
P 		118.2
(-3)
P 		227
avr 334.4
(3) 		242
(0.4) 		258.1
(0.9) 		121.3
(-3) 		213

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 295
1 2 3 4 5 6 range
A 158.5
(0.5)
P 		191.3
(2.7)
P 		122.4
(-1.9)
P 		106.3
(-3)
P 		182.4
(2.1)
P 		195.8
(3)
P 		90
B 322.9
(2.8)
P 		205.2
(-0.5)
P 		164.1
(-1.7)
P 		118
(-3)
P 		306.3
(2.3)
P 		329.4
(3)
P 		211
C 383
(3)
P 		169.8
(-1.3)
P 		139.7
(-2)
P 		88.1
(-3)
P 		281.9
(0.9)
P 		295.8
(1.2)
P 		295
avr 288.1
(3) 		188.8
(-0.2) 		142.1
(-1.8) 		104.1
(-3) 		256.9
(2) 		273.7
(2.5) 		184
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 173406_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.27783
Sequence Type Exemplar sequence
Representative Public ID AU115990 NCBI
Target Description AU115990_rc /REP_DB=TREMBL Accession /GB=AU115990 /FEA=Transcript Cluster /DEF=Caenorhabditis elegans cDNA clone:yk739c4 : 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_001027789(11), NM_001027790(10)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_001027789 NCBI Caenorhabditis elegans Y82E9BR.16a (Y82E9BR.16) mRNA, complete cds. 11/11 None
NM_001027790 NCBI Caenorhabditis elegans Y82E9BR.16b (Y82E9BR.16) mRNA, complete cds. 10/11 None
SNAP00000008914 ENSEMBL cdna:SNAP chromosome:CEL140:III:1419963:1420361:-1 10/11 None
GENEFINDER00000008941 ENSEMBL cdna:GeneFinder chromosome:CEL140:III:1419963:1427166:-1 10/11 None
Y82E9BR.16a ENSEMBL cdna:known chromosome:CEL140:III:1419857:1427216:-1 gene:Y82E9BR.16 11/11 None
Y82E9BR.16b ENSEMBL cdna:known chromosome:CEL140:III:1419963:1420559:-1 gene:Y82E9BR.16 10/11 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:1419908-1420232(-) 100.0 100.0
Public Domain and Genome References
Ensembl Y82E9BR.16
Functional Annotations
Protein Similarities
Method ID Description E-Value
blast AAK26156 Hypothetical protein Y82E9BR.16a [Caenorhabditis elegans] ref|NP_001022960.1| Y82E9BR.16a [Caenorhabditis elegans] 0.0
blast CAE66434 Hypothetical protein CBG11705 [Caenorhabditis briggsae] 0.0
blast CAE59577 Hypothetical protein CBG02977 [Caenorhabditis briggsae] 1.0E-103
blast AAP46262 Hypothetical protein Y82E9BR.16b [Caenorhabditis elegans] ref|NP_001022961.1| Y82E9BR.16b [Caenorhabditis elegans] 4.0E-70
blast AAK26156 Hypothetical protein Y82E9BR.16a [Caenorhabditis elegans] ref|NP_001022960.1| Y82E9BR.16a [Caenorhabditis elegans] 4.0E-70
Protein Domains
Database ID Description E-Value
Pfam IPR005828 EMBL-EBI General substrate transporter 6.0E-11
Pfam IPR005828 EMBL-EBI General substrate transporter 1.4E-10
Pfam IPR005828 EMBL-EBI General substrate transporter 2.2E-27
Pfam IPR005828 EMBL-EBI General substrate transporter 1.2E-8
Pfam IPR005828 EMBL-EBI General substrate transporter 5.1E-25
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_001022960.1 11 20-42,163-185,195-213,220-242,246-263,369-386,396-418,425-444,454-476,488-510,516-538
NP_001022961.1 3 7-29,44-66,73-95
Y82E9BR.16a 11 20-42,163-185,195-213,220-242,246-263,369-386,396-418,425-444,454-476,488-510,516-538
Y82E9BR.16b 3 7-29,44-66,73-95
SNAP00000008914 3 7-29,44-66,73-95
GENEFINDER00000008941 11 7-29,150-172,182-201,278-297,302-321,394-411,421-443,450-469,479-501,513-535,541-563
Sequence
Target Sequence 
>C. ELEGANS:173406_AT
tctgctcgacgattgctcgtgtcggcgcgatcgccgcttcgtacatctccatgtggatcg
ctgagcagtttgggaaggttttcatgattattccgttcgggtgtatggctgtgctcgccg
cagtgatgacgttgctcttttngcctgaaactatgggaaaaccactgccggagagtattg
aagagatcgaggagggagattcgtaccgcagctcgcatgaaatgcaacctctttcgaaaa
gcactgaagaaaccgcataaat

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
TCTGCTCGACGATTGCTCGTGTCGG 428 607 23 Antisense
CTCCATGTGGATCGCTGAGCAGTTT 605 235 69 Antisense
CGCTGAGCAGTTTGGGAAGGTTTTC 372 255 81 Antisense
AGGTTTTCATGATTATTCCGTTCGG 526 57 98 Antisense
TATTCCGTTCGGGTGTATGGCTGTG 419 663 111 Antisense
AACTATGGGAAAACCACTGCCGGAG 490 139 171 Antisense
GAGGAGGGAGATTCGTACCGCAGCT 657 403 211 Antisense
TCGTACCGCAGCTCGCATGAAATGC 665 603 223 Antisense
GCAGCTCGCATGAAATGCAACCTCT 420 313 230 Antisense
ATGCAACCTCTTTCGAAAAGCACTG 557 43 244 Antisense
AAAGCACTGAAGAAACCGCATAAAT 505 123 260 Antisense
Sequence Source Affymetrix Proprietary Database