[Home] | [Total List]

[188739_at] cadherin

Description Y55H10A.1 /REP_DB=WormBase Gene ID /WP=CE19628 /TR=Q9TYW1 /GB=AAC69004.1 /SUBMIT=ST.LOUIS /CHR=4 /FEA=Sanger Annotation /DEF=cadherin
Cluster 6grp_highest_10_10 > 40      6grp_high1_10_10 > 04      4grp_highest_8_8 > 25      4grp_high_8_8 > 59      6grp_highest_nonorm > 11      6grp_total > 15      4grp_total > 60      6grp_highest_sub > De      6grp_high1_sub > De      6grp_total_sub > Decrease      6grp_rule_based > S1      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 4172
1 2 3 4 range
A 4023.6
(2.5)
P 		4074.9
(2.6)
P 		4267
(3)
P 		1061.4
(-3)
P 		3206
B 3530.5
(2)
P 		3212.1
(1.3)
P 		3995.3
(3)
P 		1248.1
(-3)
P 		2747
C 4316.9
(2.4)
P 		4053.8
(2)
P 		4724.2
(3)
P 		552.5
(-3)
P 		4172
avr 3957
(2.3) 		3780.3
(2) 		4328.8
(3) 		954
(-3) 		3375

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 2857
1 2 3 4 5 6 range
A 1913.6
(0.7)
P 		2690.7
(3)
P 		1456.4
(-0.7)
P 		858
(-2.5)
P 		856.5
(-2.5)
P 		673.1
(-3)
P 		2018
B 2226.9
(3)
P 		1633.1
(0.7)
P 		1446.8
(0)
P 		1476.6
(0.1)
P 		836.2
(-2.3)
P 		650.9
(-3)
P 		1576
C 3507.6
(3)
P 		1672.8
(-0.9)
P 		1693.1
(-0.8)
P 		1023
(-2.2)
P 		1228.8
(-1.8)
P 		661.6
(-3)
P 		2846
avr 2549.4
(3) 		1998.9
(1.3) 		1532.1
(-0.2) 		1119.2
(-1.5) 		973.8
(-2) 		661.9
(-3) 		1888
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 1553
1 2 3 4 range
A 1465
(3)
P 		884.5
(0.3)
P 		1115.5
(1.4)
P 		155.4
(-3)
P 		1310
B 1125.8
(3)
P 		793.3
(0.7)
P 		925.8
(1.6)
P 		266
(-3)
P 		860
C 1429
(2.2)
P 		1165.5
(1.1)
P 		1646.5
(3)
P 		93.2
(-3)
P 		1553
avr 1339.9
(3) 		947.8
(1) 		1229.3
(2.4) 		171.5
(-3) 		1168

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 1136
1 2 3 4 5 6 range
A 352.8
(-1.6)
P 		957
(3)
P 		317.2
(-1.8)
P 		217.6
(-2.6)
P 		258.4
(-2.3)
P 		163.9
(-3)
P 		793
B 774.8
(3)
P 		543.6
(0.4)
P 		351.3
(-1.8)
P 		391.1
(-1.3)
P 		339.7
(-1.9)
P 		242.7
(-3)
P 		532
C 1300.1
(3)
P 		510.4
(-1.3)
P 		430.9
(-1.8)
P 		205.7
(-3)
P 		397.6
(-1.9)
P 		221.5
(-2.9)
P 		1094
avr 809.2
(3) 		670.3
(1.6) 		366.5
(-1.4) 		271.5
(-2.4) 		331.9
(-1.8) 		209.4
(-3) 		600
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 188739_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.10687
Sequence Type Exemplar sequence
Representative Public ID Y55H10A.1 NCBI
Target Description Y55H10A.1 /REP_DB=WormBase Gene ID /WP=CE19628 /TR=Q9TYW1 /GB=AAC69004.1 /SUBMIT=ST.LOUIS /CHR=4 /FEA=Sanger Annotation /DEF=cadherin
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_067931(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_067931 NCBI Caenorhabditis elegans Y55H10A.1 (cadherin) mRNA, complete cds. 11/11 None
GENEFINDER00000012668 ENSEMBL cdna:GeneFinder chromosome:CEL140:IV:3369194:3373063:1 11/11 None
Y55H10A.1.2 ENSEMBL cdna:known chromosome:CEL140:IV:3369191:3373352:1 gene:Y55H10A.1 11/11 None
Y55H10A.1.1 ENSEMBL cdna:known chromosome:CEL140:IV:3369193:3373463:1 gene:Y55H10A.1 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
chrIV:3369199-3372922(+) 100.0 100.0
Public Domain and Genome References
Gene Title cadherin
Ensembl Y55H10A.1
Entrez Gene 177103 Entrez gene
SwissProt Q9TYW1 EMBL-EBI
WormBase CE19628 Wormbase
Functional Annotations
Gene Ontology
GO Biological Process (view graph)
ID Description Evidence Links
15986 ATP synthesis coupled proton transport inferred from electronic annotation QuickGO AmiGO
GO Cellular Component (view graph)
ID Description Evidence Links
16021 integral to membrane inferred from electronic annotation QuickGO AmiGO
16469 proton-transporting two-sector ATPase complex inferred from electronic annotation QuickGO AmiGO
GO Molecular Function (view graph)
ID Description Evidence Links
46933 hydrogen-transporting ATP synthase activity, rotational mechanism inferred from electronic annotation QuickGO AmiGO
46961 hydrogen-transporting ATPase activity, rotational mechanism inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast AAC69004 Hypothetical protein Y55H10A.1 [Caenorhabditis elegans] ref|NP_500332.1| Y55H10A.1 [Caenorhabditis elegans] 0.0
blast CAE73571 Hypothetical protein CBG21042 [Caenorhabditis briggsae] 1.0E-159
blast CAE73571 Hypothetical protein CBG21042 [Caenorhabditis briggsae] 1.0E-153
blast CAE69615 Hypothetical protein CBG15848 [Caenorhabditis briggsae] 4.0E-97
Protein Domains
Database ID Description E-Value
Pfam IPR008388 EMBL-EBI Vacuolar ATP synthase subunit S1 1.0E-126
Pfam IPR008388 EMBL-EBI Vacuolar ATP synthase subunit S1 4.5E-50
Pfam IPR008388 EMBL-EBI Vacuolar ATP synthase subunit S1 1.0E-126
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_500332.1 1 406-428
Y55H10A.1.2 1 406-428
Y55H10A.1.1 1 406-428
GENEFINDER00000012668 1 434-456
Sequence
Target Sequence 
>C. ELEGANS:188739_AT
ccgatgtaacctgcccgaatggaacaattggagatttcatttttaagattcatctcaccc
tcgaaaacgatattactggaatgcagggtaccagcaagaaggctttcacaatgaaaaaag
gagataaaatcgattttgacctcacttttactggagatttgtttggttattgggcactta
acaaggcttcggccagtaatcttgctatcagtggatatgatccatataagagtgcctccg
ttgacggcagcaaagtggtaaatggctcagcaacccaatacacaaagcttaactcagtcg
ccggatggtcgttggcctgtggacaatctcaagcagtctttttcccaacaaatgaacaat
ccgtccgaattggtgtggctcttatgaacactcaaattcaacttttcaactatcaaaacc
ccgaaaaatgggtcgaatctgcccatttcacactacaaaccgaagattgtactggaacat
tctcctcgggatcctggatgggaatcgtatcggcacttgttctgattgctggcctaatgt
tcggatatgttatgcttcagtccgttca

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
CCGATGTAACCTGCCCGAATGGAAC 104 265 740 Antisense
TTAAGATTCATCTCACCCTCGAAAA 329 683 782 Antisense
GCTTCGGCCAGTAATCTTGCTATCA 144 307 925 Antisense
GTGCCTCCGTTGACGGCAGCAAAGT 534 463 971 Antisense
ACAAAGCTTAACTCAGTCGCCGGAT 513 109 1021 Antisense
GATGGTCGTTGGCCTGTGGACAATC 166 407 1043 Antisense
CAATCTCAAGCAGTCTTTTTCCCAA 703 179 1063 Antisense
TGGGTCGAATCTGCCCATTTCACAC 455 553 1168 Antisense
TTCTCCTCGGGATCCTGGATGGGAA 7 681 1219 Antisense
TCGGCACTTGTTCTGATTGCTGGCC 51 605 1249 Antisense
GATATGTTATGCTTCAGTCCGTTCA 593 425 1283 Antisense
Sequence Source Affymetrix Proprietary Database