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[173689_s_at]

Description AV198447 /REP_DB=TREMBL Accession /5_PRIME_EXT_ID=K09H9.6 /5_PRIME_EXT_DB=WormBase Gene ID /GB=AV198447 /WB_GENE_ID=K09H9.6 /WP=CE18041 /CHR=1 /FEA=Genomic Cluster /DEF=Caenorhabditis elegans cDNA clone:yk679b8 : 5prime end, single read.
Cluster 4grp_highest_8_8 > 45      4grp_high_8_8 > 01      6grp_total > 45      4grp_total > 15      6grp_cgc > 45      6grp_total_sub > Cup      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 129
1 2 3 4 range
A 167
(2.9)
P 		89
(-1.2)
P 		55.4
(-3)
P 		169.4
(3)
P 		114
B 180.3
(3)
P 		51.5
(-3)
P 		118.5
(0.1)
P 		176.8
(2.8)
P 		129
C 158.3
(2.1)
P 		96.6
(-3)
P 		104.2
(-2.4)
P 		169.2
(3)
P 		73
avr 168.5
(2.8) 		79
(-3) 		92.7
(-2.1) 		171.8
(3) 		93

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 100
1 2 3 4 5 6 range
A 89.8
(0.2)
A 		70.3
(-2.8)
P 		107.7
(3)
P 		69.1
(-3)
A 		69.6
(-2.9)
M 		94.6
(1)
P 		39
B 54.2
(0.6)
P 		83.3
(2.8)
P 		76.4
(2.3)
A 		7.3
(-3)
A 		48.9
(0.2)
A 		85.8
(3)
P 		79
C 76.8
(1.4)
P 		79.6
(1.6)
A 		97.5
(3)
A 		21.1
(-3)
A 		74.8
(1.2)
A 		94
(2.7)
P 		76
avr 73.6
(1) 		77.7
(1.4) 		93.9
(3) 		32.5
(-3) 		64.4
(0.1) 		91.5
(2.8) 		61
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 48
1 2 3 4 range
A 60.8
(3)
P 		19.3
(-2.4)
P 		14.5
(-3)
P 		24.8
(-1.7)
P 		46
B 57.5
(3)
P 		12.7
(-3)
P 		27.5
(-1)
P 		37.7
(0.3)
P 		45
C 52.4
(3)
P 		27.8
(-3)
P 		36.3
(-0.9)
P 		28.5
(-2.8)
P 		25
avr 56.9
(3) 		19.9
(-3) 		26.1
(-2) 		30.3
(-1.3) 		37

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 30
1 2 3 4 5 6 range
A 16.6
(-3)
A 		25
(3)
P 		23.4
(1.9)
P 		17.5
(-2.4)
A 		21
(0.1)
M 		23
(1.6)
P 		8
B 18.8
(0.4)
P 		27.7
(2.1)
P 		18.6
(0.3)
A 		1.9
(-3)
A 		19.9
(0.6)
A 		32
(3)
P 		30
C 28.5
(2.3)
P 		24.3
(1.4)
A 		24.8
(1.5)
A 		4.3
(-3)
A 		24.2
(1.4)
A 		31.5
(3)
P 		27
avr 21.3
(0.8) 		25.7
(2.1) 		22.3
(1.1) 		7.9
(-3) 		21.7
(1) 		28.8
(3) 		21
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 173689_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.22536
Sequence Type Exemplar sequence
Representative Public ID AV198447 NCBI
Target Description AV198447 /REP_DB=TREMBL Accession /5_PRIME_EXT_ID=K09H9.6 /5_PRIME_EXT_DB=WormBase Gene ID /GB=AV198447 /WB_GENE_ID=K09H9.6 /WP=CE18041 /CHR=1 /FEA=Genomic Cluster /DEF=Caenorhabditis elegans cDNA clone:yk679b8 : 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_058707(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_058707 NCBI Caenorhabditis elegans LiPid Depleted family member (lpd-6) (lpd-6) mRNA, complete cds. 11/11 None
SNAP00000035325 ENSEMBL cdna:SNAP chromosome:CEL140:I:3144522:3151980:-1 11/11 None
GENEFINDER00000035331 ENSEMBL cdna:GeneFinder chromosome:CEL140:I:3144522:3147785:-1 11/11 None
K09H9.6 ENSEMBL cdna:known chromosome:CEL140:I:3144429:3147794:-1 gene:K09H9.6 11/11 None
Annotation Notes
Cross Hybridizing mRNA Matched Probes Nature of Assignment Related Probesets by Grade
GENEFINDER00000028628 1/11 Cross Hyb Matching Probes None
SNAP00000028623 1/11 Cross Hyb Matching Probes None
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrI:3144481-3147786(-) 97.43 100.0
Public Domain and Genome References
Gene Title
Gene Symbol lpd-6
Ensembl K09H9.6
Entrez Gene 171886 Entrez gene
SwissProt O44991 EMBL-EBI
WormBase CE37030 Wormbase
Functional Annotations
Ortholog
ID Title Organism
ATH1-121501:247497_AT brix domain-containing protein at
CANINE:1601986_AT similar to Suppressor of SWI4 1 homolog (Ssf-1) (Peter Pan homolog) cfa
CANINE_2:CFA.17551.2.S1_S_AT similar to Suppressor of SWI4 1 homolog (Ssf-1) (Peter Pan homolog) cfa
CANINE_2:CFA.8183.1.A1_AT similar to Suppressor of SWI4 1 homolog (Ssf-1) (Peter Pan homolog) cfa
CANINE_2:CFAAFFX.27419.1.S1_AT similar to Suppressor of SWI4 1 homolog (Ssf-1) (Peter Pan homolog) cfa
CANINE_2:CFAAFFX.27424.1.S1_AT similar to Suppressor of SWI4 1 homolog (Ssf-1) (Peter Pan homolog) cfa
DROSOPHILA_2:1628216_AT peter pan dm
DROSGENOME1:143634_AT peter pan dm
HG-U133_PLUS_2:221649_S_AT peter pan homolog (Drosophila) hs
HG-FOCUS:221649_S_AT peter pan homolog (Drosophila) hs
HG-U133A:221649_S_AT peter pan homolog (Drosophila) hs
HG-U133A_2:221649_S_AT peter pan homolog (Drosophila) hs
HU35KSUBC:RC_AA600054_AT peter pan homolog (Drosophila) hs
U133_X3P:G12653526_3P_X_AT peter pan homolog (Drosophila) hs
U133_X3P:G12653526_3P_A_AT peter pan homolog (Drosophila) hs
HG-U95B:46597_AT peter pan homolog (Drosophila) hs
HG-U95D:88479_S_AT peter pan homolog (Drosophila) hs
MU11KSUBA:AA265569_S_AT peter pan homolog (Drosophila) mm
MG-U74AV2:160802_AT peter pan homolog (Drosophila) mm
MG-U74CV2:170991_AT peter pan homolog (Drosophila) mm
MOE430A:1423703_AT peter pan homolog (Drosophila) mm
MOUSE430A_2:1423703_AT peter pan homolog (Drosophila) mm
MOUSE430_2:1423703_AT peter pan homolog (Drosophila) mm
MU19KSUBC:TC38006_AT Peter pan homolog (Drosophila) (Ppan), mRNA mm
MU19KSUBC:TC40685_AT Peter pan homolog (Drosophila) (Ppan), mRNA mm
RAE230A:1374326_AT peter pan homolog (Drosophila) (predicted) rn
RAT230_2:1374326_AT peter pan homolog (Drosophila) (predicted) rn
YEAST_2:1774186_AT Constituent of 66S pre-ribosomal particles, required for ribosomal large subunit maturation; functionally redundant with Ssf2p; member of the Brix family Sc
Protein Similarities
Method ID Description E-Value
blast NP_491108 LiPid Depleted family member (lpd-6) [Caenorhabditis elegans] gb|AAB97575.2| Lipid depleted protein 6 [Caenorhabditis elegans] 0.0
blast CAE60550 Hypothetical protein CBG04177 [Caenorhabditis briggsae] 0.0
blast EAL28350 GA19127-PA [Drosophila pseudoobscura] 7.0E-62
Protein Domains
Database ID Description E-Value
Pfam IPR007109 EMBL-EBI Brix domain 4.4E-120
Pfam IPR007109 EMBL-EBI Brix domain 6.4E-117
Pfam IPR007109 EMBL-EBI Brix domain 4.4E-120
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_491108.2 1 100-122
K09H9.6 1 100-122
GENEFINDER00000035331 1 100-122
Sequence
Target Sequence 
>C. ELEGANS:173689_S_AT
gaatgctgctcgtaagcaagctgccgctactggacaagttgaagaagttgagaatcagaa
ggagaaggatagagagattgcgatgaatcgggaaagagatctgaagcgtgccaacgagga
atggggtacatctgaagcctcgaagcgtccaagatatgaggatagtcgtgggggattccg
aggtggattcagaggaagaggagaagatcgtggaggcttccgcggacgtggcggagatcg
tggaggcttcagaggtcgcgatcgtgatggaggtggctttagaggaagatccgtggatcg
tggtggcttccgtggaggtggtggcgaccgaggaggcttcagaggacgttcatcagatcg
tggtggagatcgtggaggcttccgtggaagatcgggagatcgtgatggaggatttagagg
tggattcggaggacgtggtggcggtggtttccgtggaggcgatcgaggaggattcagagg
acgcggcggaggtggtggattccgtggtgggcgaggtggagatcgaggcggcggtttccg
a

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GAATGCTGCTCGTAAGCAAGCTGCC 170 331 1285 Antisense
TAAGCAAGCTGCCGCTACTGGACAA 9 639 1297 Antisense
GTCGTGGGGGATTCCGAGGTGGATT 74 473 1449 Antisense
GAGAAGATCGTGGAGGCTTCCGCGG 479 391 1485 Antisense
GGCTTCCGCGGACGTGGCGGAGATC 424 537 1499 Antisense
CGTGGAGGCTTCAGAGGTCGCGATC 365 245 1523 Antisense
GGTCGCGATCGTGATGGAGGTGGCT 603 501 1538 Antisense
GAAGATCCGTGGATCGTGGTGGCTT 598 337 1569 Antisense
GGCTTCAGAGGACGTTCATCAGATC 558 537 1619 Antisense
AGGATTCAGAGGACGCGGCGGAGGT 388 55 1753 Antisense
TGGAGATCGAGGCGGCGGTTTCCGA 622 545 1801 Antisense
Sequence Source Affymetrix Proprietary Database