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[189945_at] leucine rich repeats

Description T01G9.3 /REP_DB=WormBase Gene ID /WP=CE06340 /TR=Q22075 /GB=CAB00050.1 /SUBMIT=HINXTON /CHR=1 /FEA=Sanger Annotation /DEF=leucine rich repeats
Cluster 6grp_highest_10_10 > 53      6grp_high1_10_10 > 25      4grp_highest_8_8 > 04      4grp_high_8_8 > 29      6grp_highest_nonorm > 70      6grp_total > 02      4grp_total > 35      6grp_highest_sub > 02      6grp_high1_sub > 01_02      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 175
1 2 3 4 range
A 232.4
(-2.2)
P 		370
(3)
P 		210.4
(-3)
P 		297.3
(0.3)
P 		160
B 194.6
(-3)
P 		344.4
(3)
P 		209.2
(-2.4)
P 		327.8
(2.3)
P 		150
C 198.6
(-3)
P 		319.5
(3)
P 		229.7
(-1.5)
P 		266.7
(0.4)
P 		121
avr 208.5
(-3) 		344.6
(3) 		216.4
(-2.7) 		297.3
(0.9) 		136

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 216
1 2 3 4 5 6 range
A 361.6
(1.4)
P 		402.6
(3)
P 		253
(-2.8)
P 		298.4
(-1)
P 		247
(-3)
P 		301.6
(-0.9)
P 		156
B 346.4
(1.4)
P 		397.6
(3)
P 		201.5
(-3)
P 		311.8
(0.4)
P 		214.6
(-2.6)
P 		247.8
(-1.6)
P 		196
C 340.6
(0.5)
P 		417.6
(3)
P 		267.2
(-2)
P 		313.2
(-0.4)
P 		256.5
(-2.3)
P 		235.6
(-3)
P 		182
avr 349.5
(1) 		405.9
(3) 		240.6
(-3) 		307.8
(-0.5) 		239.4
(-3) 		261.7
(-2.2) 		167
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 48
1 2 3 4 range
A 84.6
(3)
P 		80.3
(2.4)
P 		55
(-1.3)
P 		43.5
(-3)
P 		41
B 62.1
(-0.8)
P 		85.1
(3)
P 		48.5
(-3)
P 		69.8
(0.5)
P 		37
C 65.7
(-0.4)
P 		91.9
(3)
P 		80.1
(1.5)
P 		45
(-3)
P 		47
avr 70.8
(0.3) 		85.8
(3) 		61.2
(-1.5) 		52.8
(-3) 		33

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 94
1 2 3 4 5 6 range
A 66.7
(-2.2)
P 		143.2
(3)
P 		55.1
(-3)
P 		75.7
(-1.6)
P 		74.5
(-1.7)
P 		73.4
(-1.8)
P 		88
B 120.5
(2.1)
P 		132.4
(3)
P 		48.9
(-3)
P 		82.6
(-0.6)
P 		87.2
(-0.2)
P 		92.4
(0.1)
P 		84
C 126.2
(2.9)
P 		127.4
(3)
P 		68
(-2.5)
P 		63
(-3)
P 		83
(-1.1)
P 		78.9
(-1.5)
P 		64
avr 104.5
(0.7) 		134.3
(3) 		57.3
(-3) 		73.8
(-1.7) 		81.6
(-1.1) 		81.6
(-1.1) 		77
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 189945_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.1356
Sequence Type Exemplar sequence
Representative Public ID T01G9.3 NCBI
Target Description T01G9.3 /REP_DB=WormBase Gene ID /WP=CE06340 /TR=Q22075 /GB=CAB00050.1 /SUBMIT=HINXTON /CHR=1 /FEA=Sanger Annotation /DEF=leucine rich repeats
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_059852(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_059852 NCBI Caenorhabditis elegans T01G9.3 (T01G9.3) mRNA, complete cds. 11/11 None
SNAP00000040992 ENSEMBL cdna:SNAP chromosome:CEL140:I:8290190:8292422:1 11/11 None
GENEFINDER00000040998 ENSEMBL cdna:GeneFinder chromosome:CEL140:I:8290190:8292422:1 11/11 None
T01G9.3 ENSEMBL cdna:known chromosome:CEL140:I:8290112:8292584:1 gene:T01G9.3 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:8290120-8292353(+) 100.0 100.0
Public Domain and Genome References
Gene Title leucine rich repeats
Ensembl T01G9.3
Entrez Gene 187968 Entrez gene
SwissProt Q22075 EMBL-EBI
WormBase CE06340 Wormbase
Functional Annotations
Ortholog
ID Title Organism
DROSOPHILA_2:1629025_AT Pray For Elves dm
DROSOPHILA_2:1637869_AT Pray For Elves dm
DROSGENOME1:152111_AT Pray For Elves dm
Protein Similarities
Method ID Description E-Value
blast CAB00050 Hypothetical protein T01G9.3 [Caenorhabditis elegans] ref|NP_492253.1| T01G9.3 [Caenorhabditis elegans] 0.0
blast CAE60478 Hypothetical protein CBG04090 [Caenorhabditis briggsae] 0.0
blast AAF53643 CG15151-PA [Drosophila melanogaster] ref|NP_609861.1| CG15151-PA [Drosophila melanogaster] gb|AAO42666.1| GH07373p [Drosophila melanogaster] 5.0E-29
Protein Domains
Database ID Description E-Value
Pfam IPR000483 EMBL-EBI Cysteine-rich flanking region, C-terminal 4.5E-4
Pfam IPR001611 EMBL-EBI Leucine-rich repeat 0.01
Pfam IPR001611 EMBL-EBI Leucine-rich repeat 5.5E-4
Pfam IPR001611 EMBL-EBI Leucine-rich repeat 0.032
Pfam IPR001611 EMBL-EBI Leucine-rich repeat 0.93
Pfam IPR001611 EMBL-EBI Leucine-rich repeat 0.059
Pfam IPR001611 EMBL-EBI Leucine-rich repeat 0.62
Pfam IPR001611 EMBL-EBI Leucine-rich repeat 0.014
Pfam IPR001611 EMBL-EBI Leucine-rich repeat 0.051
Pfam IPR001611 EMBL-EBI Leucine-rich repeat 0.41
Pfam IPR001611 EMBL-EBI Leucine-rich repeat 0.0027
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_492253.1 1 508-530
T01G9.3 1 508-530
SNAP00000040992 1 508-530
GENEFINDER00000040998 1 508-530
Sequence
Target Sequence 
>C. ELEGANS:189945_AT
gaaaactttcgacatcacagccaaccgattccacaccttctcgcatacagatttggcatt
cctaaataatgttgaacaagtgtacgtagatggaaatccttgggattgttcatgtgctat
tcaaggacttcaagttcatatgcgagatcgttatgcgatgagacacattctcaactacga
taatgtccgatgcgcgacaccatcgcttgtggaaggtcattcagttctggcaattaccga
cgtaaacgactgtgccgttttgtttggtgcacggtatggattaacgcaaacaagtgaaat
gctcatacttctcgcaggagttctcctttttgccgcactacttcttatgattcttggatg
catctatttccttcgtgagcgacagtacaaaggatcatatgtgacacgagaacactctcg
aactccactcacgatggcaaacacacatagttgctcttcgagtacaaatgatacacatgg
tccattatcaccaccatttgatccattcttggttagtactgaaacatttaaagccactcc
tcca

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GAAAACTTTCGACATCACAGCCAAC 666 353 1230 Antisense
GATAATGTCCGATGCGCGACACCAT 391 423 1408 Antisense
GCGACACCATCGCTTGTGGAAGGTC 89 289 1423 Antisense
ACGACTGTGCCGTTTTGTTTGGTGC 121 93 1475 Antisense
GAAATGCTCATACTTCTCGCAGGAG 27 363 1525 Antisense
TCGCAGGAGTTCTCCTTTTTGCCGC 181 601 1541 Antisense
GCCGCACTACTTCTTATGATTCTTG 413 285 1561 Antisense
TGGATGCATCTATTTCCTTCGTGAG 41 551 1584 Antisense
TCGAACTCCACTCACGATGGCAAAC 287 599 1647 Antisense
ACACACATAGTTGCTCTTCGAGTAC 105 111 1670 Antisense
TGAAACATTTAAAGCCACTCCTCCA 319 573 1749 Antisense
Sequence Source Affymetrix Proprietary Database