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[187852_at]

Description F41B4.4 /REP_DB=WormBase Gene ID /WP=CE07214 /SUBMIT=ST.LOUIS /CHR=X /FEA=Sanger Annotation /DEF=ligand-gated ionic channel
Cluster 6grp_high1_10_10 > 33      6grp_total > 21      4grp_total > 30      6grp_cgc > 62      6grp_high1_sub > 02      6grp_cgc_sub > 02      6grp_total_sub > Hat      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 127
1 2 3 4 range
A 138.2
(0.6)
P 		132.4
(0)
P 		101.8
(-3)
A 		162.5
(3)
P 		61
B 186.3
(3)
P 		107.3
(-1.1)
A 		70.4
(-3)
A 		135.6
(0.4)
P 		116
C 191.6
(3)
P 		76.2
(-2.5)
A 		64.6
(-3)
A 		164.3
(1.7)
P 		127
avr 172
(3) 		105.3
(-1.3) 		78.9
(-3) 		154.1
(1.8) 		93

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 105
1 2 3 4 5 6 range
A 143.3
(-0.8)
A 		193
(3)
P 		163.7
(0.8)
P 		181.9
(2.2)
P 		113.7
(-3)
P 		130.6
(-1.7)
P 		79
B 119.5
(-0.2)
P 		155.3
(3)
P 		112.2
(-0.8)
P 		112.6
(-0.8)
P 		115.4
(-0.5)
P 		87.7
(-3)
P 		68
C 165.4
(1.9)
P 		165.7
(1.9)
P 		178.6
(3)
P 		126.3
(-1.4)
P 		137.4
(-0.5)
P 		107.3
(-3)
P 		71
avr 142.7
(0.3) 		171.3
(3) 		151.5
(1.1) 		140.3
(0) 		122.2
(-1.7) 		108.5
(-3) 		63
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 47
1 2 3 4 range
A 50.3
(3)
P 		28.7
(-1.9)
P 		26.6
(-2.4)
A 		23.8
(-3)
P 		27
B 59.4
(3)
P 		26.5
(-1.6)
A 		16.3
(-3)
A 		28.9
(-1.2)
P 		43
C 63.4
(3)
P 		21.9
(-3)
A 		22.5
(-2.9)
A 		27.7
(-2.2)
P 		42
avr 57.7
(3) 		25.7
(-2.3) 		21.8
(-3) 		26.8
(-2.2) 		36

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 43
1 2 3 4 5 6 range
A 26.4
(-3)
A 		68.6
(3)
P 		35.7
(-1.7)
P 		46.1
(-0.2)
P 		34.3
(-1.9)
P 		31.8
(-2.2)
P 		42
B 41.6
(0.5)
P 		51.7
(3)
P 		27.2
(-3)
P 		29.8
(-2.4)
P 		46.9
(1.8)
P 		32.7
(-1.7)
P 		25
C 61.3
(3)
P 		50.6
(1.2)
P 		45.5
(0.4)
P 		25.4
(-3)
P 		44.5
(0.2)
P 		35.9
(-1.2)
P 		36
avr 43.1
(-0.5) 		57
(3) 		36.1
(-2.3) 		33.8
(-2.9) 		41.9
(-0.9) 		33.5
(-3) 		24
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 187852_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.17278
Sequence Type Exemplar sequence
Representative Public ID F41B4.4 NCBI
Target Description F41B4.4 /REP_DB=WormBase Gene ID /WP=CE07214 /SUBMIT=ST.LOUIS /CHR=X /FEA=Sanger Annotation /DEF=ligand-gated ionic channel
Cluster Evidence This cluster is supported by a 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_171712(11), NM_171713(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_171712 NCBI Caenorhabditis elegans GLutamate Receptor family (AMPA) family member (glr-6) (glr-6) mRNA, complete cds. 11/11 None
NM_171713 NCBI Caenorhabditis elegans GLutamate Receptor family (AMPA) family member (glr-6) (glr-6) mRNA, complete cds. 11/11 None
F41B4.4a ENSEMBL cdna:known chromosome:CEL140:X:6836338:6840567:-1 gene:F41B4.4 11/11 None
F41B4.4b ENSEMBL cdna:known chromosome:CEL140:X:6836372:6838010:-1 gene:F41B4.4 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
chrX:6836371-6840567(-) 100.0 100.0
Public Domain and Genome References
Ensembl F41B4.4
Functional Annotations
Protein Similarities
Method ID Description E-Value
blast AAM54176 Glutamate receptor family (ampa) protein 6, isoform a [Caenorhabditis elegans] ref|NP_741822.2| GLutamate Receptor family (AMPA) family member (glr-6) [Caenorhabditis elegans] 0.0
blast CAE65798 Hypothetical protein CBG10905 [Caenorhabditis briggsae] 0.0
blast AAK01098 ionotropic glutamate receptor GLR-6 [Caenorhabditis elegans] 0.0
blast AAM54177 Glutamate receptor family (ampa) protein 6, isoform b [Caenorhabditis elegans] ref|NP_741823.1| GLutamate Receptor family (AMPA) family member (glr-6) [Caenorhabditis elegans] 1.0E-178
blast AAM54176 Glutamate receptor family (ampa) protein 6, isoform a [Caenorhabditis elegans] ref|NP_741822.2| GLutamate Receptor family (AMPA) family member (glr-6) [Caenorhabditis elegans] 1.0E-166
Protein Domains
Database ID Description E-Value
Pfam IPR001320 EMBL-EBI Ionotropic glutamate receptor 1.2E-87
Pfam IPR001320 EMBL-EBI Ionotropic glutamate receptor 1.5E-85
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_741822.2 4 539-561,574-596,600-622,787-809
NP_741823.1 4 23-45,58-80,84-106,271-293
F41B4.4a 4 539-561,574-596,600-622,787-809
F41B4.4b 4 23-45,58-80,84-106,271-293
Sequence
Target Sequence 
>C. ELEGANS:187852_AT
caattctcggtggatcgacaatgcaattcttcaaatactccagaattgagacttttcgtc
gtttgtgggagcgtatgcaaagtgccgaaccttcagcgtttgtaggcaccaatcacgaag
gagttaaccgggtgttaaatgagaaatatgtcttcctaatggaatctgccacactagact
atcaagtgactcaaaactgcaatcttactcgtgttggcaacgttgttcttggatccaatg
gatatagtattgcacttccaaagggatcaaagtggagggaaaagcttacaagacaaatcc
tcgatctgaatgaaaaaggcataattctaatgttgaagaataattggtggaaaaaatccc
aacaagaatgtcagtcaagtgagcccgaagatttacaaactgctctgggcgctgaaaatg
tgtacggtttgtttcttctcctcgctcttggaagtggaattggagttctttgtgcggtgc
tggaacatacacatttcatattcttcgagaaaaataaacgaaatggtcaaactcccaaat
tgcaacaa

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
CAATTCTCGGTGGATCGACAATGCA 1 181 1952 Antisense
GACTTTTCGTCGTTTGTGGGAGCGT 130 371 2001 Antisense
CAAAGTGCCGAACCTTCAGCGTTTG 39 191 2029 Antisense
CAGCGTTTGTAGGCACCAATCACGA 599 203 2045 Antisense
ATGTCTTCCTAATGGAATCTGCCAC 486 47 2099 Antisense
GAATCTGCCACACTAGACTATCAAG 367 329 2113 Antisense
AACTGCAATCTTACTCGTGTTGGCA 442 141 2146 Antisense
GTGTTGGCAACGTTGTTCTTGGATC 579 469 2162 Antisense
AAGCTTACAAGACAAATCCTCGATC 437 147 2233 Antisense
TTTACAAACTGCTCTGGGCGCTGAA 305 673 2343 Antisense
TGGTCAAACTCCCAAATTGCAACAA 8 553 2475 Antisense
Sequence Source Affymetrix Proprietary Database