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[192597_at] ligand-gated ionic channel protein

Description ZC196.7 /REP_DB=WormBase Gene ID /WP=CE15078 /TR=O01623 /GB=AAB52291.1 /SUBMIT=ST.LOUIS /CHR=5 /FEA=Sanger Annotation /DEF=ligand-gated ionic channel protein
Cluster 6grp_highest_10_10 > 20      6grp_high1_10_10 > 13      4grp_highest_8_8 > 51      4grp_high_8_8 > 24      6grp_highest_nonorm > 61      6grp_total > 13      4grp_total > 47      6grp_highest_sub > De      6grp_cgc > 30      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.
4 545
1 2 3 4 range
A 710.1
(3)
P 		272.2
(-3)
P 		320.5
(-2.3)
P 		312.8
(-2.4)
P 		438
B 649.1
(3)
P 		383.5
(-0.8)
P 		235.1
(-3)
P 		322.2
(-1.7)
P 		414
C 779.6
(3)
P 		330.9
(-3)
P 		333.5
(-3)
P 		454.8
(-1.3)
P 		449
avr 712.9
(3) 		328.9
(-2.5) 		296.4
(-3) 		363.3
(-2) 		417

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 382
1 2 3 4 5 6 range
A 480.2
(3)
P 		468.3
(2.7)
P 		425.4
(1.7)
P 		339
(-0.3)
P 		306.3
(-1)
P 		221.9
(-3)
P 		258
B 604
(3)
P 		521.7
(1.6)
P 		438.7
(0.1)
P 		380.7
(-0.9)
P 		399.4
(-0.6)
P 		261
(-3)
P 		343
C 483.8
(1.7)
P 		539.1
(3)
P 		377.7
(-0.9)
P 		500.3
(2.1)
P 		288.3
(-3)
P 		301.9
(-2.7)
P 		251
avr 522.7
(3) 		509.7
(2.7) 		413.9
(0.5) 		406.7
(0.3) 		331.3
(-1.4) 		261.6
(-3) 		261
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 213
1 2 3 4 range
A 258.6
(3)
P 		59.1
(-2.6)
P 		83.8
(-1.9)
P 		45.8
(-3)
P 		213
B 207
(3)
P 		94.7
(-1.4)
P 		54.5
(-3)
P 		68.7
(-2.4)
P 		153
C 258.1
(3)
P 		95.1
(-2.4)
P 		116.2
(-1.7)
P 		76.7
(-3)
P 		181
avr 241.2
(3) 		83
(-2.3) 		84.8
(-2.3) 		63.7
(-3) 		178

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 156
1 2 3 4 5 6 range
A 88.5
(-1.2)
P 		166.6
(3)
P 		92.6
(-0.9)
P 		86
(-1.3)
P 		92.4
(-1)
P 		54
(-3)
P 		113
B 210.2
(3)
P 		173.7
(1.1)
P 		106.5
(-2.5)
P 		100.8
(-2.8)
P 		162.3
(0.5)
P 		97.3
(-3)
P 		113
C 179.3
(3)
P 		164.5
(2)
P 		96.1
(-2.8)
P 		100.6
(-2.5)
P 		93.3
(-3)
P 		101.1
(-2.5)
P 		86
avr 159.3
(2.4) 		168.3
(3) 		98.4
(-2) 		95.8
(-2.2) 		116
(-0.7) 		84.1
(-3) 		84
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 192597_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.12420
Sequence Type Exemplar sequence
Representative Public ID ZC196.7 NCBI
Target Description ZC196.7 /REP_DB=WormBase Gene ID /WP=CE15078 /TR=O01623 /GB=AAB52291.1 /SUBMIT=ST.LOUIS /CHR=5 /FEA=Sanger Annotation /DEF=ligand-gated ionic channel protein
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_072843(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_072843 NCBI Caenorhabditis elegans GLutamate Receptor family (AMPA) family member (glr-5) (glr-5) mRNA, complete cds. 11/11 None
SNAP00000023098 ENSEMBL cdna:SNAP chromosome:CEL140:V:8718544:8723078:1 11/11 None
GENEFINDER00000023110 ENSEMBL cdna:GeneFinder chromosome:CEL140:V:8719267:8723078:1 11/11 None
ZC196.7 ENSEMBL cdna:known chromosome:CEL140:V:8719083:8723481:1 gene:ZC196.7 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
chrV:8719127-8723079(+) 100.0 100.0
Public Domain and Genome References
Gene Title ligand-gated ionic channel protein
Gene Symbol glr-5
Ensembl ZC196.7
Entrez Gene 179251 Entrez gene
SwissProt O01623 EMBL-EBI
WormBase CE15078 Wormbase
Functional Annotations
Ortholog
ID Title Organism
CANINE_2:CFAAFFX.5954.1.S1_AT similar to glutamate receptor 7 precursor cfa
CANINE_2:CFAAFFX.5968.1.S1_S_AT similar to glutamate receptor 7 precursor cfa
DROSOPHILA_2:1626426_AT dm
DROSGENOME1:142525_AT dm
DROSOPHILA_2:1634140_A_AT dm
DROSGENOME1:151607_AT dm
CHICKEN:GGAAFFX.1387.1.S1_S_AT similar to glutamate receptor, ionotropic, kainate 3; glutamate receptor subunit kainate subtype; kainate receptor gga
HG-U133_PLUS_2:207454_AT glutamate receptor, ionotropic, kainate 3 hs
HG-U133A:207454_AT glutamate receptor, ionotropic, kainate 3 hs
HG-FOCUS:207454_AT glutamate receptor, ionotropic, kainate 3 hs
HG-U133A_2:207454_AT glutamate receptor, ionotropic, kainate 3 hs
HUGENEFL:U16127_AT glutamate receptor, ionotropic, kainate 3 hs
U133_X3P:G4504118_3P_AT glutamate receptor, ionotropic, kainate 3 hs
HG-U95AV2:34540_AT glutamate receptor, ionotropic, kainate 3 hs
MOE430A:1427709_AT glutamate receptor, ionotropic, kainate 3 mm
MOUSE430_2:1427709_AT glutamate receptor, ionotropic, kainate 3 mm
MOUSE430A_2:1427709_AT glutamate receptor, ionotropic, kainate 3 mm
MU19KSUBC:TC38688_AT PREDICTED: glutamate receptor 7 [Mus musculus], mRNA sequence mm
RAT230_2:1370587_AT glutamate receptor, ionotropic, kainate 3 rn
RAE230A:1370587_AT glutamate receptor, ionotropic, kainate 3 rn
RN-U34:AF027331_AT glutamate receptor, ionotropic, kainate 3 rn
RG-U34A:AF027331_AT glutamate receptor, ionotropic, kainate 3 rn
Gene Ontology
GO Biological Process (view graph)
ID Description Evidence Links
6811 ion transport inferred from electronic annotation QuickGO AmiGO
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
4872 receptor activity inferred from electronic annotation QuickGO AmiGO
4970 ionotropic glutamate receptor 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
Protein Similarities
Method ID Description E-Value
blast AAB52291 Glutamate receptor family (ampa) protein 5 [Caenorhabditis elegans] ref|NP_505244.1| GLutamate Receptor family (AMPA) family member (glr-5) [Caenorhabditis elegans] 0.0
blast CAE58402 Hypothetical protein CBG01531 [Caenorhabditis briggsae] 0.0
blast AAK01097 ionotropic glutamate receptor GLR-5 [Caenorhabditis elegans] 0.0
Protein Domains
Database ID Description E-Value
Pfam IPR001320 EMBL-EBI Ionotropic glutamate receptor 1.0E-126
Pfam IPR001828 EMBL-EBI Extracellular ligand-binding receptor 5.5E-11
Pfam IPR001320 EMBL-EBI Ionotropic glutamate receptor 1.0E-126
Pfam IPR001828 EMBL-EBI Extracellular ligand-binding receptor 5.5E-11
Pfam IPR001320 EMBL-EBI Ionotropic glutamate receptor 1.0E-126
Pfam IPR001828 EMBL-EBI Extracellular ligand-binding receptor 5.5E-11
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_505244.1 4 7-29,567-589,660-682,844-866
ZC196.7 4 7-29,567-589,660-682,844-866
SNAP00000023098 3 550-572,643-665,827-849
GENEFINDER00000023110 3 578-600,671-693,855-877
Sequence
Target Sequence 
>C. ELEGANS:192597_AT
aaaggttatggaatcgcactcgcaaaaaaatccgaatggacagatcgaatttctcgtcaa
attctattgtatgccaaacgtggaatcattgaaatgaaaaagacaaagtggtggagaagc
aaaggagccgcatgtgcgagtacagcgtctgcggtcaagcatgaccgatttgctcttagc
atgtacaacgttgctggtctcttcatcactttgggggtcggaatcgtgttggccgcaatt
gtagtgatatttgagttaattcatagatgccatcacattgccaaaaaagaaggaaaacct
ttcttagaagaacttttgtacgaactcaggtttgctttgaatatgaactcgctctccgat
ca

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
AAAGGTTATGGAATCGCACTCGCAA 528 121 2353 Antisense
GGACAGATCGAATTTCTCGTCAAAT 235 525 2390 Antisense
AGCCGCATGTGCGAGTACAGCGTCT 102 83 2478 Antisense
TACAGCGTCTGCGGTCAAGCATGAC 79 639 2493 Antisense
GCATGACCGATTTGCTCTTAGCATG 692 309 2511 Antisense
GCATGTACAACGTTGCTGGTCTCTT 666 309 2531 Antisense
TCATCACTTTGGGGGTCGGAATCGT 15 619 2555 Antisense
CGGAATCGTGTTGGCCGCAATTGTA 307 243 2571 Antisense
CATAGATGCCATCACATTGCCAAAA 243 195 2614 Antisense
GTACGAACTCAGGTTTGCTTTGAAT 589 457 2670 Antisense
TGAATATGAACTCGCTCTCCGATCA 687 575 2690 Antisense
Sequence Source Affymetrix Proprietary Database