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[174211_s_at]

Description C54214_rc /REP_DB=TREMBL Accession /GB=C54214 /CHR=4 /FEA=Genomic Cluster /DEF=C.elegans cDNA clone yk354d9 : 3prime end, single read.
Cluster 6grp_highest_10_10 > 52      6grp_high1_10_10 > 25      4grp_highest_8_8 > 51      4grp_high_8_8 > 25      6grp_highest_nonorm > 60      6grp_total > 15      4grp_total > 39      6grp_highest_sub > 01_02      6grp_cgc > 23      6grp_high1_sub > 01_02      6grp_cgc_sub > De      6grp_total_sub > Decrease      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 497
1 2 3 4 range
A 692
(3)
P 		222.1
(-2.8)
P 		208
(-3)
P 		241.4
(-2.6)
P 		484
B 681.7
(3)
P 		275.5
(-2)
P 		195.5
(-3)
P 		355
(-1)
P 		486
C 572.7
(3)
P 		314.6
(-2.5)
P 		291.4
(-3)
P 		363.5
(-1.5)
P 		281
avr 648.8
(3) 		270.7
(-2.4) 		231.6
(-3) 		320
(-1.7) 		417

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 431
1 2 3 4 5 6 range
A 571.8
(3)
P 		500.9
(1.8)
P 		262.1
(-2.2)
P 		316.2
(-1.3)
P 		332.7
(-1)
P 		213.6
(-3)
P 		358
B 607.1
(2.4)
P 		644.3
(3)
P 		266.1
(-3)
P 		353.1
(-1.6)
P 		283.9
(-2.7)
P 		290.2
(-2.6)
P 		378
C 506.2
(1.9)
P 		565.4
(3)
P 		289.8
(-2.1)
P 		331.2
(-1.3)
P 		238.7
(-3)
P 		276.6
(-2.3)
P 		327
avr 561.7
(2.8) 		570.2
(3) 		272.7
(-2.8) 		333.5
(-1.6) 		285.1
(-2.5) 		260.1
(-3) 		310
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 217
1 2 3 4 range
A 251.9
(3)
P 		48.2
(-2.6)
P 		54.4
(-2.5)
P 		35.3
(-3)
P 		217
B 217.4
(3)
P 		68
(-2.2)
P 		45.3
(-3)
P 		75.6
(-1.9)
P 		172
C 189.6
(3)
P 		90.5
(-1.6)
P 		101.6
(-1.1)
P 		61.3
(-3)
P 		128
avr 219.6
(3) 		68.9
(-2.6) 		67.1
(-2.6) 		57.4
(-3) 		162

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 163
1 2 3 4 5 6 range
A 105.4
(-0.5)
P 		178.1
(3)
P 		57.1
(-2.8)
P 		80.2
(-1.7)
P 		100.4
(-0.7)
P 		52
(-3)
P 		126
B 211.2
(2.9)
P 		214.5
(3)
P 		64.6
(-3)
P 		93.5
(-1.8)
P 		115.4
(-1)
P 		108.2
(-1.3)
P 		150
C 187.6
(3)
P 		172.5
(2.3)
P 		73.8
(-2.6)
P 		66.6
(-3)
P 		77.3
(-2.5)
P 		92.6
(-1.7)
P 		121
avr 168.1
(2) 		188.4
(3) 		65.2
(-3) 		80.1
(-2.3) 		97.7
(-1.4) 		84.3
(-2.1) 		123
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 174211_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.21643
Sequence Type Exemplar sequence
Representative Public ID C54214 NCBI
Target Description C54214_rc /REP_DB=TREMBL Accession /GB=C54214 /CHR=4 /FEA=Genomic Cluster /DEF=C.elegans cDNA clone yk354d9 : 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_171352(11), NM_171353(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_171352 NCBI Caenorhabditis elegans Novel Channel type/putative Nematode CAlcium channel family member (nca-1) (nca-1) mRNA, complete cds. 11/11 A 
NM_171353 NCBI Caenorhabditis elegans Novel Channel type/putative Nematode CAlcium channel family member (nca-1) (nca-1) mRNA, complete cds. 11/11 A 
SNAP00000030429 ENSEMBL cdna:SNAP chromosome:CEL140:IV:6157427:6158845:-1 11/11 None
GENEFINDER00000030436 ENSEMBL cdna:GeneFinder chromosome:CEL140:IV:6156964:6179312:-1 11/11 None
C11D2.6d ENSEMBL cdna:known chromosome:CEL140:IV:6157296:6173024:-1 gene:C11D2.6 11/11 A 
C11D2.6c ENSEMBL cdna:known chromosome:CEL140:IV:6157299:6171656:-1 gene:C11D2.6 11/11 A 
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
177379 4 2 NM_068525 188103_s_at (11)
NM_171352 174211_s_at (11), 183134_at (10), 188103_s_at (11)
NM_171353 174211_s_at (11), 183134_at (11), 188103_s_at (11)
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrIV:6157352-6157827(-) 100.0 100.0
Public Domain and Genome References
Ensembl C11D2.6
Functional Annotations
Protein Similarities
Method ID Description E-Value
blast AAU05590 Novel channel type/putative nematode calcium channel protein 1, isoform d [Caenorhabditis elegans] ref|NP_741413.2| Novel Channel type/putative Nematode CAlcium channel family member (nca-1) [Caenorhabditis elegans] 0.0
blast AAS65871 four domain-type voltage-gated ion channel alpha-1 subunit [Caenorhabditis elegans] 0.0
blast AAM81121 Novel channel type/putative nematode calcium channel protein 1, isoform c [Caenorhabditis elegans] ref|NP_741414.1| Novel Channel type/putative Nematode CAlcium channel family member (nca-1) [Caenorhabditis elegans] 0.0
Protein Domains
Database ID Description E-Value
Pfam IPR005821 EMBL-EBI Ion transport protein 7.8E-28
Pfam IPR005821 EMBL-EBI Ion transport protein 6.5E-34
Pfam IPR005821 EMBL-EBI Ion transport protein 2.8E-37
Pfam IPR005821 EMBL-EBI Ion transport protein 9.0E-30
Pfam IPR005821 EMBL-EBI Ion transport protein 7.8E-28
Pfam IPR005821 EMBL-EBI Ion transport protein 6.5E-34
Pfam IPR005821 EMBL-EBI Ion transport protein 2.8E-37
Pfam IPR005821 EMBL-EBI Ion transport protein 9.0E-30
Pfam IPR005821 EMBL-EBI Ion transport protein 7.8E-28
Pfam IPR005821 EMBL-EBI Ion transport protein 6.5E-34
Pfam IPR005821 EMBL-EBI Ion transport protein 2.8E-37
Pfam IPR005821 EMBL-EBI Ion transport protein 9.0E-30
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_741413.2 20 149-171,186-208,229-248,343-365,429-451,466-488,553-575,624-646,924-946,973-995,1002-1021,1066-1088,1150-1169,1184-1206,1261-1283,1298-1320,1333-1352,1367-1384,1404-1426,1490-1512
NP_741414.1 21 138-160,180-199,214-236,257-276,371-393,503-525,540-562,627-649,698-720,1005-1027,1054-1076,1083-1102,1147-1169,1231-1250,1265-1287,1342-1364,1379-1401,1414-1433,1448-1465,1485-1507,1571-1593
C11D2.6d 20 149-171,186-208,229-248,343-365,429-451,466-488,553-575,624-646,924-946,973-995,1002-1021,1066-1088,1150-1169,1184-1206,1261-1283,1298-1320,1333-1352,1367-1384,1404-1426,1490-1512
C11D2.6c 21 138-160,180-199,214-236,257-276,371-393,503-525,540-562,627-649,698-720,1005-1027,1054-1076,1083-1102,1147-1169,1231-1250,1265-1287,1342-1364,1379-1401,1414-1433,1448-1465,1485-1507,1571-1593
GENEFINDER00000030436 20 155-177,192-214,235-254,349-371,478-500,515-537,602-624,673-695,939-961,988-1010,1017-1036,1081-1103,1165-1184,1199-1221,1276-1298,1313-1335,1348-1367,1382-1399,1419-1441,1505-1527
Sequence
Target Sequence 
>C. ELEGANS:174211_S_AT
tccagctaaacgtctatgatctacctgacgtagaagaacgtggagaagattctccatttt
ctcccaaaaacttgtctgatgattttaatggagagcattcaccattggtgataactccat
ccttgcctgtaccaccgacacatggaagccctcgaccacttatgccatgtgaaacgacaa
aagatattgaaaaatggtggaattcccttgttgatta

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
TCCAGCTAAACGTCTATGATCTACC 518 587 24 Antisense
ACGTCTATGATCTACCTGACGTAGA 428 91 33 Antisense
GAGAAGATTCTCCATTTTCTCCCAA 613 391 66 Antisense
TTCTCCATTTTCTCCCAAAAACTTG 567 687 73 Antisense
TTCTCCCAAAAACTTGTCTGATGAT 520 693 82 Antisense
ATGGAGAGCATTCACCATTGGTGAT 68 53 111 Antisense
CATTGGTGATAACTCCATCCTTGCC 178 217 126 Antisense
GCCTGTACCACCGACACATGGAAGC 337 283 148 Antisense
CCTCGACCACTTATGCCATGTGAAA 250 267 173 Antisense
GACCACTTATGCCATGTGAAACGAC 593 383 177 Antisense
AATGGTGGAATTCCCTTGTTGATTA 620 161 216 Antisense
Sequence Source Affymetrix Proprietary Database