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[173570_s_at] calcium channel subunit /// ---

Description C55100_rc /REP_DB=TREMBL Accession /5_PRIME_EXT_ID=F17C8.6 /5_PRIME_EXT_DB=WormBase Gene ID /GB=C55100 /WB_GENE_ID=F17C8.6 /WP=CE00960 /CHR=3 /FEA=Genomic Cluster /DEF=C.elegans cDNA clone yk429b4 : 3prime end, single read.
Cluster 6grp_highest_10_10 > 41      6grp_high1_10_10 > 15      4grp_highest_8_8 > 52      4grp_high_8_8 > 16      6grp_highest_nonorm > 80      6grp_total > 15      4grp_total > 39      6grp_highest_sub > De      6grp_cgc > 23      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.
4 310
1 2 3 4 range
A 374.5
(3)
P 		97.1
(-2.8)
P 		85.6
(-3)
P 		196.2
(-0.7)
P 		289
B 265.2
(3)
P 		64.3
(-3)
P 		89.1
(-2.3)
P 		158.7
(-0.2)
P 		201
C 330.8
(3)
P 		75.1
(-3)
P 		82.7
(-2.8)
P 		148.9
(-1.3)
P 		256
avr 323.5
(3) 		78.8
(-3) 		85.8
(-2.8) 		167.9
(-0.8) 		245

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 270
1 2 3 4 5 6 range
A 258.6
(3)
P 		231.6
(2.1)
P 		178.2
(0.4)
P 		173.3
(0.2)
P 		103.5
(-2.1)
P 		74.7
(-3)
P 		184
B 344.5
(3)
P 		300.1
(1.8)
P 		149.8
(-2.3)
P 		178.9
(-1.5)
P 		134.5
(-2.7)
P 		123.3
(-3)
P 		221
C 289.3
(3)
P 		265.3
(2.2)
P 		160.9
(-1.5)
P 		130.6
(-2.6)
P 		119.6
(-3)
P 		132.6
(-2.5)
P 		170
avr 297.5
(3) 		265.7
(2) 		163
(-1.3) 		160.9
(-1.4) 		119.2
(-2.7) 		110.2
(-3) 		187
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 121
1 2 3 4 range
A 136.4
(3)
P 		21.1
(-3)
P 		22.4
(-2.9)
P 		28.7
(-2.6)
P 		115
B 84.6
(3)
P 		15.9
(-3)
P 		20.6
(-2.6)
P 		33.8
(-1.4)
P 		69
C 109.5
(3)
P 		21.6
(-3)
P 		28.8
(-2.5)
P 		25.1
(-2.8)
P 		88
avr 110.2
(3) 		19.5
(-3) 		23.9
(-2.7) 		29.2
(-2.4) 		91

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 102
1 2 3 4 5 6 range
A 47.7
(-0.2)
P 		82.4
(3)
P 		38.8
(-1.1)
P 		43.9
(-0.6)
P 		31.2
(-1.8)
P 		18.2
(-3)
P 		64
B 119.9
(3)
P 		99.9
(1.6)
P 		36.4
(-3)
P 		47.4
(-2.2)
P 		54.6
(-1.7)
P 		46
(-2.3)
P 		84
C 107.2
(3)
P 		80.9
(1)
P 		40.9
(-1.9)
P 		26.3
(-3)
P 		38.7
(-2.1)
P 		44.4
(-1.7)
P 		81
avr 91.6
(3) 		87.7
(2.6) 		38.7
(-2.7) 		39.2
(-2.7) 		41.5
(-2.4) 		36.2
(-3) 		55
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 173570_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.23846
Sequence Type Exemplar sequence
Representative Public ID C55100 NCBI
Target Description C55100_rc /REP_DB=TREMBL Accession /5_PRIME_EXT_ID=F17C8.6 /5_PRIME_EXT_DB=WormBase Gene ID /GB=C55100 /WB_GENE_ID=F17C8.6 /WP=CE00960 /CHR=3 /FEA=Genomic Cluster /DEF=C.elegans cDNA clone yk429b4 : 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_065573(11), NM_065653(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_065573 NCBI Caenorhabditis elegans F17C8.6 (F17C8.6) mRNA, complete cds. 11/11 None
NM_065653 NCBI Caenorhabditis elegans Novel Channel type/putative Nematode CAlcium channel family member (nca-2) (nca-2) mRNA, complete cds. 11/11 None
SNAP00000012149 ENSEMBL cdna:SNAP chromosome:CEL140:III:4744832:4745987:-1 11/11 None
GENEFINDER00000012156 ENSEMBL cdna:GeneFinder chromosome:CEL140:III:4744832:4745987:-1 11/11 None
GENEFINDER00000001024 ENSEMBL cdna:GeneFinder chromosome:CEL140:III:4970209:4979536:1 11/11 None
SNAP00000001014 ENSEMBL cdna:SNAP chromosome:CEL140:III:4971288:4979536:1 11/11 None
F17C8.6 ENSEMBL cdna:known chromosome:CEL140:III:4744832:4745987:-1 gene:F17C8.6 11/11 None
C27F2.2 ENSEMBL cdna:known chromosome:CEL140:III:4965531:4979690:1 gene:C27F2.2 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
chrIII:4978332-4979612(+) 99.56 99.56
chrIII:4744754-4745988(-) 100.0 100.0
Public Domain and Genome References
Gene Title calcium channel subunit

Gene Symbol nca-2
Ensembl F17C8.6
C27F2.2
Entrez Gene 175626 Entrez gene
175674 Entrez gene
SwissProt Q19526 EMBL-EBI
WormBase CE38941 Wormbase
CE00960 Wormbase
Functional Annotations
Ortholog
ID Title Organism
CANINE_2:CFAAFFX.9832.1.S1_AT similar to voltage gated channel like 1 cfa
CANINE_2:CFAAFFX.9835.1.S1_S_AT similar to voltage gated channel like 1 cfa
DROSOPHILA_2:1635546_A_AT narrow abdomen dm
DROSGENOME1:145060_AT narrow abdomen dm
CHICKEN:GGAAFFX.10801.1.S1_AT similar to bA430M15.1 (novel protein (ortholog of rat four repeat ion channel)) gga
CHICKEN:GGAAFFX.10801.3.S1_S_AT similar to bA430M15.1 (novel protein (ortholog of rat four repeat ion channel)) gga
CHICKEN:GGAAFFX.10801.7.S1_AT similar to bA430M15.1 (novel protein (ortholog of rat four repeat ion channel)) gga
HU35KSUBB:RC_AA157945_AT voltage gated channel like 1 hs
U133_X3P:HS2.367949.2.S1_3P_AT voltage gated channel like 1 hs
U133_X3P:HS.279224.0.A1_3P_S_AT voltage gated channel like 1 hs
HG-U133_PLUS_2:1554702_AT voltage gated channel like 1 hs
HG-U133_PLUS_2:242880_AT voltage gated channel like 1 hs
HG-U133B:242880_AT voltage gated channel like 1 hs
HG-U133_PLUS_2:232828_AT Voltage gated channel like 1 hs
HG-U133B:232828_AT Voltage gated channel like 1 hs
HU35KSUBC:RC_N63403_AT Voltage gated channel like 1 hs
U133_X3P:HS.45080.0.S1_3P_AT Voltage gated channel like 1 hs
U133_X3P:HS.133142.0.S1_3P_AT Voltage gated channel like 1 hs
HG-U133_PLUS_2:228608_AT Voltage gated channel like 1 hs
HG-U133B:228608_AT Voltage gated channel like 1 hs
HG-U95B:51064_AT Voltage gated channel like 1 hs
HG-U95AV2:31753_AT Voltage gated channel like 1 hs
YEAST_2:1772170_AT Voltage-gated calcium channel involved in calcium influx in response to mating pheromones Sc
Protein Similarities
Method ID Description E-Value
blast NP_498054 Novel Channel type/putative Nematode CAlcium channel family member (nca-2) [Caenorhabditis elegans] 0.0
blast AAS65872 four domain-type voltage-gated ion channel alpha-1 subunit [Caenorhabditis elegans] gb|AAA81424.3| Novel channel type/putative nematode calcium channel protein 2 [Caenorhabditis elegans] 0.0
blast CAE71314 Hypothetical protein CBG18206 [Caenorhabditis briggsae] 0.0
Protein Domains
Database ID Description E-Value
Pfam IPR005821 EMBL-EBI Ion transport protein 5.7E-34
Pfam IPR005821 EMBL-EBI Ion transport protein 7.2E-36
Pfam IPR005821 EMBL-EBI Ion transport protein 1.3E-38
Pfam IPR005821 EMBL-EBI Ion transport protein 1.1E-35
Pfam IPR005821 EMBL-EBI Ion transport protein 1.3E-30
Pfam IPR005821 EMBL-EBI Ion transport protein 7.2E-36
Pfam IPR005821 EMBL-EBI Ion transport protein 1.3E-38
Pfam IPR005821 EMBL-EBI Ion transport protein 1.1E-35
Pfam IPR005821 EMBL-EBI Ion transport protein 1.4E-29
Pfam IPR005821 EMBL-EBI Ion transport protein 7.2E-36
Pfam IPR005821 EMBL-EBI Ion transport protein 5.8E-20
Pfam IPR005821 EMBL-EBI Ion transport protein 1.1E-35
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_498054.1 20 7-29,61-83,125-147,238-260,317-339,359-378,399-421,453-475,518-540,821-843,856-878,893-915,960-982,1076-1098,1153-1175,1185-1207,1227-1249,1259-1277,1298-1320,1384-1406
C27F2.2 20 7-29,61-83,125-147,238-260,317-339,359-378,399-421,453-475,518-540,821-843,856-878,893-915,960-982,1076-1098,1153-1175,1185-1207,1227-1249,1259-1277,1298-1320,1384-1406
GENEFINDER00000001024 20 84-106,126-148,209-231,322-344,401-423,443-462,483-505,537-559,602-624,905-927,940-962,977-999,1044-1066,1160-1182,1237-1259,1269-1291,1311-1333,1343-1361,1382-1404,1468-1490
SNAP00000001014 18 29-51,72-94,99-121,134-156,247-269,326-348,368-390,459-481,530-552,876-898,908-930,1031-1053,1112-1131,1138-1160,1180-1202,1214-1231,1251-1273,1339-1361
Sequence
Target Sequence 
>C. ELEGANS:173570_S_AT
gcaaagcacactattcgggcgtggctagagaattgtttgaaaaacatcaaagccaagcag
aataagactcttggaaaaatgagctcaattgggtcaacatttgcatttccacaatctcaa
gaagtattaacaaaaggagttgtgctcacggaggcttctcctgaagaagattcattgcaa
ggagataagggcagtggaaagaagaaggctcagagaggcaactctattacagagatagtg
gcagaagcgcaaaagaaaagtgtaaaacgagcaactgataaaataagtgaacgtcgtgga
acacttcgtcaaatgcaaatgggaacatatgatgaattggaagaagttgaagaagacgaa
gatactgacggagaaatcagaagatcatcatttgaatattcaggagttgatatgattcaa
atgtcacatgaaaaacaactggaagatgtgaaaacttggtggacgttgtgtgat

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GCAAAGCACACTATTCGGGCGTGGC 32 317 377 Antisense
CGGGCGTGGCTAGAGAATTGTTTGA 125 241 392 Antisense
GAGCTCAATTGGGTCAACATTTGCA 680 387 457 Antisense
TCAACATTTGCATTTCCACAATCTC 125 631 470 Antisense
AAGGAGTTGTGCTCACGGAGGCTTC 459 159 510 Antisense
TGCTCACGGAGGCTTCTCCTGAAGA 195 581 519 Antisense
GAAGGCTCAGAGAGGCAACTCTATT 694 331 580 Antisense
TTACAGAGATAGTGGCAGAAGCGCA 703 681 603 Antisense
GTGAACGTCGTGGAACACTTCGTCA 609 481 663 Antisense
GGAACACTTCGTCAAATGCAAATGG 309 529 674 Antisense
GAAAACTTGGTGGACGTTGTGTGAT 262 355 826 Antisense
Sequence Source Affymetrix Proprietary Database