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[189872_at] ligand-gated ion channel subunit

Description F25G6.4 /REP_DB=WormBase Gene ID /WP=CE20721 /GEN=acr-15 /SUBMIT=ST.LOUIS /CHR=5 /FEA=Sanger Annotation /DEF=ligand-gated ion channel subunit
Cluster 4grp_high_8_8 > 20      6grp_total > 41      4grp_total > 05      6grp_cgc > 83      6grp_cgc_sub > 03      6grp_total_sub > Hat      6grp_rule_based > S3      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 94
1 2 3 4 range
A 125.7
(2.6)
A 		85.9
(-3)
A 		107.2
(-0)
A 		128.6
(3)
P 		43
B 91.1
(-2.6)
M 		119.7
(0.8)
P 		87.7
(-3)
P 		138.3
(3)
P 		51
C 112.2
(0)
P 		65.3
(-3)
A 		92.9
(-1.2)
P 		158.8
(3)
P 		94
avr 109.7
(-0.7) 		90.3
(-3) 		95.9
(-2.3) 		141.9
(3) 		52

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 117
1 2 3 4 5 6 range
A 103.9
(0.9)
A 		131.5
(3)
A 		112.2
(1.6)
P 		118.1
(2)
A 		71.6
(-1.5)
A 		51.2
(-3)
A 		80
B 107.8
(-0.7)
P 		93
(-1.6)
A 		167.7
(3)
A 		106.6
(-0.8)
A 		95
(-1.5)
A 		70.4
(-3)
A 		97
C 94.8
(-1.1)
P 		126.5
(1)
A 		112.4
(0)
P 		157
(3)
P 		77.2
(-2.3)
P 		66.3
(-3)
P 		91
avr 102.2
(0.5) 		117
(1.8) 		130.8
(3) 		127.2
(2.7) 		81.3
(-1.4) 		62.6
(-3) 		68
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 27
1 2 3 4 range
A 45.8
(3)
A 		18.6
(-3)
A 		28
(-0.9)
A 		18.8
(-3)
P 		27
B 29.1
(2.7)
M 		29.6
(3)
P 		20.3
(-3)
P 		29.5
(2.9)
P 		9
C 37.1
(3)
P 		18.8
(-3)
A 		32.4
(1.5)
P 		26.8
(-0.4)
P 		18
avr 37.3
(3) 		22.3
(-3) 		26.9
(-1.2) 		25
(-1.9) 		15

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 34
1 2 3 4 5 6 range
A 19.1
(-1.8)
A 		46.8
(3)
A 		24.4
(-0.9)
P 		30
(0.1)
A 		21.6
(-1.4)
A 		12.5
(-3)
A 		34
B 37.5
(1.7)
P 		30.9
(-1.1)
A 		40.7
(3)
A 		28.2
(-2.2)
A 		38.6
(2.1)
A 		26.3
(-3)
A 		14
C 35.1
(1.7)
P 		38.6
(3)
A 		28.6
(-0.7)
P 		31.6
(0.4)
P 		25
(-2)
P 		22.2
(-3)
P 		16
avr 30.6
(0.3) 		38.8
(3) 		31.2
(0.5) 		29.9
(0.1) 		28.4
(-0.4) 		20.3
(-3) 		19
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 189872_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.11860
Sequence Type Exemplar sequence
Representative Public ID F25G6.4 NCBI
Target Description F25G6.4 /REP_DB=WormBase Gene ID /WP=CE20721 /GEN=acr-15 /SUBMIT=ST.LOUIS /CHR=5 /FEA=Sanger Annotation /DEF=ligand-gated ion channel subunit
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_072805(9)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_072805 NCBI Caenorhabditis elegans AcetylCholine Receptor family member (acr-15) (acr-15) mRNA, complete cds. 9/11 None
GENEFINDER00000003990 ENSEMBL cdna:GeneFinder chromosome:CEL140:V:8552647:8557935:1 9/11 None
F25G6.4 ENSEMBL cdna:known chromosome:CEL140:V:8555283:8557958:1 gene:F25G6.4 9/11 None
Annotation Notes
Cross Hybridizing mRNA Matched Probes Nature of Assignment Related Probesets by Grade
SNAP00000003978 7/11 Cross Hyb Matching Probes None
SNAP00000003979 2/11 Cross Hyb Matching Probes None
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrV:8555308-8557936(+) 100.0 100.0
Public Domain and Genome References
Gene Title ligand-gated ion channel subunit
Gene Symbol acr-15
Ensembl F25G6.4
Entrez Gene 191602 Entrez gene
SwissProt O16926 EMBL-EBI
WormBase CE37637 Wormbase
Functional Annotations
Ortholog
ID Title Organism
HG-U133_PLUS_2:210123_S_AT CHRNA7 (cholinergic receptor, nicotinic, alpha polypeptide 7, exons 5-10) and FAM7A (family with sequence similarity 7A, exons A-E) fusion hs
HG-U133A:210123_S_AT CHRNA7 (cholinergic receptor, nicotinic, alpha polypeptide 7, exons 5-10) and FAM7A (family with sequence similarity 7A, exons A-E) fusion hs
HG-FOCUS:210123_S_AT CHRNA7 (cholinergic receptor, nicotinic, alpha polypeptide 7, exons 5-10) and FAM7A (family with sequence similarity 7A, exons A-E) fusion hs
HG-U133A_2:210123_S_AT CHRNA7 (cholinergic receptor, nicotinic, alpha polypeptide 7, exons 5-10) and FAM7A (family with sequence similarity 7A, exons A-E) fusion hs
HU35KSUBD:RC_N54079_S_AT CHRNA7 (cholinergic receptor, nicotinic, alpha polypeptide 7, exons 5-10) and FAM7A (family with sequence similarity 7A, exons A-E) fusion hs
HUGENEFL:X70297_AT CHRNA7 (cholinergic receptor, nicotinic, alpha polypeptide 7, exons 5-10) and FAM7A (family with sequence similarity 7A, exons A-E) fusion hs
U133_X3P:G1458119_3P_A_AT CHRNA7 (cholinergic receptor, nicotinic, alpha polypeptide 7, exons 5-10) and FAM7A (family with sequence similarity 7A, exons A-E) fusion hs
HG-U95AV2:39566_AT CHRNA7 (cholinergic receptor, nicotinic, alpha polypeptide 7, exons 5-10) and FAM7A (family with sequence similarity 7A, exons A-E) fusion hs
HG-U95D:70426_AT CHRNA7 (cholinergic receptor, nicotinic, alpha polypeptide 7, exons 5-10) and FAM7A (family with sequence similarity 7A, exons A-E) fusion hs
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
GO Cellular Component (view graph)
ID Description Evidence Links
16020 membrane inferred from electronic annotation QuickGO AmiGO
16021 integral to membrane inferred from electronic annotation QuickGO AmiGO
45211 postsynaptic membrane inferred from electronic annotation QuickGO AmiGO
GO Molecular Function (view graph)
ID Description Evidence Links
4889 nicotinic acetylcholine-activated cation-selective channel activity inferred from electronic annotation QuickGO AmiGO
5216 ion channel activity inferred from electronic annotation QuickGO AmiGO
5230 extracellular ligand-gated ion channel activity inferred from electronic annotation QuickGO AmiGO
30594 neurotransmitter receptor activity inferred from electronic annotation QuickGO AmiGO
15464 acetylcholine receptor activity inferred from sequence similarity QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast AAC25797 Acetylcholine receptor protein 15 [Caenorhabditis elegans] ref|NP_505206.2| AcetylCholine Receptor family member (acr-15) [Caenorhabditis elegans] 0.0
blast CAE58367 Hypothetical protein CBG01493 [Caenorhabditis briggsae] 0.0
blast AAC25798 Temporarily assigned gene name protein 57 [Caenorhabditis elegans] ref|NP_505205.1| F25G6.5 [Caenorhabditis elegans] sp|O16925|DHBY_CAEEL Putative steroid dehydrogenase F25G6.5 1.0E-128
blast CAE58366 Hypothetical protein CBG01491 [Caenorhabditis briggsae] 1.0E-113
Protein Domains
Database ID Description E-Value
Pfam IPR006029 EMBL-EBI Neurotransmitter-gated ion-channel transmembrane region 1.5E-7
Pfam IPR006029 EMBL-EBI Neurotransmitter-gated ion-channel transmembrane region 3.8E-5
Pfam IPR006202 EMBL-EBI Neurotransmitter-gated ion-channel ligand binding domain 3.6E-92
Pfam IPR006029 EMBL-EBI Neurotransmitter-gated ion-channel transmembrane region 3.8E-5
Pfam IPR002198 EMBL-EBI Short-chain dehydrogenase/reductase SDR 1.9E-31
Pfam IPR006202 EMBL-EBI Neurotransmitter-gated ion-channel ligand binding domain 3.6E-92
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_505206.2 4 228-250,257-276,291-313,454-476
F25G6.4 4 228-250,257-276,291-313,454-476
GENEFINDER00000003990 6 10-29,474-496,511-530,550-568,578-600,744-766
Sequence
Target Sequence 
>C. ELEGANS:189872_AT
gaaaccaacatgtacacgaacggatggatttctgggtatttcttctttttttttcatatc
aaaatataaaattccagatgaggttcattctcttggagtggtcaccgtggctattgcgaa
tgaaaatgccggatagagaaaataactttcagacactgacagaaagttggaagggaagga
atcgaagagaatctatggcaagaacagcgttcgaatatgcagatggaccggttacacaga
tacattccatgggaattatgttgaaagataattttgaagagcttatttatcaagttaaac
aggagaagattgctgatgaaaaaggaattgagagattgcgggtgttacagaagatttacg
atcatgtaaagatacatgtggacgagtacagtaatagatcaagcttttcaatcagaatca
aatattgttttttccagatgatccgagaacatgacgatgacaatgatgaagacagtcgag
tagctcttgaatggagatttgctgcaattgtcgtcgatcgtc

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GAAACCAACATGTACACGAACGGAT 586 357 959 Antisense
GGATGGATTTCTGGGTATTTCTTCT 345 515 980 Antisense
GGTTCATTCTCTTGGAGTGGTCACC 552 505 1040 Antisense
AGTGGTCACCGTGGCTATTGCGAAT 564 59 1055 Antisense
GAATCTATGGCAAGAACAGCGTTCG 126 329 1147 Antisense
CAGCGTTCGAATATGCAGATGGACC 413 203 1163 Antisense
GACCGGTTACACAGATACATTCCAT 642 379 1184 Antisense
GAGAGATTGCGGGTGTTACAGAAGA 532 389 1288 Antisense
ATTGTTTTTTCCAGATGATCCGAGA 257 5 1382 Antisense
GACAGTCGAGTAGCTCTTGAATGGA 710 359 1429 Antisense
TTTGCTGCAATTGTCGTCGATCGTC 65 667 1456 Antisense
Sequence Source Affymetrix Proprietary Database