[Home] | [Total List]

[193436_s_at] Leucine Rich Repeat (2 copies) (2 domains)

Description Y39A1A.17 /REP_DB=WormBase Gene ID /WP=CE19137 /TR=Q9XX12 /GB=CAA21029.1 /SUBMIT=HINXTON /CHR=3 /FEA=Sanger Annotation /DEF=Leucine Rich Repeat (2 copies) (2 domains)
Cluster 6grp_total > 19      4grp_total > 21      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 96
1 2 3 4 range
A 48.5
(-0.1)
A 		74.6
(3)
A 		23.4
(-3)
A 		65.8
(2)
A 		51
B 38.8
(0.1)
A 		7.2
(-3)
A 		14.2
(-2.3)
A 		69.1
(3)
A 		62
C 85.1
(1.8)
A 		43.3
(-1)
A 		14
(-3)
A 		103.2
(3)
A 		89
avr 57.5
(0.9) 		41.7
(-0.6) 		17.2
(-3) 		79.4
(3) 		62

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 72
1 2 3 4 5 6 range
A 47
(3)
A 		20.9
(-1.4)
A 		11.8
(-3)
A 		33.3
(0.7)
A 		44.8
(2.6)
A 		44.6
(2.6)
A 		35
B 52.3
(3)
A 		10
(-2.6)
A 		7.1
(-3)
A 		22.5
(-1)
A 		16.1
(-1.8)
A 		42.2
(1.7)
A 		45
C 79.5
(3)
P 		29.7
(-2.2)
A 		56.2
(0.6)
A 		21.9
(-3)
A 		70.7
(2.1)
P 		34.3
(-1.7)
P 		58
avr 59.6
(3) 		20.2
(-3) 		25
(-2.3) 		25.9
(-2.1) 		43.9
(0.6) 		40.4
(0.1) 		39
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 26
1 2 3 4 range
A 17.7
(3)
A 		16.2
(2.2)
A 		6.1
(-3)
A 		9.6
(-1.2)
A 		12
B 12.4
(1.9)
A 		1.8
(-3)
A 		3.3
(-2.3)
A 		14.7
(3)
A 		13
C 28.2
(3)
A 		12.4
(-1.1)
A 		4.9
(-3)
A 		17.4
(0.2)
A 		23
avr 19.4
(3) 		10.1
(-0.8) 		4.8
(-3) 		13.9
(0.7) 		15

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 28
1 2 3 4 5 6 range
A 8.7
(0.4)
A 		7.4
(-0.4)
A 		2.6
(-3)
A 		8.4
(0.2)
A 		13.5
(3)
A 		10.9
(1.6)
A 		11
B 18.2
(3)
A 		3.3
(-2.4)
A 		1.7
(-3)
A 		6
(-1.4)
A 		6.5
(-1.3)
A 		15.7
(2.1)
A 		17
C 29.5
(3)
P 		9.1
(-1.9)
A 		14.3
(-0.6)
A 		4.4
(-3)
A 		22.9
(1.4)
P 		11.5
(-1.3)
P 		25
avr 18.8
(3) 		6.6
(-2.8) 		6.2
(-3) 		6.3
(-3) 		14.3
(0.9) 		12.7
(0.1) 		13
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 193436_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.6340
Sequence Type Exemplar sequence
Representative Public ID Y39A1A.17 NCBI
Target Description Y39A1A.17 /REP_DB=WormBase Gene ID /WP=CE19137 /TR=Q9XX12 /GB=CAA21029.1 /SUBMIT=HINXTON /CHR=3 /FEA=Sanger Annotation /DEF=Leucine Rich Repeat (2 copies) (2 domains)
Cluster Evidence This cluster is supported by a 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_001027666(11), NM_001027665(11), NM_001027667(11), NM_066953(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_001027666 NCBI Caenorhabditis elegans CeNTaurin family member (cnt-2) (cnt-2) mRNA, complete cds. 11/11 None
NM_001027665 NCBI Caenorhabditis elegans CeNTaurin family member (cnt-2) (cnt-2) mRNA, complete cds. 11/11 None
NM_001027667 NCBI Caenorhabditis elegans CeNTaurin family member (cnt-2) (cnt-2) mRNA, complete cds. 11/11 None
NM_066953 NCBI Caenorhabditis elegans Y39A1A.17 (Y39A1A.17) mRNA, complete cds. 11/11 A 
GENEFINDER00000012934 ENSEMBL cdna:GeneFinder chromosome:CEL140:III:10666837:10676645:1 11/11 None
SNAP00000012921 ENSEMBL cdna:SNAP chromosome:CEL140:III:10670141:10677031:1 11/11 None
SNAP00000012922 ENSEMBL cdna:SNAP chromosome:CEL140:III:10682868:10685904:-1 11/11 None
GENEFINDER00000012937 ENSEMBL cdna:GeneFinder chromosome:CEL140:III:10684190:10690978:-1 10/11 None
Y39A1A.15b ENSEMBL cdna:known chromosome:CEL140:III:10655650:10677334:1 gene:Y39A1A.15 11/11 A 
Y39A1A.15a ENSEMBL cdna:known chromosome:CEL140:III:10663324:10677039:1 gene:Y39A1A.15 11/11 A 
Y39A1A.15c ENSEMBL cdna:known chromosome:CEL140:III:10666768:10677031:1 gene:Y39A1A.15 11/11 A 
Y39A1A.17 ENSEMBL cdna:known chromosome:CEL140:III:10684755:10690978:-1 gene:Y39A1A.17 11/11 A 
Annotation Notes
There are no noteworthy cross hybridizing mRNAs found for this probe set.
Splice Variants
Entrez Total Refseq Isoforms Total Detected By This Probeset Refseq Probesets
176490 4 3 NM_001027665 190947_s_at (11), 193436_s_at (11)
NM_001027666 190947_s_at (11), 193436_s_at (11)
NM_001027667 190947_s_at (11), 193436_s_at (11)
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrIII:10684750-10690974(-) 98.98 100.0
Public Domain and Genome References
Gene Title Leucine Rich Repeat (2 copies) (2 domains)
Ensembl Y39A1A.15
Y39A1A.17
Entrez Gene 189711 Entrez gene
SwissProt Q9XX12 EMBL-EBI
WormBase CE19137 Wormbase
Functional Annotations
Protein Similarities
Method ID Description E-Value
blast CAA21027 Hypothetical protein Y39A1A.15b [Caenorhabditis elegans] ref|NP_001022837.1| CeNTaurin family member (cnt-2) [Caenorhabditis elegans] 0.0
blast CAA10736 centaurin gamma 1A [Caenorhabditis elegans] 0.0
blast CAA21026 Hypothetical protein Y39A1A.15a [Caenorhabditis elegans] ref|NP_001022836.1| CeNTaurin family member (cnt-2) [Caenorhabditis elegans] 0.0
blast CAA10737 centaurin gamma 1B [Caenorhabditis elegans] 0.0
blast CAA21032 Hypothetical protein Y39A1A.15c [Caenorhabditis elegans] ref|NP_001022838.1| CeNTaurin family member (cnt-2) [Caenorhabditis elegans] 0.0
blast CAA21029 Hypothetical protein Y39A1A.17 [Caenorhabditis elegans] ref|NP_499354.1| Y39A1A.17 [Caenorhabditis elegans] 0.0
Protein Domains
Database ID Description E-Value
Pfam IPR001164 EMBL-EBI Human Rev interacting-like protein (hRIP) 6.2E-51
Pfam IPR002110 EMBL-EBI Ankyrin 6.5E-8
Pfam IPR002110 EMBL-EBI Ankyrin 0.52
Pfam IPR001806 EMBL-EBI Ras GTPase superfamily 1.5E-8
Pfam IPR001849 EMBL-EBI Pleckstrin-like 8.9E-16
Pfam IPR001164 EMBL-EBI Human Rev interacting-like protein (hRIP) 6.2E-51
Pfam IPR002110 EMBL-EBI Ankyrin 6.5E-8
Pfam IPR002110 EMBL-EBI Ankyrin 0.52
Pfam IPR001806 EMBL-EBI Ras GTPase superfamily 1.5E-8
Pfam IPR001849 EMBL-EBI Pleckstrin-like 8.9E-16
Pfam IPR001164 EMBL-EBI Human Rev interacting-like protein (hRIP) 6.2E-51
Pfam IPR002110 EMBL-EBI Ankyrin 6.5E-8
Pfam IPR002110 EMBL-EBI Ankyrin 0.52
Pfam IPR001806 EMBL-EBI Ras GTPase superfamily 1.5E-8
Pfam IPR001849 EMBL-EBI Pleckstrin-like 8.9E-16
Pfam IPR001164 EMBL-EBI Human Rev interacting-like protein (hRIP) 6.2E-51
Pfam IPR002110 EMBL-EBI Ankyrin 6.5E-8
Pfam IPR002110 EMBL-EBI Ankyrin 0.52
Pfam IPR001849 EMBL-EBI Pleckstrin-like 8.9E-16
Pfam IPR001611 EMBL-EBI Leucine-rich repeat 0.11
Pfam IPR001611 EMBL-EBI Leucine-rich repeat 0.038
Sequence
Target Sequence 
>C. ELEGANS:193436_S_AT
tcccatcgtgtcgcaagttctgtggatctgttgaatggcggtggaggtggtggcacaccg
acgctcaagagctacgaaccacggcggagtgacgttggagccaactctggcgatggaact
tctggtggtggatcggatgatgcgattaaggagaatcagagacaacacttctcaccgcct
gccatgcctcaaaccgtagctgggaagaagaagcgagagtcgaggaagatcggaacgaat
tcgaagcataatgatgaggaggacgagtgttttgaagtta

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
TCCCATCGTGTCGCAAGTTCTGTGG 184 599 1255 Antisense
CATCGTGTCGCAAGTTCTGTGGATC 424 211 1258 Antisense
GGAGCCAACTCTGGCGATGGAACTT 200 523 1351 Antisense
AACTCTGGCGATGGAACTTCTGGTG 632 139 1357 Antisense
ATGGAACTTCTGGTGGTGGATCGGA 254 51 1367 Antisense
GTGGATCGGATGATGCGATTAAGGA 43 489 1382 Antisense
AATCAGAGACAACACTTCTCACCGC 121 171 1408 Antisense
CATGCCTCAAACCGTAGCTGGGAAG 113 47 1437 Antisense
GAGAGTCGAGGAAGATCGGAACGAA 349 393 1469 Antisense
GGAACGAATTCGAAGCATAATGATG 50 529 1486 Antisense
GAGGAGGACGAGTGTTTTGAAGTTA 260 239 1510 Antisense
Sequence Source Affymetrix Proprietary Database