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[173484_at]

Description C43638 /REP_DB=TREMBL Accession /5_PRIME_EXT_ID=F53H8.4 /5_PRIME_EXT_DB=WormBase Gene ID /GB=C43638 /WB_GENE_ID=F53H8.4 /WP=CE04657 /CHR=X /FEA=Genomic Cluster /DEF=C.elegans cDNA clone yk331b1 : 5prime end, single read.
Cluster 6grp_highest_10_10 > 71      6grp_high1_10_10 > 28      4grp_highest_8_8 > 60      4grp_high_8_8 > 26      6grp_highest_nonorm > 70      6grp_total > 28      4grp_total > 37      6grp_highest_sub > De      6grp_cgc > 12      6grp_high1_sub > De      6grp_cgc_sub > De      6grp_total_sub > Cup      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 229
1 2 3 4 range
A 473.4
(3)
P 		323.8
(-0.9)
P 		244.3
(-3)
P 		337.4
(-0.6)
P 		229
B 373.8
(3)
P 		374.3
(3)
P 		248.3
(-3)
P 		305.1
(-0.3)
P 		126
C 421
(3)
P 		350.3
(-0.2)
P 		289.5
(-3)
P 		336.5
(-0.9)
P 		132
avr 422.7
(3) 		349.5
(0.3) 		260.7
(-3) 		326.3
(-0.6) 		162

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 351
1 2 3 4 5 6 range
A 442.2
(3)
P 		304.7
(0)
P 		225.9
(-1.7)
P 		164.4
(-3)
P 		290.6
(-0.3)
P 		292.1
(-0.2)
P 		278
B 515
(3)
P 		340.7
(-0.5)
P 		211.9
(-3)
P 		244.7
(-2.4)
P 		275.7
(-1.7)
P 		282.4
(-1.6)
P 		303
C 421.9
(3)
P 		280.3
(-1)
P 		262.1
(-1.5)
P 		209.5
(-3)
P 		234.4
(-2.3)
P 		251.5
(-1.8)
P 		212
avr 459.7
(3) 		308.6
(-0.6) 		233.3
(-2.4) 		206.2
(-3) 		266.9
(-1.6) 		275.3
(-1.4) 		254
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 123
1 2 3 4 range
A 172.4
(3)
P 		70.3
(-2)
P 		63.9
(-2.3)
P 		49.4
(-3)
P 		123
B 119.2
(3)
P 		92.5
(0.4)
P 		57.5
(-3)
P 		65
(-2.3)
P 		62
C 139.4
(3)
P 		100.7
(0.2)
P 		100.9
(0.2)
P 		56.7
(-3)
P 		83
avr 143.7
(3) 		87.8
(-0.9) 		74.1
(-1.8) 		57
(-3) 		87

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 138
1 2 3 4 5 6 range
A 81.5
(0.6)
P 		108.4
(3)
P 		49.2
(-2.3)
P 		41.7
(-3)
P 		87.7
(1.1)
P 		71.1
(-0.4)
P 		67
B 179.2
(3)
P 		113.4
(-0.1)
P 		51.4
(-3)
P 		64.8
(-2.4)
P 		112
(-0.2)
P 		105.3
(-0.5)
P 		128
C 156.4
(3)
P 		85.5
(-0.7)
P 		66.7
(-1.7)
P 		42.1
(-3)
P 		75.8
(-1.2)
P 		84.2
(-0.8)
P 		114
avr 139
(3) 		102.4
(0.5) 		55.8
(-2.6) 		49.5
(-3) 		91.8
(-0.2) 		86.9
(-0.5) 		90
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 173484_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.26215
Sequence Type Exemplar sequence
Representative Public ID C43638 NCBI
Target Description C43638 /REP_DB=TREMBL Accession /5_PRIME_EXT_ID=F53H8.4 /5_PRIME_EXT_DB=WormBase Gene ID /GB=C43638 /WB_GENE_ID=F53H8.4 /WP=CE04657 /CHR=X /FEA=Genomic Cluster /DEF=C.elegans cDNA clone yk331b1 : 5prime 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_075781(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_075781 NCBI Caenorhabditis elegans SphingoMyelin Synthase family member (sms-2) (sms-2) mRNA, complete cds. 11/11 None
F53H8.4 ENSEMBL cdna:known chromosome:CEL140:X:944827:948882:-1 gene:F53H8.4 11/11 A 
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
chrX:944896-948881(-) 94.92 100.0
Public Domain and Genome References
Gene Title
Gene Symbol sms-2
Ensembl F53H8.4
Entrez Gene 180445 Entrez gene
SwissProt Q20735 EMBL-EBI
WormBase CE04657 Wormbase
Functional Annotations
Protein Similarities
Method ID Description E-Value
blast AAA82341 Sphingomyelin synthase protein 2 [Caenorhabditis elegans] ref|NP_508182.1| SphingoMyelin Synthase family member (sms-2) [Caenorhabditis elegans] sp|Q20735|SMS2_CAEEL Putative phosphatidylcholine:ceramide cholinephosphotransferase 2 (Sphingomyelin synthase 2) 0.0
blast CAE63595 Hypothetical protein CBG08086 [Caenorhabditis briggsae] 0.0
blast XP_392299 PREDICTED: similar to ENSANGP00000021414 [Apis mellifera] 9.0E-42
Protein Domains
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_508182.1 6 60-82,102-124,136-155,200-222,229-249,259-276
F53H8.4 6 60-82,102-124,136-155,200-222,229-249,259-276
Sequence
Target Sequence 
>C. ELEGANS:173484_AT
gtatcattttattttatcccagttttggtttaatttcaaatcaaaatttaatcccttccc
ctcagtttcgacattttgcttatctcatttttttgttgttaatgttttgttttgtatttc
ccccaaagcggtttttcctacttcttttccagtacaatacgatgctccatacgagatatt
tcaattaaacacaacgaacaacacattttctttcccgcaaaaatgcccctcctgctcatt
tctttcgatttctccccctttgaaactcataatttttcctcctgca

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GTATCATTTTATTTTATCCCAGTTT 236 455 1069 Antisense
CCCTCAGTTTCGACATTTTGCTTAT 692 259 1127 Antisense
GTTTCGACATTTTGCTTATCTCATT 371 451 1133 Antisense
TTGTTGTTAATGTTTTGTTTTGTAT 576 705 1161 Antisense
TTTCCTACTTCTTTTCCAGTACAAT 28 671 1202 Antisense
TCCAGTACAATACGATGCTCCATAC 440 589 1216 Antisense
GATGCTCCATACGAGATATTTCAAT 538 413 1229 Antisense
CGAACAACACATTTTCTTTCCCGCA 139 253 1263 Antisense
CACATTTTCTTTCCCGCAAAAATGC 2 195 1270 Antisense
TTTCTCCCCCTTTGAAACTCATAAT 384 671 1317 Antisense
GAAACTCATAATTTTTCCTCCTGCA 195 357 1330 Antisense
Sequence Source Affymetrix Proprietary Database