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[173777_s_at] CNG channel protein

Description CEK001A8R_rc /REP_DB=TREMBL Accession /5_PRIME_EXT_ID=F14H8.6 /5_PRIME_EXT_DB=WormBase Gene ID /GB=D32651 /WB_GENE_ID=F14H8.6 /WP=CE28435 /CHR=5 /FEA=Genomic Cluster /DEF=CNG channel protein; C.elegans cDNA clone yk1a8 : 3prime end, single read.
Cluster 6grp_total > 15      4grp_total > 14      6grp_cgc > 32      6grp_cgc_sub > De      6grp_total_sub > Decrease      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 69
1 2 3 4 range
A 55.8
(1.9)
P 		4.4
(-2.8)
A 		2.6
(-3)
A 		67.4
(3)
A 		65
B 60.1
(1.9)
P 		9.4
(-3)
A 		13.1
(-2.6)
A 		71.4
(3)
A 		62
C 54.8
(1.5)
P 		21.9
(-3)
A 		33.1
(-1.5)
P 		65.4
(3)
M 		44
avr 56.9
(1.8) 		11.9
(-3) 		16.3
(-2.5) 		68.1
(3) 		56

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 79
1 2 3 4 5 6 range
A 80.8
(3)
A 		59
(1.2)
P 		35.8
(-0.7)
A 		6.9
(-3)
A 		35.8
(-0.7)
A 		24.1
(-1.6)
A 		74
B 50.5
(3)
P 		44.7
(2.3)
P 		40.3
(1.7)
P 		1.9
(-3)
A 		22.7
(-0.4)
A 		13.6
(-1.6)
A 		49
C 68
(2.2)
P 		76.4
(3)
P 		40.3
(-0.3)
A 		54.7
(1)
P 		31.3
(-1.2)
A 		11.3
(-3)
A 		65
avr 66.4
(3) 		60
(2.2) 		38.8
(-0.3) 		21.2
(-2.4) 		29.9
(-1.4) 		16.3
(-3) 		50
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 20
1 2 3 4 range
A 20.3
(3)
P 		0.9
(-2.9)
A 		0.7
(-3)
A 		9.9
(-0.2)
A 		20
B 19.2
(3)
P 		2.3
(-3)
A 		3
(-2.8)
A 		15.2
(1.6)
A 		17
C 18.1
(3)
P 		6.3
(-3)
A 		11.5
(-0.4)
P 		11
(-0.6)
M 		12
avr 19.2
(3) 		3.2
(-3) 		5.1
(-2.3) 		12
(0.3) 		16

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 25
1 2 3 4 5 6 range
A 14.9
(1.1)
A 		21
(3)
P 		7.8
(-1.1)
A 		1.7
(-3)
A 		10.8
(-0.2)
A 		5.9
(-1.7)
A 		19
B 17.6
(3)
P 		14.9
(2.1)
P 		9.8
(0.3)
P 		0.5
(-3)
A 		9.2
(0.1)
A 		5.1
(-1.4)
A 		17
C 25.2
(3)
P 		23.3
(2.5)
P 		10.3
(-1.2)
A 		11
(-1)
P 		10.1
(-1.2)
A 		3.8
(-3)
A 		21
avr 19.2
(2.8) 		19.7
(3) 		9.3
(-1.1) 		4.4
(-3) 		10
(-0.8) 		4.9
(-2.8) 		15
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 173777_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.25488
Sequence Type Exemplar sequence
Representative Public ID CEK001A8R NCBI
Target Description CEK001A8R_rc /REP_DB=TREMBL Accession /5_PRIME_EXT_ID=F14H8.6 /5_PRIME_EXT_DB=WormBase Gene ID /GB=D32651 /WB_GENE_ID=F14H8.6 /WP=CE28435 /CHR=5 /FEA=Genomic Cluster /DEF=CNG channel protein; C.elegans cDNA clone yk1a8 : 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_074298(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_074298 NCBI Caenorhabditis elegans Cyclic Nucleotide Gated channel family member (cng-1) (cng-1) mRNA, complete cds. 11/11 None
SNAP00000006135 ENSEMBL cdna:SNAP chromosome:CEL140:V:15028371:15031325:-1 11/11 None
GENEFINDER00000006142 ENSEMBL cdna:GeneFinder chromosome:CEL140:V:15028371:15031325:-1 11/11 None
F14H8.6 ENSEMBL cdna:known chromosome:CEL140:V:15028326:15034219:-1 gene:F14H8.6 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:15028371-15034136(-) 100.0 100.0
Public Domain and Genome References
Gene Title CNG channel protein
Gene Symbol cng-1
Ensembl F14H8.6
Entrez Gene 180004 Entrez gene
SwissProt Q93486 EMBL-EBI
WormBase CE28435 Wormbase
Functional Annotations
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
5216 ion channel activity inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast CAB02935 Hypothetical protein F14H8.6 [Caenorhabditis elegans] ref|NP_506699.1| Cyclic Nucleotide Gated channel family member (cng-1) [Caenorhabditis elegans] 0.0
blast T20936 hypothetical protein F14H8.6a - Caenorhabditis elegans 0.0
blast CAE66332 Hypothetical protein CBG11583 [Caenorhabditis briggsae] 0.0
Protein Domains
Database ID Description E-Value
Pfam IPR005821 EMBL-EBI Ion transport protein 7.8E-14
Pfam IPR000595 EMBL-EBI Cyclic nucleotide-binding domain 3.1E-28
Pfam IPR000595 EMBL-EBI Cyclic nucleotide-binding domain 3.1E-28
Pfam IPR005821 EMBL-EBI Ion transport protein 7.8E-14
Pfam IPR000595 EMBL-EBI Cyclic nucleotide-binding domain 3.1E-28
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_506699.1 3 114-136,245-267,383-405
F14H8.6 3 114-136,245-267,383-405
SNAP00000006135 2 81-103,299-321
GENEFINDER00000006142 4 81-103,154-176,211-233,349-371
Sequence
Target Sequence 
>C. ELEGANS:173777_S_AT
gcggctattgtatgagctaattttgaagttgcagctccgagtatacagcccaatggatta
tatctgcaaaaagggagatgttggaaccgaaatgtacattgtcaaggaaggatttgtgga
agttgtcagtgaggatggtcaaacgatttttgtaactctaccggcaggctttgtatttgg
agaactttccattctaaacatacctggaaataaaaacaagaatttaagaactgcttctgt
tagatccaagggatattctgatctttatgttctcgataaagaagatctttgggaggctct
tcatgaatatccgcaagcaaaagattcactgattcaaaaaggaattcaaattctcgagaa
ggacaaaatgattgacccgaatatggtagatgacgaggatgaaagttttaatgggcctat
tgaagattatatggaacatttggaacatgaaattttgaaaataacaaagatgattgatca
agcagaggacaagattcagaaatcaaaccagaaaatgaagacacggctatttggaatgga
aatggaccttgttcacgagata

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GCGGCTATTGTATGAGCTAATTTTG 420 287 1516 Antisense
TTGCAGCTCCGAGTATACAGCCCAA 166 703 1544 Antisense
TACAGCCCAATGGATTATATCTGCA 423 643 1559 Antisense
GATTTTTGTAACTCTACCGGCAGGC 368 421 1660 Antisense
ACCGGCAGGCTTTGTATTTGGAGAA 521 87 1675 Antisense
GAACTTTCCATTCTAAACATACCTG 525 349 1697 Antisense
GAACTGCTTCTGTTAGATCCAAGGG 398 347 1743 Antisense
GATATTCTGATCTTTATGTTCTCGA 397 427 1767 Antisense
GGGAGGCTCTTCATGAATATCCGCA 96 497 1806 Antisense
TGAAGACACGGCTATTTGGAATGGA 536 573 2031 Antisense
GGAAATGGACCTTGTTCACGAGATA 147 527 2053 Antisense
Sequence Source Affymetrix Proprietary Database