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[174295_at] serine palmitoyltransferase

Description C33118_rc /REP_DB=TREMBL Accession /GB=C33118 /CHR=5 /FEA=Genomic Cluster /DEF=C.elegans cDNA clone yk340h9 : 3prime end, single read.
Cluster 6grp_highest_10_10 > 74      6grp_high1_10_10 > 56      4grp_highest_8_8 > 45      4grp_high_8_8 > 01      6grp_highest_nonorm > 74      6grp_total > 47      4grp_total > 15      6grp_highest_sub > Cu      6grp_cgc > 26      6grp_high1_sub > Cu      6grp_total_sub > Cup      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 528
1 2 3 4 range
A 546.6
(3)
P 		250.4
(-3)
P 		308.5
(-1.8)
P 		374.1
(-0.5)
P 		296
B 539.5
(3)
P 		293.5
(-3)
P 		429
(0.3)
P 		531.6
(2.8)
P 		246
C 632.3
(1.1)
P 		304.9
(-3)
P 		389
(-1.9)
P 		778.3
(3)
P 		473
avr 572.8
(3) 		282.9
(-3) 		375.5
(-1.1) 		561.3
(2.8) 		290

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 418
1 2 3 4 5 6 range
A 871.5
(3)
P 		671.7
(-0.9)
P 		757.9
(0.8)
P 		568
(-3)
P 		805.1
(1.7)
P 		688.7
(-0.6)
P 		304
B 524.1
(-3)
P 		740.2
(0.5)
P 		676.3
(-0.5)
P 		871.4
(2.6)
P 		682.6
(-0.4)
P 		895.3
(3)
P 		371
C 924.6
(3)
P 		732.1
(0.2)
P 		680.6
(-0.5)
P 		788.3
(1)
P 		507
(-3)
P 		819.1
(1.5)
P 		418
avr 773.4
(1.8) 		714.7
(-0.8) 		704.9
(-1.2) 		742.6
(0.4) 		664.9
(-3) 		801
(3) 		136
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 155
1 2 3 4 range
A 199
(3)
P 		54.4
(-3)
P 		80.6
(-1.9)
P 		54.8
(-3)
P 		145
B 172.1
(3)
P 		72.5
(-3)
P 		99.4
(-1.4)
P 		113.3
(-0.5)
P 		100
C 209.3
(3)
P 		87.7
(-3)
P 		135.6
(-0.6)
P 		131.2
(-0.9)
P 		122
avr 193.5
(3) 		71.5
(-3) 		105.2
(-1.3) 		99.8
(-1.6) 		122

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 199
1 2 3 4 5 6 range
A 160.7
(-2)
P 		238.9
(2.8)
P 		165.1
(-1.7)
P 		144.1
(-3)
P 		242.9
(3)
P 		167.7
(-1.6)
P 		99
B 182.4
(-2.4)
P 		246.4
(-0.1)
P 		164.2
(-3)
P 		230.8
(-0.6)
P 		277.4
(1)
P 		333.8
(3)
P 		170
C 342.7
(3)
P 		223.4
(-0.9)
P 		173.2
(-2.5)
P 		158.5
(-3)
P 		164.1
(-2.8)
P 		274.2
(0.8)
P 		184
avr 228.6
(1) 		236.2
(1.5) 		167.5
(-3) 		177.8
(-2.3) 		228.1
(1) 		258.6
(3) 		91
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 174295_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.21921
Sequence Type Exemplar sequence
Representative Public ID C33118 NCBI
Target Description C33118_rc /REP_DB=TREMBL Accession /GB=C33118 /CHR=5 /FEA=Genomic Cluster /DEF=C.elegans cDNA clone yk340h9 : 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_074044(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_074044 NCBI Caenorhabditis elegans Serine Palmitoyl Transferase famiLy family member (sptl-3) (sptl-3) mRNA, complete cds. 11/11 None
T22G5.5.1 ENSEMBL cdna:known chromosome:CEL140:V:13895992:13898994:1 gene:T22G5.5 11/11 None
Annotation Notes
Cross Hybridizing mRNA Matched Probes Nature of Assignment Related Probesets by Grade
GENEFINDER00000016901 1/11 Cross Hyb Matching Probes None
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrV:13898636-13898932(+) 100.0 100.0
Public Domain and Genome References
Gene Title serine palmitoyltransferase
Gene Symbol sptl-3
Ensembl T22G5.5
Entrez Gene 179884 Entrez gene
SwissProt Q9XVI6 EMBL-EBI
WormBase CE31996 Wormbase
Functional Annotations
Gene Ontology
GO Biological Process (view graph)
ID Description Evidence Links
8152 metabolism inferred from electronic annotation QuickGO AmiGO
9058 biosynthesis inferred from electronic annotation QuickGO AmiGO
GO Molecular Function (view graph)
ID Description Evidence Links
8483 transaminase activity inferred from electronic annotation QuickGO AmiGO
16740 transferase activity inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast CAB03390 Hypothetical protein T22G5.5 [Caenorhabditis elegans] ref|NP_506445.2| Serine Palmitoyl Transferase famiLy family member (sptl-3) [Caenorhabditis elegans] 0.0
blast CAE66206 Hypothetical protein CBG11447 [Caenorhabditis briggsae] 0.0
blast AAA92303 Serine palmitoyl transferase family protein 2, isoform a [Caenorhabditis elegans] ref|NP_505065.1| Serine Palmitoyl Transferase famiLy family member (sptl-2) [Caenorhabditis elegans] 1.0E-137
Protein Domains
Database ID Description E-Value
Pfam IPR004839 EMBL-EBI Aminotransferase, class I and II 3.6E-27
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_506445.2 1 35-57
T22G5.5.1 1 35-57
Sequence
Target Sequence 
>C. ELEGANS:174295_AT
gtatttattaactatcctcgttatttgtcagttcttccctgtttcacttctacatatata
ttcccattaccccaattcttgccctttgaataattttttttctgacttttattttttatc
taccaaaaactatcgaattcctaggatcttcttcttatataaatttaaattttctctttt
tctatttgtttgttttatgtattttcccattgttttttacacttatttctttctaggcaa
acaattttcatgac

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GTATTTATTAACTATCCTCGTTATT 238 453 14 Antisense
ATCCTCGTTATTTGTCAGTTCTTCC 425 39 27 Antisense
TCGTTATTTGTCAGTTCTTCCCTGT 365 603 31 Antisense
TACATATATATTCCCATTACCCCAA 566 643 64 Antisense
CCCCAATTCTTGCCCTTTGAATAAT 603 261 83 Antisense
TGCCCTTTGAATAATTTTTTTTCTG 253 585 93 Antisense
AAAACTATCGAATTCCTAGGATCTT 205 131 139 Antisense
ATTCCTAGGATCTTCTTCTTATATA 253 9 150 Antisense
TGTTTTATGTATTTTCCCATTGTTT 564 561 204 Antisense
TTTACACTTATTTCTTTCTAGGCAA 348 673 229 Antisense
TTTCTAGGCAAACAATTTTCATGAC 375 667 243 Antisense
Sequence Source Affymetrix Proprietary Database