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[186036_at]

Description C54F6.13 /REP_DB=WormBase Gene ID /WP=CE08985 /TR=O16452 /GB=AAG24015.1 /SUBMIT=ST.LOUIS /CHR=5 /FEA=Sanger Annotation
Cluster 6grp_highest_10_10 > 39      6grp_high1_10_10 > 92      4grp_highest_8_8 > 11      4grp_high_8_8 > 47      6grp_highest_nonorm > 63      6grp_total > 84      4grp_total > 40      6grp_highest_sub > 04      6grp_cgc > 77      6grp_high1_sub > 04_05      6grp_cgc_sub > 04_05_06      6grp_total_sub > Hat      6grp_rule_based > S4      4grp_rule_based > L3      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 356
1 2 3 4 range
A 143.5
(-3)
P 		402.1
(3)
P 		369
(2.2)
P 		275.3
(0.1)
P 		259
B 82.3
(-3)
P 		279.8
(0.3)
P 		438
(3)
P 		246.4
(-0.2)
P 		356
C 106.5
(-3)
P 		291.4
(0.5)
P 		427.4
(3)
P 		230.5
(-0.7)
P 		321
avr 110.8
(-3) 		324.4
(1.3) 		411.5
(3) 		250.7
(-0.2) 		301

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 900
1 2 3 4 5 6 range
A 161.2
(-3)
P 		327.2
(-1.9)
P 		338.1
(-1.8)
P 		1052.1
(3)
P 		690.3
(0.6)
P 		601
(-0)
P 		891
B 151.8
(-3)
P 		264.7
(-1.8)
P 		349.1
(-1)
P 		696.2
(2.6)
P 		736.8
(3)
P 		541.1
(1)
P 		585
C 166.6
(-3)
P 		254
(-2.3)
P 		334.2
(-1.7)
P 		907.8
(2.9)
P 		921.5
(3)
P 		616.1
(0.6)
P 		755
avr 159.9
(-3) 		282
(-2) 		340.5
(-1.5) 		885.4
(3) 		782.9
(2.2) 		586.1
(0.5) 		726
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 123
1 2 3 4 range
A 52.2
(-1.7)
P 		87.3
(2)
P 		96.5
(3)
P 		40.3
(-3)
P 		56
B 26.3
(-3)
P 		69.1
(0.4)
P 		101.5
(3)
P 		52.5
(-0.9)
P 		75
C 35.2
(-3)
P 		83.8
(-0.4)
P 		148.9
(3)
P 		38.9
(-2.8)
P 		114
avr 37.9
(-3) 		80.1
(0.3) 		115.6
(3) 		43.9
(-2.5) 		78

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 270
1 2 3 4 5 6 range
A 29.7
(-3)
P 		116.4
(-0.8)
P 		73.6
(-1.9)
P 		266.8
(3)
P 		208.3
(1.5)
P 		146.3
(-0)
P 		237
B 52.8
(-3)
P 		88.1
(-2.1)
P 		84.8
(-2.2)
P 		184.4
(0.2)
P 		299.4
(3)
P 		201.8
(0.6)
P 		247
C 61.7
(-3)
P 		77.5
(-2.6)
P 		85.1
(-2.4)
P 		182.5
(0.1)
P 		298.2
(3)
P 		206.2
(0.7)
P 		237
avr 48.1
(-3) 		94
(-1.8) 		81.2
(-2.1) 		211.2
(1.4) 		268.6
(3) 		184.8
(0.7) 		221
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 186036_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.12208
Sequence Type Exemplar sequence
Representative Public ID C54F6.13 NCBI
Target Description C54F6.13 /REP_DB=WormBase Gene ID /WP=CE08985 /TR=O16452 /GB=AAG24015.1 /SUBMIT=ST.LOUIS /CHR=5 /FEA=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_001028564(11), NM_001028565(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_001028564 NCBI Caenorhabditis elegans Na/H eXchanger family member (nhx-3) (nhx-3) mRNA, complete cds. 11/11 None
NM_001028565 NCBI Caenorhabditis elegans Na/H eXchanger family member (nhx-3) (nhx-3) mRNA, complete cds. 11/11 None
SNAP00000031626 ENSEMBL cdna:SNAP chromosome:CEL140:V:7543551:7547430:-1 11/11 None
GENEFINDER00000031628 ENSEMBL cdna:GeneFinder chromosome:CEL140:V:7539511:7547430:-1 11/11 None
C54F6.13a ENSEMBL cdna:known chromosome:CEL140:V:7543485:7547430:-1 gene:C54F6.13 11/11 None
C54F6.13b ENSEMBL cdna:known chromosome:CEL140:V:7543551:7546417:-1 gene:C54F6.13 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:7543551-7546418(-) 100.0 100.0
Public Domain and Genome References
Ensembl C54F6.13
Functional Annotations
Protein Similarities
Method ID Description E-Value
blast NP_001023735 Na/H eXchanger family member (nhx-3) [Caenorhabditis elegans] gb|AAM18103.1| putative Na-H exchanger isoform 3 [Caenorhabditis elegans] gb|AAG24015.2| Na/h exchanger protein 3, isoform a [Caenorhabditis elegans] sp|O16452|NHX3_CAEEL Probable Na(+)/H(+) antiporter nhx-3 (Na(+)-H(+) exchanger protein 3) 0.0
blast NP_001023736 Na/H eXchanger family member (nhx-3) [Caenorhabditis elegans] gb|AAR30208.1| Na/h exchanger protein 3, isoform b [Caenorhabditis elegans] 0.0
blast CAE57801 Hypothetical protein CBG00825 [Caenorhabditis briggsae] 0.0
Protein Domains
Database ID Description E-Value
Pfam IPR006153 EMBL-EBI Sodium/hydrogen exchanger 1.0E-126
Pfam IPR006153 EMBL-EBI Sodium/hydrogen exchanger 1.0E-126
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_001023735.1 11 41-60,73-95,99-121,128-150,165-184,193-215,237-259,272-294,347-369,390-409,419-441
NP_001023736.1 11 22-41,54-76,80-102,109-131,146-165,174-196,218-240,253-275,328-350,371-390,400-422
C54F6.13a 11 41-60,73-95,99-121,128-150,165-184,193-215,237-259,272-294,347-369,390-409,419-441
C54F6.13b 11 22-41,54-76,80-102,109-131,146-165,174-196,218-240,253-275,328-350,371-390,400-422
SNAP00000031626 11 41-60,73-95,99-121,128-150,165-184,193-215,237-259,272-294,347-369,390-409,419-441
GENEFINDER00000031628 10 41-60,73-95,99-121,128-150,165-184,193-215,237-259,272-294,347-369,390-412
Sequence
Target Sequence 
>C. ELEGANS:186036_AT
gacattgcgggtcaacgtggtcattatagttttattgagaactttgaacgtttcaatgca
aaagttatcaaaccagtacttatgcggcatgaaaaacgacaaagcttcgacgccacatca
attatcagagcatatgagaaaattacgctggaggacgcgatcaagcttactaaagtgaaa
agtacactgcaaaataaacgactggaaaaagttaaaagtgaagttcgagtggccccggaa
caaactacagttactccgaaagatgttcagttggccagatttatgcaatctggtgagaac
attgatcaactttacacactatttagtgaccttcttgataagaaacttaatgaattgaaa
gtccaagcagataaggttgacaaagcgaatgatgatgatattcaagacgattacatggcg
gaaatgggatcacattcaaatcttggatttatgcatcacagtgccgatcagcttgactcc
gactcagtattccaacgaagaggccgacgactttcaacaggagatttgaaagggcactgc
gggaccagca

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GACATTGCGGGTCAACGTGGTCATT 391 371 1378 Antisense
ATCAAACCAGTACTTATGCGGCATG 634 25 1444 Antisense
AAACGACAAAGCTTCGACGCCACAT 327 127 1471 Antisense
GACGCCACATCAATTATCAGAGCAT 654 379 1486 Antisense
TACGCTGGAGGACGCGATCAAGCTT 22 649 1521 Antisense
AACATTGATCAACTTTACACACTAT 324 139 1675 Antisense
ACACTATTTAGTGACCTTCTTGATA 423 109 1693 Antisense
ATCACAGTGCCGATCAGCTTGACTC 9 27 1832 Antisense
ACTCCGACTCAGTATTCCAACGAAG 600 97 1853 Antisense
AGGCCGACGACTTTCAACAGGAGAT 158 41 1878 Antisense
TTGAAAGGGCACTGCGGGACCAGCA 392 701 1903 Antisense
Sequence Source Affymetrix Proprietary Database