[Home] | [Total List]

[174128_at]

Description C59705_rc /REP_DB=TREMBL Accession /GB=C59705 /CHR=3 /FEA=Genomic Cluster /DEF=C.elegans cDNA clone yk440f1 : 3prime end, single read.
Cluster 6grp_highest_10_10 > 96      6grp_high1_10_10 > 68      4grp_highest_8_8 > 46      4grp_high_8_8 > 02      6grp_highest_nonorm > 87      6grp_total > 59      4grp_total > 14      6grp_highest_sub > Cu      6grp_high1_sub > Cu      6grp_total_sub > Cup      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 922
1 2 3 4 range
A 1207.8
(0.4)
P 		795
(-2.9)
P 		779.4
(-3)
P 		1543.6
(3)
P 		764
B 1329
(3)
P 		763.2
(-1.8)
P 		621.4
(-3)
P 		1332
(3)
P 		711
C 1113.3
(-0.7)
P 		930.7
(-3)
P 		929.2
(-3)
P 		1401.4
(3)
P 		472
avr 1216.7
(1.1) 		829.6
(-2.5) 		776.7
(-3) 		1425.7
(3) 		649

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 1071
1 2 3 4 5 6 range
A 1533.6
(3)
P 		818.8
(-2.1)
P 		759.2
(-2.6)
P 		697.6
(-3)
P 		1248.9
(1)
P 		1469.6
(2.5)
P 		836
B 1027.6
(-1)
P 		989.6
(-1.2)
P 		686.6
(-3)
P 		1038.7
(-0.9)
P 		944.6
(-1.5)
P 		1691.1
(3)
P 		1005
C 964.4
(-0.2)
P 		958.2
(-0.2)
P 		620.5
(-3)
P 		950.3
(-0.3)
P 		915.6
(-0.6)
P 		1346.8
(3)
P 		726
avr 1175.2
(0.6) 		922.2
(-1.3) 		688.8
(-3) 		895.5
(-1.5) 		1036.4
(-0.4) 		1502.5
(3) 		814
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 296
1 2 3 4 range
A 439.8
(3)
P 		172.6
(-3)
P 		203.8
(-2.3)
P 		226
(-1.8)
P 		267
B 423.8
(3)
P 		188.5
(-2)
P 		144
(-3)
P 		283.9
(-0)
P 		280
C 368.5
(3)
P 		267.6
(-1.6)
P 		323.8
(1)
P 		236.3
(-3)
P 		132
avr 410.7
(3) 		209.6
(-3) 		223.9
(-2.6) 		248.7
(-1.8) 		201

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 473
1 2 3 4 5 6 range
A 282.7
(0.3)
P 		291.2
(0.6)
P 		165.3
(-3)
P 		176.9
(-2.7)
P 		376.9
(3)
P 		357.8
(2.5)
P 		212
B 357.5
(-0.5)
P 		329.4
(-0.9)
P 		166.7
(-3)
P 		275.1
(-1.6)
P 		383.8
(-0.2)
P 		630.6
(3)
P 		464
C 357.5
(1.1)
P 		292.4
(-0.2)
P 		157.9
(-3)
P 		191.1
(-2.3)
P 		296.3
(-0.2)
P 		450.8
(3)
P 		293
avr 332.6
(0.2) 		304.3
(-0.3) 		163.3
(-3) 		214.4
(-2) 		352.3
(0.6) 		479.7
(3) 		316
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 174128_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.21159
Sequence Type Exemplar sequence
Representative Public ID C59705 NCBI
Target Description C59705_rc /REP_DB=TREMBL Accession /GB=C59705 /CHR=3 /FEA=Genomic Cluster /DEF=C.elegans cDNA clone yk440f1 : 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_066446(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_066446 NCBI Caenorhabditis elegans R05D3.2 (R05D3.2) mRNA, complete cds. 11/11 None
R05D3.2 ENSEMBL cdna:known chromosome:CEL140:III:8372170:8375080:1 gene:R05D3.2 11/11 A 
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
chrIII:8374706-8375017(+) 100.0 100.0
Public Domain and Genome References
Gene Title
Ensembl R05D3.2
Entrez Gene 176182 Entrez gene
SwissProt P34535 EMBL-EBI
WormBase CE00281 Wormbase
Functional Annotations
Ortholog
ID Title Organism
CANINE_2:CFAAFFX.8652.1.S1_S_AT similar to limb region 1 protein cfa
CANINE_2:CFAAFFX.8653.1.S1_S_AT similar to limb region 1 protein cfa
CHICKEN:GGA.1918.1.S1_AT limb region 1 homolog (mouse) gga
CHICKEN:GGA.1918.1.S2_AT limb region 1 homolog (mouse) gga
HG-U133_PLUS_2:224036_S_AT limb region 1 homolog (mouse) hs
HG-U133B:224036_S_AT limb region 1 homolog (mouse) hs
HG-U133_PLUS_2:224410_S_AT limb region 1 homolog (mouse) hs
HG-U133B:224410_S_AT limb region 1 homolog (mouse) hs
HU35KSUBA:RC_AA485147_AT limb region 1 homolog (mouse) hs
HU35KSUBB:RC_AA205320_AT limb region 1 homolog (mouse) hs
HU35KSUBD:RC_AA476728_AT limb region 1 homolog (mouse) hs
U133_X3P:G13591769_3P_S_AT limb region 1 homolog (mouse) hs
U133_X3P:G12002015_3P_A_AT limb region 1 homolog (mouse) hs
U133_X3P:HS.107537.0.S3_3P_AT limb region 1 homolog (mouse) hs
HG-U133_PLUS_2:222505_AT limb region 1 homolog (mouse) hs
HG-U133B:222505_AT limb region 1 homolog (mouse) hs
HG-U133_PLUS_2:222506_AT limb region 1 homolog (mouse) hs
HG-U133B:222506_AT limb region 1 homolog (mouse) hs
HG-U95B:56376_AT limb region 1 homolog (mouse) hs
HG-U95B:42173_AT Limb region 1 homolog (mouse) hs
HG-U95D:71569_AT Limb region 1 homolog (mouse) hs
HG-U95D:91218_AT Limb region 1 homolog (mouse) hs
HU35KSUBC:RC_T90672_AT Limb region 1 homolog (mouse) hs
HU35KSUBD:RC_AA425162_AT Limb region 1 homolog (mouse) hs
MOUSE430A_2:1426272_AT limb region 1 mm
MOE430A:1426272_AT limb region 1 mm
MOUSE430_2:1426272_AT limb region 1 mm
MOE430A:1426273_AT limb region 1 mm
MOUSE430A_2:1426273_AT limb region 1 mm
MOUSE430_2:1426273_AT limb region 1 mm
MOE430A:1425605_A_AT limb region 1 mm
MOUSE430A_2:1425605_A_AT limb region 1 mm
MOUSE430_2:1425605_A_AT limb region 1 mm
MOUSE430_2:1459606_AT Limb region 1, mRNA (cDNA clone MGC:28737 IMAGE:4481088) mm
MOE430B:1459606_AT Limb region 1, mRNA (cDNA clone MGC:28737 IMAGE:4481088) mm
MG-U74AV2:95880_S_AT Limb region 1, mRNA (cDNA clone MGC:28737 IMAGE:4481088) mm
Protein Similarities
Method ID Description E-Value
blast AAK21441 Hypothetical protein R05D3.2 [Caenorhabditis elegans] ref|NP_498847.1| R05D3.2 [Caenorhabditis elegans] sp|P34535|YNC2_CAEEL Hypothetical protein R05D3.2 in chromosome III 0.0
blast CAE71275 Hypothetical protein CBG18158 [Caenorhabditis briggsae] 0.0
blast AAF56340 CG5807-PA [Drosophila melanogaster] ref|NP_651290.1| CG5807-PA [Drosophila melanogaster] 5.0E-34
Protein Domains
Database ID Description E-Value
Pfam IPR006876 EMBL-EBI LMBR1-like conserved region 1.0E-126
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_498847.1 10 5-27,65-87,113-135,161-183,204-226,241-263,541-563,601-623,636-658,673-695
R05D3.2 10 5-27,65-87,113-135,161-183,204-226,241-263,541-563,601-623,636-658,673-695
Sequence
Target Sequence 
>C. ELEGANS:174128_AT
cttcttacccatgttcatcattttaatcttttcattacaaaaacaaggtcctattttttt
tctcgggtactactcgccttttctaataattcagaatcatcaatttttgccaacctctag
ctttacatgtctgtttttcatcattttctctcaagcattctcctaatatattatgttccc
tagtatttcccctcagtcagcaattttctcgtcgtcgaaaccgtttagctttactttcaa
tcaaaacgt

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
CTTCTTACCCATGTTCATCATTTTA 460 221 13 Antisense
CATGTTCATCATTTTAATCTTTTCA 581 209 22 Antisense
GTACTACTCGCCTTTTCTAATAATT 97 461 79 Antisense
ATCAATTTTTGCCAACCTCTAGCTT 183 25 111 Antisense
CCAACCTCTAGCTTTACATGTCTGT 288 277 122 Antisense
TACATGTCTGTTTTTCATCATTTTC 221 645 136 Antisense
CATCATTTTCTCTCAAGCATTCTCC 469 213 151 Antisense
TTCTCTCAAGCATTCTCCTAATATA 88 693 158 Antisense
TATATTATGTTCCCTAGTATTTCCC 63 663 179 Antisense
TTCTCGTCGTCGAAACCGTTTAGCT 441 683 218 Antisense
TTAGCTTTACTTTCAATCAAAACGT 458 681 237 Antisense
Sequence Source Affymetrix Proprietary Database