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Cluster Members
Consensus/Exemplar
Group Members

GeneChip Array Information

Probe Set ID

186609_s_at

GeneChip Array

C. elegans Genome Array

Organism Common Name

Nematode

Probe Design Information

Transcript ID(Array Design)

affy.Ce.200

Sequence Type

Exemplar sequence

Representative Public ID

Y47G6A.23 NCBI

Target Description

Y47G6A.23 /REP_DB=WormBase Gene ID /WP=CE27261 /TR=Q9N3R9 /GB=AAF60650.2 /SUBMIT=ST.LOUIS /CHR=1 /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_058781(11)

Transcript Assignments

Representative Transcript	Description	Matching Probes	Related Probesets by Grade
NM_058781 NCBI	Caenorhabditis elegans LiPid Depleted family member (lpd-3) (lpd-3) mRNA, complete cds.	11/11	None
SNAP00000033994 ENSEMBL	cdna:SNAP chromosome:CEL140:I:3565245:3600679:-1	11/11	None
GENEFINDER00000034084 ENSEMBL	cdna:GeneFinder chromosome:CEL140:I:3565245:3594952:-1	11/11	None
Y47G6A.23 ENSEMBL	cdna:known chromosome:CEL140:I:3565042:3578690:-1 gene:Y47G6A.23	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
chrI:3565260-3600679(-)	99.21	100.0

Public Domain and Genome References

Gene Title

Gene Symbol

lpd-3

Ensembl

Y47G6A.23

Entrez Gene

171926 Entrez gene

SwissProt

Q9N3R9 EMBL-EBI

WormBase

CE31376 Wormbase

Functional Annotations

Ortholog

ID	Title	Organism
CANINE_2:CFAAFFX.6962.1.S1_AT	similar to CG15133-PA	cfa
CANINE_2:CFAAFFX.7004.1.S1_S_AT	similar to CG15133-PA	cfa
CANINE_2:CFAAFFX.7015.1.S1_AT	similar to CG15133-PA	cfa
CANINE_2:CFAAFFX.7015.1.S1_S_AT	similar to CG15133-PA	cfa
DROSOPHILA_2:1640750_AT		dm
DROSGENOME1:153051_AT		dm
CHICKEN:GGA.15070.1.S1_S_AT	similar to KIAA1109 protein	gga
CHICKEN:GGA.16369.1.S1_AT	similar to KIAA1109 protein	gga
CHICKEN:GGAAFFX.23690.1.S1_S_AT	similar to KIAA1109 protein	gga
CHICKEN:GGAAFFX.7538.1.S1_AT	similar to KIAA1109 protein	gga
CHICKEN:GGAAFFX.7538.2.S1_S_AT	similar to KIAA1109 protein	gga
CHICKEN:GGAAFFX.7539.1.S1_AT	similar to KIAA1109 protein	gga
CHICKEN:GGAAFFX.7543.1.S1_AT	similar to KIAA1109 protein	gga
HG-U133_PLUS_2:214929_S_AT	KIAA1109	hs
HG-U133A_2:214929_S_AT	KIAA1109	hs
HG-U133A:214929_S_AT	KIAA1109	hs
HU35KSUBA:RC_AA250974_AT	KIAA1109	hs
HU35KSUBC:RC_N90419_AT	KIAA1109	hs
U133_X3P:HS2.6606.1.S1_3P_X_AT	KIAA1109	hs
U133_X3P:HS2.6606.1.S1_3P_AT	KIAA1109	hs
U133_X3P:HS.6606.2.S1_3P_A_AT	KIAA1109	hs
U133_X3P:HS.6606.1.S1_3P_A_AT	KIAA1109	hs
U133_X3P:HS.6606.0.S1_3P_AT	KIAA1109	hs
U133_X3P:HS.272255.0.S1_3P_AT	KIAA1109	hs
HG-U133_PLUS_2:1553792_AT	KIAA1109	hs
HG-U133_PLUS_2:1553793_A_AT	KIAA1109	hs
HG-U133A_2:212779_AT	KIAA1109	hs
HG-U133_PLUS_2:212779_AT	KIAA1109	hs
HG-U133A:212779_AT	KIAA1109	hs
HG-U133A_2:216294_S_AT	KIAA1109	hs
HG-U133_PLUS_2:216294_S_AT	KIAA1109	hs
HG-U133A:216294_S_AT	KIAA1109	hs
HG-U133_PLUS_2:233096_AT	KIAA1109	hs
HG-U133B:233096_AT	KIAA1109	hs
HG-U95AV2:36814_AT	KIAA1109	hs
HG-U95E:69839_AT	KIAA1109	hs
HG-U95E:69841_G_AT	KIAA1109	hs
HG-U95E:69844_AT	KIAA1109	hs
HG-U95E:83903_AT	KIAA1109	hs
HG-U133_PLUS_2:233227_AT	KIAA1109	hs
HG-U133B:233227_AT	KIAA1109	hs
HG-U95B:56717_R_AT	KIAA1109	hs
HU35KSUBC:RC_N20598_AT	KIAA1109	hs

Protein Similarities

Method	ID	Description	E-Value
blast	NP_491182	LiPid Depleted family member (lpd-3) [Caenorhabditis elegans] gb\|AAL32249.2\| Lipid depleted protein 3 [Caenorhabditis elegans]	0.0
blast	CAE68951	Hypothetical protein CBG14931 [Caenorhabditis briggsae]	0.0
blast	NP_740830	Y47G6A.29 [Caenorhabditis elegans] gb\|AAL32250.2\| Hypothetical protein Y47G6A.29 [Caenorhabditis elegans]	0.0

Protein Domains

Database	ID	Description	E-Value
scop	a.2.7.Methicillin resistance protein FemA probable tRNA-binding arm	All alpha proteins; Long alpha-hairpin; tRNA-binding arm; Methicillin resistance protein FemA probable tRNA-binding arm	4.30000019073486

Trans Membrane
ID	Number Of Domains	Domain Boundaries
SNAP00000033994	1	20-42

Sequence

Target Sequence

>C. ELEGANS:186609_S_AT
aaatgccaatggacgtgctcacgacatttgtgtgtgatttcttcagtgaagtggcgattg
agacgaatttcaacgcacaagtctcattcttgccggaacttttgaaaagctatctgaaag
aatcacacagtggcacatcatcatctcattcgacaaattcgtctccggcagtgtcttcaa
gtaaagaatcagttgtatcggaaactagcaaagatcctcgaatcttcacgtgccaagaat
ggaaagtagagccgagaatattcgatcatcgaaatacgattccaaaagttattcagcgag
cagtgctcgatccacttgacgccacacttgccgcttcagtgattgccactttgcaaattg
tggataacaagaaaacgattcagaaattcaaaaaggttaggatttcggagttaaaaagac
atatttctggaaaaaaagccaaaaaaaaacagtcgaacggactcgatggcaccgacacca
aaacgacgagacagccgtcgttcgagcgaagaagtttccgtttcaatcgatattc

BLASTn GenBank NR

Probe Info

Probe Sequence(5'-3')	Probe X	Probe Y	Probe Interrogation Position	Strandedness
AAATGCCAATGGACGTGCTCACGAC	496	119	11918	Antisense
AATTTCAACGCACAAGTCTCATTCT	451	175	11983	Antisense
GTCTCATTCTTGCCGGAACTTTTGA	682	469	11998	Antisense
CACAGTGGCACATCATCATCTCATT	69	197	12043	Antisense
CATTCGACAAATTCGTCTCCGGCAG	109	215	12064	Antisense
TCTCCGGCAGTGTCTTCAAGTAAAG	681	609	12079	Antisense
AAAGATCCTCGAATCTTCACGTGCC	276	123	12127	Antisense
CACACTTGCCGCTTCAGTGATTGCC	337	195	12240	Antisense
GTCGAACGGACTCGATGGCACCGAC	49	473	12369	Antisense
GACAGCCGTCGTTCGAGCGAAGAAG	481	365	12407	Antisense
GAAGTTTCCGTTTCAATCGATATTC	149	337	12428	Antisense

Sequence Source

Affymetrix Proprietary Database

Description	Y47G6A.23 /REP_DB=WormBase Gene ID /WP=CE27261 /TR=Q9N3R9 /GB=AAF60650.2 /SUBMIT=ST.LOUIS /CHR=1 /FEA=Sanger Annotation
Cluster	6grp_highest_10_10 > 51 6grp_high1_10_10 > 16 4grp_highest_8_8 > 50 4grp_high_8_8 > 40 6grp_highest_nonorm > 61 6grp_total > 16 4grp_total > 46 6grp_highest_sub > De 6grp_cgc > 23 6grp_high1_sub > De 6grp_cgc_sub > De 6grp_total_sub > Decrease 6grp_rule_based > S1 4grp_rule_based > L1