[Home] | [Total List]

[193572_at]

Description C10G8.5 /REP_DB=WormBase Gene ID /WP=CE20495 /CHR=5 /FEA=Sanger Annotation /DEF=locus:ncx-2 sodium-calcium exchanger protein 1 (ST.LOUIS) TR:Q94161 protein_id:AAB09172.2
Cluster 6grp_total > 15      4grp_total > 29      6grp_cgc > 23      6grp_cgc_sub > De      6grp_total_sub > Decrease      6grp_rule_based > S1      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 146
1 2 3 4 range
A 151.4
(2.9)
P 		97.7
(-1)
A 		69.6
(-3)
A 		152.7
(3)
A 		83
B 145
(3)
P 		109.8
(1.1)
A 		35.9
(-3)
A 		96.1
(0.3)
A 		109
C 97.4
(1.8)
M 		119.8
(2.9)
A 		6.3
(-3)
A 		121.2
(3)
A 		115
avr 131.3
(3) 		109.1
(1.6) 		37.3
(-3) 		123.3
(2.5) 		94

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 203
1 2 3 4 5 6 range
A 220.7
(3)
P 		134.6
(0.2)
A 		82.5
(-1.5)
A 		43.4
(-2.7)
A 		62.4
(-2.1)
A 		34.9
(-3)
A 		186
B 191.9
(2.8)
P 		196.3
(3)
P 		80.3
(-1.4)
M 		43.7
(-2.8)
A 		47.1
(-2.7)
A 		39.2
(-3)
A 		157
C 141
(1.7)
P 		174.9
(3)
P 		79.6
(-0.6)
A 		72.7
(-0.9)
A 		17.6
(-3)
A 		53.4
(-1.6)
A 		157
avr 184.5
(3) 		168.6
(2.3) 		80.8
(-1.4) 		53.3
(-2.5) 		42.4
(-3) 		42.5
(-3) 		142
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 53
1 2 3 4 range
A 55.1
(3)
P 		21.2
(-2.5)
A 		18.2
(-3)
A 		22.4
(-2.3)
A 		37
B 46.3
(3)
P 		27.1
(-0)
A 		8.3
(-3)
A 		20.5
(-1.1)
A 		38
C 32.2
(2.6)
M 		34.4
(3)
A 		2.2
(-3)
A 		20.4
(0.4)
A 		32
avr 44.5
(3) 		27.6
(0.1) 		9.6
(-3) 		21.1
(-1) 		35

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 61
1 2 3 4 5 6 range
A 40.7
(1.9)
P 		47.9
(3)
A 		18
(-1.6)
A 		11
(-2.6)
A 		18.8
(-1.4)
A 		8.5
(-3)
A 		39
B 66.8
(3)
P 		65.3
(2.8)
P 		19.5
(-2.1)
M 		11.6
(-3)
A 		19.2
(-2.2)
A 		14.6
(-2.7)
A 		55
C 52.2
(2.8)
P 		53.4
(3)
P 		20.3
(-1.2)
A 		14.6
(-1.9)
A 		5.7
(-3)
A 		17.9
(-1.5)
A 		48
avr 53.2
(2.7) 		55.5
(3) 		19.3
(-2) 		12.4
(-3) 		14.6
(-2.7) 		13.7
(-2.8) 		43
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 193572_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.11973
Sequence Type Exemplar sequence
Representative Public ID C10G8.5 NCBI
Target Description C10G8.5 /REP_DB=WormBase Gene ID /WP=CE20495 /CHR=5 /FEA=Sanger Annotation /DEF=locus:ncx-2 sodium-calcium exchanger protein 1 (ST.LOUIS) TR:Q94161 protein_id:AAB09172.2
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_072014(11), NM_072013(11), NM_001028473(11), NM_001028472(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_072014 NCBI Caenorhabditis elegans Na/Ca eXchangers family member (ncx-2) (ncx-2) mRNA, complete cds. 11/11 None
NM_072013 NCBI Caenorhabditis elegans Na/Ca eXchangers family member (ncx-2) (ncx-2) mRNA, complete cds. 11/11 A 
NM_001028473 NCBI Caenorhabditis elegans Na/Ca eXchangers family member (ncx-2) (ncx-2) mRNA, complete cds. 11/11 None
NM_001028472 NCBI Caenorhabditis elegans Na/Ca eXchangers family member (ncx-2) (ncx-2) mRNA, complete cds. 11/11 None
SNAP00000038000 ENSEMBL cdna:SNAP chromosome:CEL140:V:5303505:5310281:1 11/11 None
GENEFINDER00000038011 ENSEMBL cdna:GeneFinder chromosome:CEL140:V:5303505:5310281:1 11/11 None
C10G8.5d ENSEMBL cdna:known chromosome:CEL140:V:5303501:5309556:1 gene:C10G8.5 11/11 None
C10G8.5b ENSEMBL cdna:known chromosome:CEL140:V:5303501:5311058:1 gene:C10G8.5 11/11 A 
C10G8.5a ENSEMBL cdna:known chromosome:CEL140:V:5303505:5310657:1 gene:C10G8.5 11/11 None
C10G8.5c.2 ENSEMBL cdna:known chromosome:CEL140:V:5306891:5309481:1 gene:C10G8.5 11/11 None
C10G8.5c.1 ENSEMBL cdna:known chromosome:CEL140:V:5307470:5309481:1 gene:C10G8.5 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
chrV:5303504-5309466(+) 97.66 98.95
Public Domain and Genome References
Ensembl C10G8.5
Functional Annotations
Protein Similarities
Method ID Description E-Value
blast AAM29661 Na/ca exchangers protein 2, isoform b [Caenorhabditis elegans] ref|NP_504415.2| Na/Ca eXchangers family member (ncx-2) [Caenorhabditis elegans] 0.0
blast CAA04574 sodium-calcium exchanger [Caenorhabditis elegans] 0.0
blast AAM29660 Na/ca exchangers protein 2, isoform a [Caenorhabditis elegans] ref|NP_504414.4| Na/Ca eXchangers family member (ncx-2) [Caenorhabditis elegans] 0.0
blast AAN84873 Na/ca exchangers protein 2, isoform d [Caenorhabditis elegans] ref|NP_001023644.1| Na/Ca eXchangers family member (ncx-2) [Caenorhabditis elegans] 0.0
blast CAE62638 Hypothetical protein CBG06769 [Caenorhabditis briggsae] 0.0
blast AAN84872 Na/ca exchangers protein 2, isoform c [Caenorhabditis elegans] ref|NP_001023643.1| Na/Ca eXchangers family member (ncx-2) [Caenorhabditis elegans] 0.0
Protein Domains
Database ID Description E-Value
Pfam IPR004837 EMBL-EBI Sodium/calcium exchanger membrane region 1.7E-27
Pfam IPR004837 EMBL-EBI Sodium/calcium exchanger membrane region 5.1E-23
Pfam IPR003644 EMBL-EBI Na-Ca exchanger/integrin-beta4 3.6E-44
Pfam IPR003644 EMBL-EBI Na-Ca exchanger/integrin-beta4 5.7E-42
Pfam IPR004837 EMBL-EBI Sodium/calcium exchanger membrane region 5.0E-28
Pfam IPR003644 EMBL-EBI Na-Ca exchanger/integrin-beta4 1.0E-43
Pfam IPR003644 EMBL-EBI Na-Ca exchanger/integrin-beta4 5.7E-42
Pfam IPR004837 EMBL-EBI Sodium/calcium exchanger membrane region 5.0E-28
Pfam IPR003644 EMBL-EBI Na-Ca exchanger/integrin-beta4 5.5E-9
Pfam IPR004837 EMBL-EBI Sodium/calcium exchanger membrane region 5.1E-23
Pfam IPR004837 EMBL-EBI Sodium/calcium exchanger membrane region 5.0E-28
Pfam IPR004837 EMBL-EBI Sodium/calcium exchanger membrane region 5.0E-28
Pfam IPR003644 EMBL-EBI Na-Ca exchanger/integrin-beta4 7.4E-17
Pfam IPR003644 EMBL-EBI Na-Ca exchanger/integrin-beta4 2.8E-4
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_504415.2 11 7-24,55-77,117-139,149-171,184-206,216-238,749-771,786-808,820-842,857-879,900-922
NP_504414.4 11 7-24,55-77,117-139,149-171,184-206,216-238,799-821,836-858,870-892,907-929,950-972
NP_001023644.1 10 7-24,55-77,117-139,149-171,184-206,216-238,799-821,836-858,870-892,907-929
NP_001023643.1 3 254-276,327-349,364-384
C10G8.5d 10 7-24,55-77,117-139,149-171,184-206,216-238,799-821,836-858,870-892,907-929
C10G8.5b 11 7-24,55-77,117-139,149-171,184-206,216-238,749-771,786-808,820-842,857-879,900-922
C10G8.5a 11 7-24,55-77,117-139,149-171,184-206,216-238,799-821,836-858,870-892,907-929,950-972
C10G8.5c.2 3 254-276,327-349,364-384
C10G8.5c.1 3 254-276,327-349,364-384
SNAP00000038000 11 7-24,55-77,117-139,149-171,184-206,216-238,802-824,839-861,873-895,910-932,953-975
GENEFINDER00000038011 11 7-24,55-77,117-139,149-171,184-206,216-238,775-797,812-834,846-868,883-905,926-948
Sequence
Target Sequence 
>C. ELEGANS:193572_AT
gttatgcacgttcttactgttccatggaagctcactttcgctaccatcccaccaactgac
tacttcggaggatgggctacattcgttgtcgctatcttcatgattggagtccttaccgct
gttgtaggagatcttgcttctcaattcggatgctgggttggacttaaggatgctgtcacc
gctatctcatttgtcgctttgggaacatctgtgccagatactttcgcatcgaaggtgtcg
gccgttcaggacaagtacgctgataatgccgtcggaaacgtcaccggatccaacgctgtc
aacgttttcttgggtatcggaatcgcctggtcgatggccgcaatctaccattggaatcag
ggaaccaagttcttggttgacccaggaaatcttggattctccgtgctcattttctgcaca
gaagctgttttgtgcatcatcgtcttggtgctca

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GTTATGCACGTTCTTACTGTTCCAT 264 445 2347 Antisense
TCCATGGAAGCTCACTTTCGCTACC 433 589 2367 Antisense
TCCCACCAACTGACTACTTCGGAGG 258 597 2393 Antisense
ATTCGTTGTCGCTATCTTCATGATT 532 9 2427 Antisense
CTTGCTTCTCAATTCGGATGCTGGG 564 217 2479 Antisense
CTTAAGGATGCTGTCACCGCTATCT 82 221 2509 Antisense
GCTATCTCATTTGTCGCTTTGGGAA 675 303 2527 Antisense
ATCTGTGCCAGATACTTTCGCATCG 155 35 2553 Antisense
TCTTGGGTATCGGAATCGCCTGGTC 302 617 2654 Antisense
TTCTCCGTGCTCATTTTCTGCACAG 78 693 2743 Antisense
TTGTGCATCATCGTCTTGGTGCTCA 38 707 2776 Antisense
Sequence Source Affymetrix Proprietary Database