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[192518_at] calcium channel subunit

Description T28F2.5 /REP_DB=WormBase Gene ID /WP=CE14359 /GEN=ccb-1 /TR=O01661 /GB=AAB53056.1 /SUBMIT=ST.LOUIS /CHR=1 /FEA=Sanger Annotation /DEF=calcium channel subunit
Cluster 6grp_highest_10_10 > 20      6grp_high1_10_10 > 05      4grp_highest_8_8 > 48      4grp_high_8_8 > 42      6grp_highest_nonorm > 50      6grp_total > 04      4grp_total > 45      6grp_highest_sub > De      6grp_cgc > 31      6grp_high1_sub > De      6grp_cgc_sub > De      6grp_rule_based > S1      4grp_rule_based > L1      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 480
1 2 3 4 range
A 718.6
(3)
P 		582.9
(1)
P 		467.7
(-0.6)
P 		302.1
(-3)
P 		417
B 730
(3)
P 		511.1
(-0.2)
P 		375.2
(-2.2)
P 		322.4
(-3)
P 		408
C 687
(3)
P 		487.8
(0.3)
P 		397.9
(-1)
P 		249.6
(-3)
P 		437
avr 711.9
(3) 		527.3
(0.4) 		413.6
(-1.3) 		291.4
(-3) 		421

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 560
1 2 3 4 5 6 range
A 760.4
(3)
P 		560.3
(0.8)
P 		398.8
(-1)
P 		422.9
(-0.7)
P 		383.1
(-1.2)
P 		217.1
(-3)
P 		543
B 664.3
(3)
P 		585.5
(2)
P 		500.6
(0.9)
P 		428.8
(-0)
P 		338.3
(-1.2)
P 		200.5
(-3)
P 		464
C 755.7
(3)
P 		526.1
(0.4)
P 		489.1
(0)
P 		455.3
(-0.3)
P 		441.6
(-0.5)
P 		217.2
(-3)
P 		539
avr 726.8
(3) 		557.3
(1) 		462.8
(-0.1) 		435.7
(-0.4) 		387.7
(-0.9) 		211.6
(-3) 		515
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 220
1 2 3 4 range
A 261.6
(3)
P 		126.5
(-0.7)
P 		122.3
(-0.8)
P 		44.2
(-3)
P 		217
B 232.8
(3)
P 		126.2
(-0.9)
P 		86.9
(-2.3)
P 		68.7
(-3)
P 		164
C 227.4
(3)
P 		140.2
(0.2)
P 		138.7
(0.1)
P 		42.1
(-3)
P 		185
avr 240.6
(3) 		131
(-0.5) 		116
(-1) 		51.7
(-3) 		189

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 227
1 2 3 4 5 6 range
A 140.2
(0.6)
P 		199.3
(3)
P 		86.9
(-1.6)
P 		107.3
(-0.8)
P 		115.6
(-0.4)
P 		52.9
(-3)
P 		146
B 231.1
(3)
P 		194.9
(1.6)
P 		121.5
(-1.2)
P 		113.6
(-1.5)
P 		137.4
(-0.6)
P 		74.8
(-3)
P 		156
C 280.1
(3)
P 		160.5
(-0.5)
P 		124.5
(-1.5)
P 		91.6
(-2.5)
P 		142.9
(-1)
P 		72.7
(-3)
P 		207
avr 217.1
(3) 		184.9
(1.7) 		111
(-1.2) 		104.2
(-1.5) 		132
(-0.4) 		66.8
(-3) 		150
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 192518_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.205
Sequence Type Exemplar sequence
Representative Public ID T28F2.5 NCBI
Target Description T28F2.5 /REP_DB=WormBase Gene ID /WP=CE14359 /GEN=ccb-1 /TR=O01661 /GB=AAB53056.1 /SUBMIT=ST.LOUIS /CHR=1 /FEA=Sanger Annotation /DEF=calcium 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_058792(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_058792 NCBI Caenorhabditis elegans Calcium Channel, Beta subunit family member (ccb-1) (ccb-1) mRNA, complete cds. 11/11 None
SNAP00000038905 ENSEMBL cdna:SNAP chromosome:CEL140:I:3641960:3646883:-1 11/11 None
GENEFINDER00000038916 ENSEMBL cdna:GeneFinder chromosome:CEL140:I:3641960:3648665:-1 11/11 None
T28F2.5 ENSEMBL cdna:known chromosome:CEL140:I:3641606:3647011:-1 gene:T28F2.5 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
chrI:3641605-3646252(-) 98.94 98.94
Public Domain and Genome References
Gene Title calcium channel subunit
Gene Symbol ccb-1
Ensembl T28F2.5
Entrez Gene 171933 Entrez gene
SwissProt O01661 EMBL-EBI
WormBase CE14359 Wormbase
Functional Annotations
Ortholog
ID Title Organism
CANINE:1604893_AT similar to calcium channel, voltage-dependent, beta 2 subunit isoform 7 cfa
CANINE_2:CFA.2667.1.S1_S_AT similar to calcium channel, voltage-dependent, beta 2 subunit isoform 7 cfa
CANINE_2:CFAAFFX.7664.1.S1_S_AT similar to calcium channel, voltage-dependent, beta 2 subunit isoform 7 cfa
CANINE_2:CFAAFFX.7670.1.S1_AT similar to calcium channel, voltage-dependent, beta 2 subunit isoform 7 cfa
DROSOPHILA_2:1638440_AT Ca2+-channel-protein-subunit dm
DROSOPHILA_2:1628331_AT Ca2+-channel-protein-subunit dm
DROSGENOME1:152671_AT Ca2+-channel-protein-subunit dm
CHICKEN:GGAAFFX.5412.1.S1_S_AT similar to cardiac calcium channel beta-subunit CaB2a (splice variant of the gene CaB2 gga
CHICKEN:GGAAFFX.5412.3.S1_S_AT similar to cardiac calcium channel beta-subunit CaB2a (splice variant of the gene CaB2 gga
HG-U95AV2:39647_S_AT calcium channel, voltage-dependent, beta 2 subunit hs
HG-U133_PLUS_2:215365_AT calcium channel, voltage-dependent, beta 2 subunit hs
HG-U133A_2:215365_AT calcium channel, voltage-dependent, beta 2 subunit hs
HG-U133A:215365_AT calcium channel, voltage-dependent, beta 2 subunit hs
HG-U133_PLUS_2:213714_AT calcium channel, voltage-dependent, beta 2 subunit hs
HG-U133A_2:213714_AT calcium channel, voltage-dependent, beta 2 subunit hs
HG-U133A:213714_AT calcium channel, voltage-dependent, beta 2 subunit hs
HG-U133_PLUS_2:207776_S_AT calcium channel, voltage-dependent, beta 2 subunit hs
HG-U133A:207776_S_AT calcium channel, voltage-dependent, beta 2 subunit hs
HG-FOCUS:207776_S_AT calcium channel, voltage-dependent, beta 2 subunit hs
HG-U133A_2:207776_S_AT calcium channel, voltage-dependent, beta 2 subunit hs
HU35KSUBA:HUM_ALU_AT calcium channel, voltage-dependent, beta 2 subunit hs
HU35KSUBB:HUM_ALU_AT calcium channel, voltage-dependent, beta 2 subunit hs
HU35KSUBC:HUM_ALU_AT calcium channel, voltage-dependent, beta 2 subunit hs
HU35KSUBD:HUM_ALU_AT calcium channel, voltage-dependent, beta 2 subunit hs
HUGENEFL:HUM_ALU_AT calcium channel, voltage-dependent, beta 2 subunit hs
HC-G110:HUM_ALU_AT calcium channel, voltage-dependent, beta 2 subunit hs
HU35KSUBC:RC_AA039933_S_AT calcium channel, voltage-dependent, beta 2 subunit hs
HUGENEFL:U95019_S_AT calcium channel, voltage-dependent, beta 2 subunit hs
HUGENEFL:S60415_AT calcium channel, voltage-dependent, beta 2 subunit hs
U133_X3P:G4502532_3P_A_AT calcium channel, voltage-dependent, beta 2 subunit hs
U133_X3P:HS2.375676.1.S1_3P_X_AT calcium channel, voltage-dependent, beta 2 subunit hs
U133_X3P:HS2.375676.1.S1_3P_AT calcium channel, voltage-dependent, beta 2 subunit hs
U133_X3P:HS2.30941.2.S1_3P_S_AT calcium channel, voltage-dependent, beta 2 subunit hs
U133_X3P:HS.30941.1.A2_3P_AT calcium channel, voltage-dependent, beta 2 subunit hs
U133_X3P:HS.287522.0.S1_3P_X_AT calcium channel, voltage-dependent, beta 2 subunit hs
U133_X3P:HS.287522.0.S1_3P_AT calcium channel, voltage-dependent, beta 2 subunit hs
U133_X3P:215365_3P_AT calcium channel, voltage-dependent, beta 2 subunit hs
U133_X3P:1559419_3P_AT calcium channel, voltage-dependent, beta 2 subunit hs
HG-U133_PLUS_2:1555098_A_AT calcium channel, voltage-dependent, beta 2 subunit hs
HG-U133_PLUS_2:1559419_AT calcium channel, voltage-dependent, beta 2 subunit hs
HG-U133_PLUS_2:1559420_X_AT calcium channel, voltage-dependent, beta 2 subunit hs
HG-U95AV2:39646_AT calcium channel, voltage-dependent, beta 2 subunit hs
HG-U133_PLUS_2:237698_AT Calcium channel, voltage-dependent, beta 2 subunit hs
HG-U133B:237698_AT Calcium channel, voltage-dependent, beta 2 subunit hs
HG-U95C:50475_AT Calcium channel, voltage-dependent, beta 2 subunit hs
HG-U95E:71573_AT Calcium channel, voltage-dependent, beta 2 subunit hs
HG-U95D:73882_AT Calcium channel, voltage-dependent, beta 2 subunit hs
U133_X3P:HS.231951.0.A1_3P_AT Calcium channel, voltage-dependent, beta 2 subunit hs
MOUSE430_2:1452476_AT calcium channel, voltage-dependent, beta 2 subunit mm
MOE430A:1452476_AT calcium channel, voltage-dependent, beta 2 subunit mm
MOUSE430A_2:1452476_AT calcium channel, voltage-dependent, beta 2 subunit mm
MU11KSUBB:MSA.499.0_AT calcium channel, voltage-dependent, beta 2 subunit mm
MG-U74AV2:100757_AT calcium channel, voltage-dependent, beta 2 subunit mm
MOE430B:1456401_AT calcium channel, voltage-dependent, beta 2 subunit mm
MOUSE430_2:1456401_AT calcium channel, voltage-dependent, beta 2 subunit mm
MOE430B:1441521_AT Calcium channel, voltage-dependent, beta 2 subunit (Cacnb2), mRNA mm
MOUSE430_2:1441521_AT Calcium channel, voltage-dependent, beta 2 subunit (Cacnb2), mRNA mm
MOE430B:1446632_AT Calcium channel, voltage-dependent, beta 2 subunit (Cacnb2), mRNA mm
MOUSE430_2:1446632_AT Calcium channel, voltage-dependent, beta 2 subunit (Cacnb2), mRNA mm
MOE430B:1444693_AT Calcium channel, voltage-dependent, beta 2 subunit (Cacnb2), mRNA mm
MOUSE430_2:1444693_AT Calcium channel, voltage-dependent, beta 2 subunit (Cacnb2), mRNA mm
MU19KSUBA:TC23032_AT Calcium channel, voltage-dependent, beta 2 subunit (Cacnb2), mRNA mm
MU19KSUBB:TC32775_AT Calcium channel, voltage-dependent, beta 2 subunit (Cacnb2), mRNA mm
RN-U34:M80545_AT calcium channel, voltage-dependent, beta 2 subunit rn
RG-U34A:M80545_AT calcium channel, voltage-dependent, beta 2 subunit rn
RAE230A:1388023_A_AT calcium channel, voltage-dependent, beta 2 subunit rn
RAT230_2:1388023_A_AT calcium channel, voltage-dependent, beta 2 subunit rn
RAE230A:1370178_AT calcium channel, voltage-dependent, beta 2 subunit rn
RAT230_2:1370178_AT calcium channel, voltage-dependent, beta 2 subunit rn
RAE230B:1395263_AT Calcium channel, voltage-dependent, beta 2 subunit rn
RAT230_2:1395263_AT Calcium channel, voltage-dependent, beta 2 subunit rn
Gene Ontology
GO Biological Process (view graph)
ID Description Evidence Links
6816 calcium ion transport inferred from electronic annotation QuickGO AmiGO
GO Molecular Function (view graph)
ID Description Evidence Links
5245 voltage-gated calcium channel activity inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast AAB53056 Calcium channel, beta subunit protein 1 [Caenorhabditis elegans] ref|NP_491193.1| Calcium Channel, Beta subunit family member (ccb-1) [Caenorhabditis elegans] 0.0
blast CAE66649 Hypothetical protein CBG11986 [Caenorhabditis briggsae] 0.0
blast AAO83844 voltage-dependent calcium channel beta subunit [Lymnaea stagnalis] 1.0E-152
Protein Domains
Database ID Description E-Value
Pfam IPR000584 EMBL-EBI Dihydropyridine sensitive L-type calcium channel, beta subunit 1.0E-126
Pfam IPR000584 EMBL-EBI Dihydropyridine sensitive L-type calcium channel, beta subunit 1.0E-126
Sequence
Target Sequence 
>C. ELEGANS:192518_AT
aaaagctggcccagtgccaagcagagctcttcgacgttctgctcgacgagaatcaactgg
aagatgcgtgtgagcatcttgcagattttatggaagcctactggagagccacacatccgc
cagtcaggtcaccgcctagaataaaaagaaatccaatggaaaaccgaggaccgagcacgt
tgttcacgccggcgcagatgatgcagggtttccaaggaaacgccggtcaactgccaccgc
aactccaacctcaacaatccatagcctcaatgtcacaaatgggtggaccaatgggatcca
tgaatcctccgtacttggcacccccaatgcaaagtggtcgtccaggaatgccaagtataa
gtgtacaacaggcaactggttcctacggtggaatgcagcagcaaccacaacagcaacaac
caatgcaatcagctccacc

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
AAAAGCTGGCCCAGTGCCAAGCAGA 255 131 1052 Antisense
TGCCAAGCAGAGCTCTTCGACGTTC 443 585 1066 Antisense
TGGAAGCCTACTGGAGAGCCACACA 414 547 1142 Antisense
CCAGTCAGGTCACCGCCTAGAATAA 620 271 1171 Antisense
GTTCACGCCGGCGCAGATGATGCAG 193 445 1233 Antisense
TCCAAGGAAACGCCGGTCAACTGCC 107 585 1262 Antisense
AACAATCCATAGCCTCAATGTCACA 271 135 1304 Antisense
ATGGGATCCATGAATCCTCCGTACT 185 51 1342 Antisense
GCACCCCCAATGCAAAGTGGTCGTC 531 315 1369 Antisense
ACAGGCAACTGGTTCCTACGGTGGA 480 93 1419 Antisense
AACAACCAATGCAATCAGCTCCACC 367 135 1466 Antisense
Sequence Source Affymetrix Proprietary Database