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[193918_at]

Description C54D2.5 /REP_DB=WormBase Gene ID /WP=CE02562 /GEN=cca-1 /TR=Q18840 /GB=AAA79201.1 /SUBMIT=ST.LOUIS /CHR=X /FEA=Sanger Annotation /DEF=Skeletal muscle calcium channel alpha-1 subunit
Cluster 6grp_highest_10_10 > 41      6grp_high1_10_10 > 15      4grp_highest_8_8 > 59      4grp_high_8_8 > 25      6grp_highest_nonorm > 80      6grp_total > 15      4grp_total > 38      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.
4 277
1 2 3 4 range
A 368.1
(3)
P 		127.1
(-2.5)
P 		104.3
(-3)
P 		216.6
(-0.4)
P 		264
B 296.8
(3)
P 		195.6
(0)
P 		91.4
(-3)
P 		169.6
(-0.7)
P 		205
C 309.5
(3)
P 		149.5
(-1.9)
P 		112.5
(-3)
P 		136.6
(-2.3)
P 		197
avr 324.8
(3) 		157.4
(-1.5) 		102.7
(-3) 		174.3
(-1.1) 		222

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 195
1 2 3 4 5 6 range
A 180.2
(-0.3)
P 		275
(3)
P 		136.8
(-1.8)
P 		141
(-1.6)
P 		101.1
(-3)
P 		128.4
(-2.1)
P 		174
B 270.7
(3)
P 		213.4
(1.1)
P 		93.1
(-2.8)
P 		142.4
(-1.2)
P 		172.6
(-0.2)
P 		85.5
(-3)
P 		185
C 280.1
(3)
P 		223.5
(1.2)
P 		195
(0.2)
P 		145.5
(-1.4)
P 		112.9
(-2.4)
P 		94.9
(-3)
P 		185
avr 243.7
(3) 		237.3
(2.7) 		141.6
(-1.4) 		143
(-1.3) 		128.9
(-1.9) 		102.9
(-3) 		141
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 113
1 2 3 4 range
A 134
(3)
P 		27.6
(-3)
P 		27.3
(-3)
P 		31.7
(-2.8)
P 		107
B 94.6
(3)
P 		48.3
(-0.8)
P 		21.2
(-3)
P 		36.1
(-1.8)
P 		73
C 102.5
(3)
P 		43
(-1.5)
P 		39.2
(-1.8)
P 		23
(-3)
P 		80
avr 110.4
(3) 		39.6
(-2.2) 		29.2
(-3) 		30.3
(-2.9) 		81

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 81
1 2 3 4 5 6 range
A 33.2
(-2.7)
P 		97.8
(3)
P 		29.8
(-3)
P 		35.8
(-2.5)
P 		30.5
(-2.9)
P 		31.3
(-2.9)
P 		68
B 94.2
(3)
P 		71
(1.1)
P 		22.6
(-3)
P 		37.7
(-1.7)
P 		70.1
(1)
P 		31.9
(-2.2)
P 		72
C 103.8
(3)
P 		68.2
(0.1)
P 		49.6
(-1.4)
P 		29.3
(-3)
P 		36.5
(-2.4)
P 		31.8
(-2.8)
P 		75
avr 77.1
(2.8) 		79
(3) 		34
(-2.7) 		34.3
(-2.7) 		45.7
(-1.2) 		31.7
(-3) 		47
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 193918_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.16619
Sequence Type Exemplar sequence
Representative Public ID C54D2.5 NCBI
Target Description C54D2.5 /REP_DB=WormBase Gene ID /WP=CE02562 /GEN=cca-1 /TR=Q18840 /GB=AAA79201.1 /SUBMIT=ST.LOUIS /CHR=X /FEA=Sanger Annotation /DEF=Skeletal muscle calcium channel alpha-1 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_001029327(11), NM_001029325(11), NM_171733(11), NM_001029326(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_001029327 NCBI Caenorhabditis elegans Calcium Channel, Alpha subunit family member (cca-1) (cca-1) mRNA, complete cds. 11/11 None
NM_001029325 NCBI Caenorhabditis elegans Calcium Channel, Alpha subunit family member (cca-1) (cca-1) mRNA, complete cds. 11/11 None
NM_171733 NCBI Caenorhabditis elegans Calcium Channel, Alpha subunit family member (cca-1) (cca-1) mRNA, complete cds. 11/11 None
NM_001029326 NCBI Caenorhabditis elegans Calcium Channel, Alpha subunit family member (cca-1) (cca-1) mRNA, complete cds. 11/11 None
SNAP00000030444 ENSEMBL cdna:SNAP chromosome:CEL140:X:7848164:7857543:-1 11/11 None
GENEFINDER00000030451 ENSEMBL cdna:GeneFinder chromosome:CEL140:X:7848164:7860022:-1 11/11 None
C54D2.5a ENSEMBL cdna:known chromosome:CEL140:X:7847625:7861248:-1 gene:C54D2.5 11/11 None
C54D2.5d ENSEMBL cdna:known chromosome:CEL140:X:7847625:7861248:-1 gene:C54D2.5 11/11 None
C54D2.5e ENSEMBL cdna:known chromosome:CEL140:X:7847625:7861248:-1 gene:C54D2.5 11/11 None
C54D2.5c ENSEMBL cdna:known chromosome:CEL140:X:7847625:7861248:-1 gene:C54D2.5 11/11 None
Annotation Notes
There are no noteworthy cross hybridizing mRNAs found for this probe set.
Splice Variants
Entrez Total Refseq Isoforms Total Detected By This Probeset Refseq Probesets
181045 6 4 NM_001029325 193918_at (11)
NM_001029326 193918_at (11)
NM_001029327 193918_at (11)
NM_171733 193918_at (11)
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrX:7849505-7861119(-) 100.0 100.0
Public Domain and Genome References
Ensembl C54D2.5
Functional Annotations
Protein Similarities
Method ID Description E-Value
blast AAR25653 Calcium channel, alpha subunit protein 1, isoform e [Caenorhabditis elegans] ref|NP_001024498.1| Calcium Channel, Alpha subunit family member (cca-1) [Caenorhabditis elegans] gb|AAP84337.1| T-type voltage sensitive calcium channel alpha1 subunit isoform D [Caenorhabditis elegans] 0.0
blast AAR25652 Calcium channel, alpha subunit protein 1, isoform d [Caenorhabditis elegans] ref|NP_001024497.1| Calcium Channel, Alpha subunit family member (cca-1) [Caenorhabditis elegans] gb|AAP79882.1| T-type calcium channel alpha1 subunit isoform B [Caenorhabditis elegans] 0.0
blast AAM51534 Calcium channel, alpha subunit protein 1, isoform a [Caenorhabditis elegans] ref|NP_741848.1| Calcium Channel, Alpha subunit family member (cca-1) [Caenorhabditis elegans] gb|AAP79881.1| T-type calcium channel alpha1 subunit isoform A [Caenorhabditis elegans] gb|AAK53427.1| voltage-dependent calcium channel alpha13 subunit [Caenorhabditis elegans] 0.0
blast AAR25651 Calcium channel, alpha subunit protein 1, isoform c [Caenorhabditis elegans] ref|NP_001024496.1| Calcium Channel, Alpha subunit family member (cca-1) [Caenorhabditis elegans] gb|AAP79883.1| T-type calcium channel alpha1 subunit isoform C [Caenorhabditis elegans] 0.0
Protein Domains
Database ID Description E-Value
Pfam IPR005821 EMBL-EBI Ion transport protein 8.3E-57
Pfam IPR005821 EMBL-EBI Ion transport protein 1.1E-47
Pfam IPR005821 EMBL-EBI Ion transport protein 1.1E-63
Pfam IPR005821 EMBL-EBI Ion transport protein 3.6E-56
Pfam IPR005821 EMBL-EBI Ion transport protein 6.3E-47
Pfam IPR005821 EMBL-EBI Ion transport protein 1.1E-63
Pfam IPR005821 EMBL-EBI Ion transport protein 3.6E-56
Pfam IPR005821 EMBL-EBI Ion transport protein 5.1E-46
Pfam IPR005821 EMBL-EBI Ion transport protein 1.1E-63
Pfam IPR005821 EMBL-EBI Ion transport protein 3.6E-56
Pfam IPR005821 EMBL-EBI Ion transport protein 3.6E-56
Pfam IPR005821 EMBL-EBI Ion transport protein 4.1E-16
Pfam IPR005821 EMBL-EBI Ion transport protein 1.1E-47
Pfam IPR005821 EMBL-EBI Ion transport protein 1.1E-63
Pfam IPR005821 EMBL-EBI Ion transport protein 3.6E-56
Pfam IPR005821 EMBL-EBI Ion transport protein 1.9E-55
Pfam IPR005821 EMBL-EBI Ion transport protein 1.1E-47
Pfam IPR005821 EMBL-EBI Ion transport protein 3.6E-30
Pfam IPR005821 EMBL-EBI Ion transport protein 3.6E-56
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_001024498.1 19 131-153,174-196,268-290,391-413,428-450,655-672,692-714,775-797,861-883,1119-1137,1152-1174,1187-1209,1255-1277,1359-1381,1439-1461,1482-1504,1517-1539,1579-1601,1670-1692
NP_001024496.1 19 131-153,174-196,268-290,391-413,428-450,690-712,777-799,820-837,857-879,1112-1130,1145-1167,1180-1202,1248-1270,1352-1374,1447-1469,1490-1512,1525-1547,1587-1609,1678-1700
NP_741848.1 19 131-153,174-196,268-290,391-413,428-450,690-712,777-799,820-837,857-879,1112-1130,1145-1167,1180-1202,1248-1270,1352-1374,1432-1454,1475-1497,1510-1532,1572-1594,1663-1685
NP_001024497.1 19 131-153,174-196,268-290,391-413,428-450,690-712,775-797,823-840,902-924,1160-1178,1193-1215,1228-1250,1296-1318,1400-1422,1480-1502,1523-1545,1558-1580,1620-1642,1711-1733
C54D2.5a 19 131-153,174-196,268-290,391-413,428-450,690-712,777-799,820-837,857-879,1112-1130,1145-1167,1180-1202,1248-1270,1352-1374,1432-1454,1475-1497,1510-1532,1572-1594,1663-1685
C54D2.5d 19 131-153,174-196,268-290,391-413,428-450,690-712,775-797,823-840,902-924,1160-1178,1193-1215,1228-1250,1296-1318,1400-1422,1480-1502,1523-1545,1558-1580,1620-1642,1711-1733
C54D2.5e 19 131-153,174-196,268-290,391-413,428-450,655-672,692-714,775-797,861-883,1119-1137,1152-1174,1187-1209,1255-1277,1359-1381,1439-1461,1482-1504,1517-1539,1579-1601,1670-1692
C54D2.5c 19 131-153,174-196,268-290,391-413,428-450,690-712,777-799,820-837,857-879,1112-1130,1145-1167,1180-1202,1248-1270,1352-1374,1447-1469,1490-1512,1525-1547,1587-1609,1678-1700
SNAP00000030444 15 38-60,151-173,188-210,433-455,520-542,563-580,600-622,855-873,888-910,923-945,991-1013,1095-1117,1183-1205,1280-1302,1371-1393
GENEFINDER00000030451 14 151-173,246-268,386-408,423-445,685-707,772-794,815-832,852-874,1111-1133,1215-1237,1306-1328,1338-1360,1435-1457,1526-1548
Sequence
Target Sequence 
>C. ELEGANS:193918_AT
ctctcgaacttccaattaatccaacaatcattcgtgtcatgcgagtgctccggatagcca
gagttctgaaactgctgaaaatggccaaaggaattcgatcattgttggacacagtgggag
aagcgttgccccaggttggaaatctcgggtctctgttcttccttcttttcttcatatttg
ctgcacttggtgttgaactgtttggaaaactggagtgctctgaagatcatccgtgtgatg
gattaggagaacatgcgcattttaaaaattttggaatggcttttttaacactctttcgaa
tagcgacgggtgataattggaatggaattatgaaggatgccctccgtgatgactgtgatt
cctccgatcactgtgaaacaaactgctgcgttgatccaatcctggcaccatgcttcttcg
taattttcgtc

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
CTCTCGAACTTCCAATTAATCCAAC 160 231 4430 Antisense
TCATTCGTGTCATGCGAGTGCTCCG 574 619 4457 Antisense
AGTGCTCCGGATAGCCAGAGTTCTG 101 61 4473 Antisense
GAAGCGTTGCCCCAGGTTGGAAATC 463 169 4549 Antisense
TTCCTTCTTTTCTTCATATTTGCTG 284 701 4588 Antisense
TGGAGTGCTCTGAAGATCATCCGTG 410 549 4640 Antisense
TGGCTTTTTTAACACTCTTTCGAAT 191 537 4706 Antisense
TATGAAGGATGCCCTCCGTGATGAC 176 657 4758 Antisense
TGATTCCTCCGATCACTGTGAAACA 178 563 4785 Antisense
ACAAACTGCTGCGTTGATCCAATCC 669 111 4807 Antisense
ACCATGCTTCTTCGTAATTTTCGTC 239 85 4836 Antisense
Sequence Source Affymetrix Proprietary Database