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[187868_s_at] Glutamate receptor subunit

Description C06E1.4 /REP_DB=WormBase Gene ID /WP=CE00059 /GEN=glr-1 /SUBMIT=ST.LOUIS /CHR=3 /FEA=Sanger Annotation /DEF=Glutamate receptor
Cluster 6grp_highest_10_10 > 41      6grp_high1_10_10 > 04      4grp_highest_8_8 > 52      4grp_high_8_8 > 24      6grp_highest_nonorm > 90      6grp_total > 15      4grp_total > 39      6grp_highest_sub > De      6grp_cgc > 32      6grp_high1_sub > De      6grp_cgc_sub > De      6grp_total_sub > Decrease      6grp_rule_based > S1      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 216
1 2 3 4 range
A 292
(3)
P 		98.9
(-3)
P 		101.5
(-2.9)
P 		125.2
(-2.2)
P 		193
B 238.7
(3)
P 		118.5
(-1.5)
P 		78.4
(-3)
P 		123.2
(-1.3)
P 		160
C 234.9
(3)
P 		76.1
(-3)
P 		130.4
(-0.9)
P 		174.1
(0.7)
P 		159
avr 255.2
(3) 		97.8
(-3) 		103.4
(-2.8) 		140.8
(-1.4) 		157

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 139
1 2 3 4 5 6 range
A 225.7
(3)
P 		175.7
(0.7)
P 		128.4
(-1.5)
P 		104.9
(-2.6)
P 		125.1
(-1.7)
P 		97
(-3)
P 		129
B 184.5
(3)
P 		171.2
(2.1)
P 		157
(1.2)
P 		164.4
(1.7)
P 		102.3
(-2.4)
P 		92.9
(-3)
P 		92
C 159.4
(1.2)
P 		191.2
(3)
P 		132
(-0.4)
P 		86.7
(-3)
P 		101.7
(-2.1)
P 		105.4
(-1.9)
P 		105
avr 189.9
(3) 		179.4
(2.3) 		139.1
(-0.3) 		118.7
(-1.7) 		109.7
(-2.3) 		98.4
(-3) 		92
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 88
1 2 3 4 range
A 106.3
(3)
P 		21.5
(-2.8)
P 		26.5
(-2.4)
P 		18.3
(-3)
P 		88
B 76.1
(3)
P 		29.3
(-1.8)
P 		18.2
(-3)
P 		26.3
(-2.2)
P 		58
C 77.8
(3)
P 		21.9
(-3)
P 		45.4
(-0.5)
P 		29.4
(-2.2)
P 		56
avr 86.7
(3) 		24.2
(-3) 		30
(-2.4) 		24.7
(-3) 		63

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 47
1 2 3 4 5 6 range
A 41.6
(-0.2)
P 		62.5
(3)
P 		28
(-2.3)
P 		26.6
(-2.5)
P 		37.8
(-0.8)
P 		23.6
(-3)
P 		39
B 64.2
(3)
P 		57
(1.5)
P 		38.1
(-2.3)
P 		43.5
(-1.2)
P 		41.5
(-1.6)
P 		34.6
(-3)
P 		30
C 59.1
(3)
P 		58.3
(2.9)
P 		33.6
(-0.7)
P 		17.4
(-3)
P 		32.9
(-0.8)
P 		35.3
(-0.4)
P 		42
avr 55
(2.1) 		59.3
(3) 		33.2
(-2.2) 		29.2
(-3) 		37.4
(-1.4) 		31.2
(-2.6) 		30
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 187868_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.6611
Sequence Type Exemplar sequence
Representative Public ID C06E1.4 NCBI
Target Description C06E1.4 /REP_DB=WormBase Gene ID /WP=CE00059 /GEN=glr-1 /SUBMIT=ST.LOUIS /CHR=3 /FEA=Sanger Annotation /DEF=Glutamate receptor
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_066486(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_066486 NCBI Caenorhabditis elegans GLutamate Receptor family (AMPA) family member (glr-1) (glr-1) mRNA, complete cds. 11/11 A 
SNAP00000034816 ENSEMBL cdna:SNAP chromosome:CEL140:III:8584159:8588518:-1 11/11 None
GENEFINDER00000034832 ENSEMBL cdna:GeneFinder chromosome:CEL140:III:8584159:8588518:-1 11/11 None
C06E1.4 ENSEMBL cdna:known chromosome:CEL140:III:8584058:8588602:-1 gene:C06E1.4 11/11 A 
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:8584153-8588948(-) 100.0 100.0
Public Domain and Genome References
Gene Title Glutamate receptor subunit
Gene Symbol glr-1
Ensembl C06E1.4
Entrez Gene 176204 Entrez gene
SwissProt P34299 EMBL-EBI
WormBase CE31407 Wormbase
Functional Annotations
Ortholog
ID Title Organism
CANINE_2:CFAAFFX.27226.1.S1_S_AT similar to Glutamate receptor 1 precursor (GluR-1) (GluR-A) (GluR-K1) (Glutamate receptor ionotropic, AMPA 1) cfa
CANINE_2:CFAAFFX.27257.1.S1_S_AT similar to Glutamate receptor 1 precursor (GluR-1) (GluR-A) (GluR-K1) (Glutamate receptor ionotropic, AMPA 1) cfa
CHICKEN:GGA.942.1.S1_AT similar to AMPA receptor GluR1/A gga
CHICKEN:GGA.942.1.S1_S_AT similar to AMPA receptor GluR1/A gga
CHICKEN:GGA.943.1.S1_S_AT similar to AMPA receptor GluR1/A gga
HG-U133_PLUS_2:209793_AT glutamate receptor, ionotropic, AMPA 1 hs
HG-U133A_2:209793_AT glutamate receptor, ionotropic, AMPA 1 hs
HG-FOCUS:209793_AT glutamate receptor, ionotropic, AMPA 1 hs
HG-U133A:209793_AT glutamate receptor, ionotropic, AMPA 1 hs
HG-U133_PLUS_2:211520_S_AT glutamate receptor, ionotropic, AMPA 1 hs
HG-U133A:211520_S_AT glutamate receptor, ionotropic, AMPA 1 hs
HG-U133A_2:211520_S_AT glutamate receptor, ionotropic, AMPA 1 hs
HG-U95AV2:36854_S_AT glutamate receptor, ionotropic, AMPA 1 hs
HU35KSUBA:M81886_S_AT glutamate receptor, ionotropic, AMPA 1 hs
HUGENEFL:M81886_S_AT glutamate receptor, ionotropic, AMPA 1 hs
HUGENEFL:M64752_AT glutamate receptor, ionotropic, AMPA 1 hs
U133_X3P:G183280_3P_A_AT glutamate receptor, ionotropic, AMPA 1 hs
U133_X3P:HS.7117.1.A2_3P_AT glutamate receptor, ionotropic, AMPA 1 hs
HG-U95AV2:36853_AT glutamate receptor, ionotropic, AMPA 1 hs
HG-U95AV2:36855_R_AT glutamate receptor, ionotropic, AMPA 1 hs
U133_X3P:HS.302185.0.S1_3P_AT Glutamate receptor, ionotropic, AMPA 1 hs
HG-U133A_2:215634_AT Glutamate receptor, ionotropic, AMPA 1 hs
HG-U133_PLUS_2:215634_AT Glutamate receptor, ionotropic, AMPA 1 hs
HG-U133A:215634_AT Glutamate receptor, ionotropic, AMPA 1 hs
HG-U95AV2:32273_AT Glutamate receptor, ionotropic, AMPA 1 hs
HU35KSUBC:RC_Z41488_AT Glutamate receptor, ionotropic, AMPA 1 hs
HU35KSUBB:RC_T23452_S_AT Glutamate receptor, ionotropic, AMPA 1 hs
HUGENEFL:Z70220_AT Glutamate receptor, ionotropic, AMPA 1 hs
MU11KSUBB:X57497_S_AT glutamate receptor, ionotropic, AMPA1 (alpha 1) mm
MG-U74AV2:92943_AT glutamate receptor, ionotropic, AMPA1 (alpha 1) mm
MG-U74AV2:92944_AT glutamate receptor, ionotropic, AMPA1 (alpha 1) mm
MG-U74BV2:117291_AT glutamate receptor, ionotropic, AMPA1 (alpha 1) mm
MG-U74CV2:165781_R_AT glutamate receptor, ionotropic, AMPA1 (alpha 1) mm
MOE430A:1435239_AT glutamate receptor, ionotropic, AMPA1 (alpha 1) mm
MOUSE430A_2:1435239_AT glutamate receptor, ionotropic, AMPA1 (alpha 1) mm
MOUSE430_2:1435239_AT glutamate receptor, ionotropic, AMPA1 (alpha 1) mm
MOE430A:1448972_AT glutamate receptor, ionotropic, AMPA1 (alpha 1) mm
MOUSE430A_2:1448972_AT glutamate receptor, ionotropic, AMPA1 (alpha 1) mm
MOUSE430_2:1448972_AT glutamate receptor, ionotropic, AMPA1 (alpha 1) mm
MOUSE430_2:1458285_AT Glutamate receptor, ionotropic, AMPA1 (alpha 1) (Gria1), mRNA mm
MOE430B:1458285_AT Glutamate receptor, ionotropic, AMPA1 (alpha 1) (Gria1), mRNA mm
Gene Ontology
GO Biological Process (view graph)
ID Description Evidence Links
6810 transport inferred from electronic annotation QuickGO AmiGO
6811 ion transport inferred from electronic annotation QuickGO AmiGO
35235 ionotropic glutamate receptor signaling pathway inferred from sequence similarity QuickGO AmiGO
GO Cellular Component (view graph)
ID Description Evidence Links
16020 membrane inferred from electronic annotation QuickGO AmiGO
30288 periplasmic space (sensu Gram-negative Bacteria) inferred from electronic annotation QuickGO AmiGO
45211 postsynaptic membrane inferred from direct assay QuickGO AmiGO
43025 cell soma inferred from direct assay QuickGO AmiGO
43005 neuron projection inferred from direct assay QuickGO AmiGO
8328 ionotropic glutamate receptor complex inferred from sequence similarity QuickGO AmiGO
GO Molecular Function (view graph)
ID Description Evidence Links
4872 receptor activity inferred from electronic annotation QuickGO AmiGO
4970 ionotropic glutamate receptor activity inferred from electronic annotation QuickGO AmiGO
5215 transporter activity inferred from electronic annotation QuickGO AmiGO
5216 ion channel activity inferred from electronic annotation QuickGO AmiGO
5234 glutamate-gated ion channel activity inferred from electronic annotation QuickGO AmiGO
4971 alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity inferred from sequence similarity QuickGO AmiGO
16595 glutamate binding inferred from sequence similarity QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast AAA27933 Glutamate receptor family (ampa) protein 1 [Caenorhabditis elegans] ref|NP_498887.2| GLutamate Receptor family (AMPA) family member (glr-1) [Caenorhabditis elegans] sp|P34299|GLR1_CAEEL Glutamate receptor 1 precursor pir||S60225 ionotropic glutamate receptor - Caenorhabditis elegans gb|AAA92006.1| ionotropic glutamate receptor subunit prf||2123408A Glu receptor GLR-1 0.0
blast CAE71239 Hypothetical protein CBG18112 [Caenorhabditis briggsae] 0.0
blast AAO61447 Glutamate receptor family (ampa) protein 2, isoform b [Caenorhabditis elegans] ref|NP_001021114.1| GLutamate Receptor family (AMPA) family member (glr-2) [Caenorhabditis elegans] gb|AAK01094.2| non-NMDA ionotropic glutamate receptor subunit GLR-2 [Caenorhabditis elegans] sp|Q10914|GLR2_CAEEL Glutamate receptor 2 precursor 0.0
Protein Domains
Database ID Description E-Value
Pfam IPR001320 EMBL-EBI Ionotropic glutamate receptor 1.0E-126
Pfam IPR001320 EMBL-EBI Ionotropic glutamate receptor 1.0E-126
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_498887.2 4 594-616,636-654,669-691,858-880
C06E1.4 4 594-616,636-654,669-691,858-880
SNAP00000034816 4 595-617,637-655,670-692,859-881
GENEFINDER00000034832 4 594-616,636-654,669-691,858-880
Sequence
Target Sequence 
>C. ELEGANS:187868_S_AT
atggaatagcgacacctttcggctccgactggaaggatcatatcaacttggcaattttag
ccctccaagaacgtggtgaactgaaaaagttggaaaacaaatggtggtatgatagaggac
aatgcgatgcgggtattactgttgacgggtcatctgctagtttgaatctatcaaaagttg
ctggaatattttatattttaatgggtggtatggtcatttcaatgttggctgcactcgggg
aattcttgtatcgaagtaggattgaagcgaggaaatctaattccaattctatggtggcga
attttgcgaaaaatttgaaaagtgcattgtcatctcaattaagattatcagtcgaaggag
gtgcagttgcacaaccaggatctcaatctcataatgcaattagaagacaacaggtagctg
cattcttgcctgca

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
ATGGAATAGCGACACCTTTCGGCTC 358 53 2465 Antisense
CGGCTCCGACTGGAAGGATCATATC 141 243 2484 Antisense
GCAATTTTAGCCCTCCAAGAACGTG 185 323 2515 Antisense
GAGGACAATGCGATGCGGGTATTAC 53 405 2579 Antisense
GCGGGTATTACTGTTGACGGGTCAT 322 237 2593 Antisense
GACGGGTCATCTGCTAGTTTGAATC 258 375 2608 Antisense
GGTCATTTCAATGTTGGCTGCACTC 590 503 2676 Antisense
GCTGCACTCGGGGAATTCTTGTATC 404 297 2692 Antisense
TCAGTCGAAGGAGGTGCAGTTGCAC 304 623 2812 Antisense
GCAGTTGCACAACCAGGATCTCAAT 23 313 2827 Antisense
ACAGGTAGCTGCATTCTTGCCTGCA 237 107 2874 Antisense
Sequence Source Affymetrix Proprietary Database