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[174456_at] Glutamate receptor

Description C59681_rc /REP_DB=TREMBL Accession /GB=C59681 /CHR=2 /FEA=Genomic Cluster /DEF=C.elegans cDNA clone yk440c12 : 3prime end, single read.
Cluster 6grp_highest_10_10 > 41      6grp_high1_10_10 > 26      4grp_highest_8_8 > 51      4grp_high_8_8 > 32      6grp_highest_nonorm > 70      6grp_total > 16      4grp_total > 47      6grp_highest_sub > De      6grp_cgc > 23      6grp_high1_sub > De      6grp_cgc_sub > De      6grp_total_sub > Decrease      6grp_rule_based > S1      4grp_rule_based > L1      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 598
1 2 3 4 range
A 640.4
(3)
P 		216.6
(-2.8)
P 		200.3
(-3)
P 		290.1
(-1.8)
P 		440
B 743.1
(3)
P 		278.2
(-1.7)
P 		145.5
(-3)
P 		268.6
(-1.8)
P 		598
C 644.1
(3)
P 		231.7
(-3)
P 		254.5
(-2.7)
P 		233.5
(-3)
P 		412
avr 675.9
(3) 		242.2
(-2.5) 		200.1
(-3) 		264.1
(-2.2) 		476

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 356
1 2 3 4 5 6 range
A 401
(1.4)
P 		473.5
(3)
P 		257.9
(-1.6)
P 		229.7
(-2.2)
P 		194.3
(-3)
P 		196
(-3)
P 		279
B 548.8
(3)
P 		393.3
(0.2)
P 		301.9
(-1.5)
P 		241.7
(-2.5)
P 		242.6
(-2.5)
P 		216.3
(-3)
P 		333
C 524.6
(3)
P 		417.6
(1.1)
P 		356.3
(-0)
P 		193.1
(-3)
P 		212.6
(-2.6)
P 		302.6
(-1)
P 		332
avr 491.5
(3) 		428.1
(1.6) 		305.4
(-1.1) 		221.5
(-2.9) 		216.5
(-3) 		238.3
(-2.5) 		275
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 203
1 2 3 4 range
A 233.2
(3)
P 		47
(-2.9)
P 		52.4
(-2.7)
P 		42.5
(-3)
P 		191
B 237
(3)
P 		68.7
(-2)
P 		33.7
(-3)
P 		57.2
(-2.3)
P 		203
C 213.2
(3)
P 		66.6
(-2.1)
P 		88.7
(-1.3)
P 		39.4
(-3)
P 		174
avr 227.8
(3) 		60.8
(-2.5) 		58.3
(-2.6) 		46.4
(-3) 		181

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 156
1 2 3 4 5 6 range
A 73.9
(-1.7)
P 		168.4
(3)
P 		56.2
(-2.6)
P 		58.3
(-2.5)
P 		58.6
(-2.5)
P 		47.7
(-3)
P 		121
B 191
(3)
P 		130.9
(0.2)
P 		73.3
(-2.6)
P 		64
(-3)
P 		98.6
(-1.4)
P 		80.7
(-2.2)
P 		127
C 194.4
(3)
P 		127.4
(0.4)
P 		90.7
(-1)
P 		38.8
(-3)
P 		68.8
(-1.8)
P 		101.3
(-0.6)
P 		156
avr 153.1
(3) 		142.2
(2.3) 		73.4
(-1.8) 		53.7
(-3) 		75.3
(-1.7) 		76.6
(-1.6) 		99
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 174456_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.20736
Sequence Type Exemplar sequence
Representative Public ID C59681 NCBI
Target Description C59681_rc /REP_DB=TREMBL Accession /GB=C59681 /CHR=2 /FEA=Genomic Cluster /DEF=C.elegans cDNA clone yk440c12 : 3prime end, single read.
Cluster Evidence This cluster is supported by a Genomic 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_063238(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_063238 NCBI Caenorhabditis elegans GLutamate Receptor family (AMPA) family member (glr-4) (glr-4) mRNA, complete cds. 11/11 A 
SNAP00000042213 ENSEMBL cdna:SNAP chromosome:CEL140:II:7785184:7788687:-1 11/11 None
GENEFINDER00000042220 ENSEMBL cdna:GeneFinder chromosome:CEL140:II:7785184:7788515:-1 11/11 None
C06A8.9 ENSEMBL cdna:known chromosome:CEL140:II:7785103:7794240:-1 gene:C06A8.9 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
chrII:7785109-7785389(-) 100.0 100.0
Public Domain and Genome References
Gene Title Glutamate receptor
Gene Symbol glr-4
Ensembl C06A8.9
Entrez Gene 174258 Entrez gene
SwissProt Q17697 EMBL-EBI
WormBase CE31294 Wormbase
Functional Annotations
Ortholog
ID Title Organism
ATGENOME1:14040_AT glutamate receptor family protein (GLR3.2) (GLUR2) at
ATH1-121501:253166_AT glutamate receptor family protein (GLR3.2) (GLUR2) at
CANINE_2:CFAAFFX.6315.1.S1_S_AT similar to glutamate receptor 6 isoform 1 precursor cfa
CANINE_2:CFAAFFX.6317.1.S1_AT similar to glutamate receptor 6 isoform 1 precursor cfa
CANINE_2:CFAAFFX.6318.1.S1_AT similar to glutamate receptor 6 isoform 1 precursor cfa
CANINE_2:CFAAFFX.6318.1.S1_S_AT similar to glutamate receptor 6 isoform 1 precursor cfa
DROSGENOME1:146578_AT clumsy dm
DROSOPHILA_2:1627435_AT clumsy dm
CHICKEN:GGAAFFX.9829.1.S1_AT similar to glutamate receptor 6 isoform 1 precursor; excitatory amino acid receptor 4 gga
HUGENEFL:U16126_AT glutamate receptor, ionotropic, kainate 2 hs
U133_X3P:HS2.420694.1.A1_3P_X_AT glutamate receptor, ionotropic, kainate 2 hs
U133_X3P:HS2.420694.1.A1_3P_S_AT glutamate receptor, ionotropic, kainate 2 hs
U133_X3P:HS2.420694.1.A1_3P_AT glutamate receptor, ionotropic, kainate 2 hs
U133_X3P:HS2.301676.5.S1_3P_X_AT glutamate receptor, ionotropic, kainate 2 hs
U133_X3P:HS2.301676.5.S1_3P_AT glutamate receptor, ionotropic, kainate 2 hs
U133_X3P:HS2.301676.4.S1_3P_S_AT glutamate receptor, ionotropic, kainate 2 hs
U133_X3P:HS2.301676.4.S1_3P_AT glutamate receptor, ionotropic, kainate 2 hs
U133_X3P:HS2.301676.2.S1_3P_AT glutamate receptor, ionotropic, kainate 2 hs
U133_X3P:HS.301676.0.S2_3P_AT glutamate receptor, ionotropic, kainate 2 hs
HG-U133_PLUS_2:1555375_AT glutamate receptor, ionotropic, kainate 2 hs
HG-U133_PLUS_2:1560142_AT glutamate receptor, ionotropic, kainate 2 hs
HG-U133_PLUS_2:1560265_AT glutamate receptor, ionotropic, kainate 2 hs
HG-U133_PLUS_2:1563754_AT glutamate receptor, ionotropic, kainate 2 hs
HG-U95AV2:39573_AT glutamate receptor, ionotropic, kainate 2 hs
HG-U133_PLUS_2:215655_AT Glutamate receptor, ionotropic, kainate 2 hs
HG-U133A_2:215655_AT Glutamate receptor, ionotropic, kainate 2 hs
HG-U133A:215655_AT Glutamate receptor, ionotropic, kainate 2 hs
U133_X3P:HS.306651.0.S1_3P_AT Glutamate receptor, ionotropic, kainate 2 hs
HG-U95D:89824_AT Glutamate receptor, ionotropic, kainate 2 hs
HU35KSUBD:RC_AA479978_AT Glutamate receptor, ionotropic, kainate 2 hs
U133_X3P:1560265_3P_AT Glutamate receptor, ionotropic, kainate 2 hs
MOUSE430_2:1425790_A_AT glutamate receptor, ionotropic, kainate 2 (beta 2) mm
MOUSE430A_2:1425790_A_AT glutamate receptor, ionotropic, kainate 2 (beta 2) mm
MOE430A:1425790_A_AT glutamate receptor, ionotropic, kainate 2 (beta 2) mm
MU11KSUBB:X66117_S_AT glutamate receptor, ionotropic, kainate 2 (beta 2) mm
MG-U74AV2:98864_S_AT glutamate receptor, ionotropic, kainate 2 (beta 2) mm
MG-U74AV2:98863_AT glutamate receptor, ionotropic, kainate 2 (beta 2) mm
MOE430B:1457683_AT glutamate receptor, ionotropic, kainate 2 (beta 2) mm
MOUSE430_2:1457683_AT glutamate receptor, ionotropic, kainate 2 (beta 2) mm
MOUSE430_2:1439286_AT Glutamate receptor, ionotropic, kainate 2 (beta 2) (Grik2), mRNA mm
MOE430B:1439286_AT Glutamate receptor, ionotropic, kainate 2 (beta 2) (Grik2), mRNA mm
MOE430B:1440602_AT Glutamate receptor, ionotropic, kainate 2 (beta 2) (Grik2), mRNA mm
MOUSE430_2:1440602_AT Glutamate receptor, ionotropic, kainate 2 (beta 2) (Grik2), mRNA mm
RN-U34:Z11548_AT glutamate receptor, ionotropic, kainate 2 rn
RG-U34A:Z11548_AT glutamate receptor, ionotropic, kainate 2 rn
RAE230A:1369036_AT glutamate receptor, ionotropic, kainate 2 rn
RAT230_2:1369036_AT glutamate receptor, ionotropic, kainate 2 rn
RAE230B:1396846_AT Glutamate receptor, ionotropic, kainate 2 rn
RAT230_2:1396846_AT Glutamate receptor, ionotropic, kainate 2 rn
RG-U34B:RC_AI030150_AT Glutamate receptor, ionotropic, kainate 2 rn
Gene Ontology
GO Cellular Component (view graph)
ID Description Evidence Links
16020 membrane inferred from electronic annotation QuickGO AmiGO
GO Molecular Function (view graph)
ID Description Evidence Links
4970 ionotropic glutamate receptor activity inferred from electronic annotation QuickGO AmiGO
5234 glutamate-gated ion channel activity inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast AAA81054 Glutamate receptor family (ampa) protein 4 [Caenorhabditis elegans] ref|NP_495639.2| GLutamate Receptor family (AMPA) family member (glr-4) [Caenorhabditis elegans] 0.0
blast CAE67453 Hypothetical protein CBG12954 [Caenorhabditis briggsae] 0.0
blast T15427 hypothetical protein C06A8.9 - Caenorhabditis elegans 0.0
Protein Domains
Database ID Description E-Value
Pfam IPR001320 EMBL-EBI Ionotropic glutamate receptor 2.4E-73
Pfam IPR001320 EMBL-EBI Ionotropic glutamate receptor 1.4E-107
Pfam IPR001320 EMBL-EBI Ionotropic glutamate receptor 2.8E-116
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_495639.2 4 7-25,531-553,611-633,801-823
C06A8.9 4 7-25,531-553,611-633,801-823
SNAP00000042213 3 170-192,250-272,373-395
GENEFINDER00000042220 3 157-179,237-259,425-447
Sequence
Target Sequence 
>C. ELEGANS:174456_AT
ccagatccaactcgtctttcaatatcatctccagcaccaactatttgcgttgtgtcatgt
gatgatggtacaccgatcagtagagatagaccaccatcaattagtagagctggacttcga
agattaagtcggatgttgccagcagcaacacatgaacaactatcacgattccgtcaagga
tcaatgtctt

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
CCAGATCCAACTCGTCTTTCAATAT 168 273 30 Antisense
CGTCTTTCAATATCATCTCCAGCAC 33 247 42 Antisense
ATCTCCAGCACCAACTATTTGCGTT 462 33 56 Antisense
CTATTTGCGTTGTGTCATGTGATGA 280 223 70 Antisense
GTGATGATGGTACACCGATCAGTAG 475 483 88 Antisense
GATCAGTAGAGATAGACCACCATCA 65 421 104 Antisense
AGACCACCATCAATTAGTAGAGCTG 229 71 117 Antisense
GTAGAGCTGGACTTCGAAGATTAAG 34 445 133 Antisense
TTAAGTCGGATGTTGCCAGCAGCAA 507 683 153 Antisense
ATGAACAACTATCACGATTCCGTCA 326 43 181 Antisense
CGATTCCGTCAAGGATCAATGTCTT 594 247 195 Antisense
Sequence Source Affymetrix Proprietary Database