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[193229_at] cadherin-containing cell adhesion protein

Description R10F2.1 /REP_DB=WormBase Gene ID /WP=CE12704 /TR=O01912 /GB=AAB54266.1 /SUBMIT=ST.LOUIS /CHR=3 /FEA=Sanger Annotation /DEF=cadherin-containing cell adhesion protein
Cluster 6grp_high1_10_10 > 46      4grp_high_8_8 > 43      6grp_total > 36      4grp_total > 44      6grp_high1_sub > Cu      6grp_total_sub > Cup      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 66
1 2 3 4 range
A 97.5
(0.4)
P 		120.3
(3)
P 		68.3
(-3)
A 		71.7
(-2.6)
P 		52
B 92.8
(1)
P 		108
(3)
P 		84.8
(0)
P 		61.3
(-3)
P 		47
C 127.7
(3)
P 		94.9
(-2.5)
P 		92.1
(-3)
P 		105.5
(-0.7)
P 		36
avr 106
(2.6) 		107.7
(3) 		81.7
(-2.5) 		79.5
(-3) 		28

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 70
1 2 3 4 5 6 range
A 94.4
(3)
P 		69.6
(0.6)
P 		80.5
(1.7)
P 		47.1
(-1.5)
A 		31.1
(-3)
A 		94.3
(3)
P 		63
B 84.8
(1.6)
P 		68.5
(-1.2)
P 		63.4
(-2.1)
P 		93
(3)
P 		58.1
(-3)
P 		72
(-0.6)
P 		35
C 92.9
(2.2)
P 		101.2
(3)
P 		74
(0.5)
P 		74.1
(0.5)
P 		35.8
(-3)
M 		62.2
(-0.6)
P 		65
avr 90.7
(3) 		79.8
(1.7) 		72.6
(0.8) 		71.4
(0.6) 		41.7
(-3) 		76.2
(1.2) 		49
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 32
1 2 3 4 range
A 35.5
(3)
P 		26.1
(0.7)
P 		17.9
(-1.2)
A 		10.5
(-3)
P 		25
B 29.6
(3)
P 		26.7
(1.9)
P 		19.7
(-0.6)
P 		13.1
(-3)
P 		17
C 42.3
(3)
P 		27.3
(-0.7)
P 		32.1
(0.5)
P 		17.8
(-3)
P 		25
avr 35.8
(3) 		26.7
(0.5) 		23.2
(-0.4) 		13.8
(-3) 		22

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 25
1 2 3 4 5 6 range
A 17.4
(0.1)
P 		24.8
(3)
P 		17.5
(0.2)
P 		11.9
(-2)
A 		9.4
(-3)
A 		23
(2.3)
P 		15
B 29.5
(3)
P 		22.8
(0.1)
P 		15.4
(-3)
P 		24.6
(0.9)
P 		23.6
(0.5)
P 		26.9
(1.9)
P 		14
C 34.4
(3)
P 		30.9
(2.1)
P 		18.8
(-1.1)
P 		14.9
(-2.1)
P 		11.6
(-3)
M 		20.8
(-0.6)
P 		23
avr 27.1
(3) 		26.2
(2.6) 		17.2
(-1.9) 		17.1
(-1.9) 		14.9
(-3) 		23.6
(1.3) 		12
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 193229_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.7069
Sequence Type Exemplar sequence
Representative Public ID R10F2.1 NCBI
Target Description R10F2.1 /REP_DB=WormBase Gene ID /WP=CE12704 /TR=O01912 /GB=AAB54266.1 /SUBMIT=ST.LOUIS /CHR=3 /FEA=Sanger Annotation /DEF=cadherin-containing cell adhesion protein
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_065240(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_065240 NCBI Caenorhabditis elegans R10F2.1 (R10F2.1) mRNA, complete cds. 11/11 None
SNAP00000016977 ENSEMBL cdna:SNAP chromosome:CEL140:III:2925741:2935547:1 11/11 None
GENEFINDER00000016982 ENSEMBL cdna:GeneFinder chromosome:CEL140:III:2925789:2936916:1 11/11 None
R10F2.1 ENSEMBL cdna:known chromosome:CEL140:III:2910960:2935547:1 gene:R10F2.1 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
chrIII:2925740-2936807(+) 100.0 100.0
Public Domain and Genome References
Gene Title cadherin-containing cell adhesion protein
Ensembl R10F2.1
Entrez Gene 187783 Entrez gene
SwissProt Q5F4W0 EMBL-EBI
WormBase CE38097 Wormbase
Functional Annotations
Ortholog
ID Title Organism
CANINE:1592051_AT similar to dachsous 1 precursor cfa
CANINE_2:CFA.7443.1.S1_AT similar to dachsous 1 precursor cfa
CANINE_2:CFAAFFX.10796.1.S1_S_AT similar to dachsous 1 precursor cfa
DROSOPHILA_2:1640627_AT dachsous dm
DROSGENOME1:143132_AT dachsous dm
CHICKEN:GGAAFFX.11115.1.S1_AT similar to protocadherin 16 precursor; fibroblast cadherin FIB1; fibroblast cadherin 1; dachsous homologue gga
CHICKEN:GGAAFFX.11115.2.S1_S_AT similar to protocadherin 16 precursor; fibroblast cadherin FIB1; fibroblast cadherin 1; dachsous homologue gga
CHICKEN:GGAAFFX.11115.4.S1_S_AT similar to protocadherin 16 precursor; fibroblast cadherin FIB1; fibroblast cadherin 1; dachsous homologue gga
HG-U95AV2:1689_AT dachsous 1 (Drosophila) hs
HC-G110:1689_AT dachsous 1 (Drosophila) hs
HG-U133_PLUS_2:218892_AT dachsous 1 (Drosophila) hs
HG-U133A:218892_AT dachsous 1 (Drosophila) hs
HG-U133A_2:218892_AT dachsous 1 (Drosophila) hs
HG-U133A:222101_S_AT dachsous 1 (Drosophila) hs
HG-U133A_2:222101_S_AT dachsous 1 (Drosophila) hs
HG-U133_PLUS_2:222101_S_AT dachsous 1 (Drosophila) hs
HU35KSUBA:RC_AA453795_AT dachsous 1 (Drosophila) hs
HU35KSUBD:RC_T54160_S_AT dachsous 1 (Drosophila) hs
HUGENEFL:AB000895_AT dachsous 1 (Drosophila) hs
U133_X3P:G13375702_3P_X_AT dachsous 1 (Drosophila) hs
U133_X3P:G13375702_3P_AT dachsous 1 (Drosophila) hs
U133_X3P:G13375702_3P_A_AT dachsous 1 (Drosophila) hs
U133_X3P:HS.9658.1.S1_3P_A_AT dachsous 1 (Drosophila) hs
HG-U95B:44770_S_AT dachsous 1 (Drosophila) hs
HG-U95B:47586_S_AT dachsous 1 (Drosophila) hs
HG-U95B:47587_R_AT dachsous 1 (Drosophila) hs
HG-U133_PLUS_2:231649_AT Dachsous 1 (Drosophila) hs
HG-U133B:231649_AT Dachsous 1 (Drosophila) hs
HG-U95E:69577_AT Dachsous 1 (Drosophila) hs
HG-U95E:89623_AT Dachsous 1 (Drosophila) hs
U133_X3P:HS.199850.0.A1_3P_AT Dachsous 1 (Drosophila) hs
U133_X3P:HS.9658.1.S1_3P_X_AT Dachsous 1 (Drosophila) hs
RG-U34A:RC_H31750_AT protocadherin 16 dachsous-like (Drosophila) (predicted) rn
RAE230A:1386422_AT protocadherin 16 dachsous-like (Drosophila) (predicted) rn
RAT230_2:1386422_AT protocadherin 16 dachsous-like (Drosophila) (predicted) rn
RAE230A:1388657_AT Protocadherin 16 dachsous-like (Drosophila) (predicted) rn
RAT230_2:1388657_AT Protocadherin 16 dachsous-like (Drosophila) (predicted) rn
RG-U34B:RC_AI060199_AT Protocadherin 16 dachsous-like (Drosophila) (predicted) rn
Gene Ontology
GO Biological Process (view graph)
ID Description Evidence Links
7156 homophilic cell adhesion inferred from electronic annotation QuickGO AmiGO
GO Cellular Component (view graph)
ID Description Evidence Links
16020 membrane inferred from electronic annotation QuickGO AmiGO
GO Molecular Function (view graph)
ID Description Evidence Links
5509 calcium ion binding inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast NP_497641 R10F2.1 [Caenorhabditis elegans] gb|AAW88390.1| Hypothetical protein R10F2.1 [Caenorhabditis elegans] 0.0
blast T15276 hypothetical protein R10F2.1 - Caenorhabditis elegans 0.0
blast CAE69524 Hypothetical protein CBG15733 [Caenorhabditis briggsae] 0.0
Protein Domains
Database ID Description E-Value
Pfam IPR002126 EMBL-EBI Cadherin 1.8E-18
Pfam IPR002126 EMBL-EBI Cadherin 1.3E-7
Pfam IPR002126 EMBL-EBI Cadherin 1.8E-20
Pfam IPR002126 EMBL-EBI Cadherin 1.7E-27
Pfam IPR002126 EMBL-EBI Cadherin 6.5E-7
Pfam IPR002126 EMBL-EBI Cadherin 4.7E-8
Pfam IPR002126 EMBL-EBI Cadherin 5.2E-9
Pfam IPR002126 EMBL-EBI Cadherin 1.9E-7
Pfam IPR002126 EMBL-EBI Cadherin 5.8E-6
Pfam IPR002126 EMBL-EBI Cadherin 7.0E-17
Pfam IPR002126 EMBL-EBI Cadherin 2.4E-4
Pfam IPR002126 EMBL-EBI Cadherin 1.6E-5
Pfam IPR002126 EMBL-EBI Cadherin 2.3E-12
Pfam IPR002126 EMBL-EBI Cadherin 7.7E-9
Pfam IPR002126 EMBL-EBI Cadherin 4.9E-7
Pfam IPR002126 EMBL-EBI Cadherin 1.8E-18
Pfam IPR002126 EMBL-EBI Cadherin 1.3E-7
Pfam IPR002126 EMBL-EBI Cadherin 1.8E-20
Pfam IPR002126 EMBL-EBI Cadherin 1.7E-27
Pfam IPR002126 EMBL-EBI Cadherin 6.5E-7
Pfam IPR002126 EMBL-EBI Cadherin 4.7E-8
Pfam IPR002126 EMBL-EBI Cadherin 5.2E-9
Pfam IPR002126 EMBL-EBI Cadherin 1.9E-7
Pfam IPR002126 EMBL-EBI Cadherin 5.8E-6
Pfam IPR002126 EMBL-EBI Cadherin 7.0E-17
Pfam IPR002126 EMBL-EBI Cadherin 2.4E-4
Pfam IPR002126 EMBL-EBI Cadherin 1.6E-5
Pfam IPR002126 EMBL-EBI Cadherin 2.3E-12
Pfam IPR002126 EMBL-EBI Cadherin 7.7E-9
Pfam IPR002126 EMBL-EBI Cadherin 4.9E-7
Pfam IPR002126 EMBL-EBI Cadherin 2.5E-5
Pfam IPR002126 EMBL-EBI Cadherin 1.3E-9
Pfam IPR002126 EMBL-EBI Cadherin 3.0E-22
Pfam IPR002126 EMBL-EBI Cadherin 1.6E-10
Pfam IPR002126 EMBL-EBI Cadherin 1.3E-10
Pfam IPR002126 EMBL-EBI Cadherin 1.8E-18
Pfam IPR002126 EMBL-EBI Cadherin 1.3E-7
Pfam IPR002126 EMBL-EBI Cadherin 1.8E-20
Pfam IPR002126 EMBL-EBI Cadherin 1.7E-27
Pfam IPR002126 EMBL-EBI Cadherin 6.5E-7
Pfam IPR002126 EMBL-EBI Cadherin 4.7E-8
Pfam IPR002126 EMBL-EBI Cadherin 5.2E-9
Pfam IPR002126 EMBL-EBI Cadherin 1.9E-7
Pfam IPR002126 EMBL-EBI Cadherin 5.8E-6
Pfam IPR002126 EMBL-EBI Cadherin 7.0E-17
Pfam IPR002126 EMBL-EBI Cadherin 2.4E-4
Pfam IPR002126 EMBL-EBI Cadherin 1.6E-5
Pfam IPR002126 EMBL-EBI Cadherin 2.3E-12
Pfam IPR002126 EMBL-EBI Cadherin 7.7E-9
Pfam IPR002126 EMBL-EBI Cadherin 4.9E-7
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_497641.2 2 9-31,2552-2574
R10F2.1 2 9-31,2552-2574
SNAP00000016977 1 1978-2000
GENEFINDER00000016982 1 1962-1984
Sequence
Target Sequence 
>C. ELEGANS:193229_AT
aaccatcacttccgaagcttctacttcactcgaaacctgtccaaatcgcggtggcatctt
taattctactcttgtttcttctcattgtggttatctgcatttgcatgtgcaaatctagaa
ggaaaactcagaatgagaaggagaaaaagcatccggatgtgattgtcaccgccgaacgga
ggccctcatctcagaagccaacgcttcagaaacaggtctactcagtgaaaaccggagaaa
tccgaacactctccgacgcccaacatcatcaccatcatccaactcactcgatgacgtcat
cagtttccacgtcatcagatgctcttcgaatggttcgaggcagctcgcggagccaaatgg
actcgggaattgatccggacaacgtatcaatcaactcatcggtcacagattatctggtgt
cactcggagtgaatgcaaacccgattccacctaggataaggcccaatacgacatacgact
cgctgatgaacgagtacatatacgcacgcgtcgaggatgtcctaccacccggaccaatca
gtctaacgaccccaaatcaacattc

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
AACCATCACTTCCGAAGCTTCTACT 638 147 5876 Antisense
AAACCTGTCCAAATCGCGGTGGCAT 317 125 5908 Antisense
GCGGTGGCATCTTTAATTCTACTCT 70 293 5923 Antisense
TAATTCTACTCTTGTTTCTTCTCAT 96 635 5936 Antisense
ATCCGGATGTGATTGTCACCGCCGA 151 39 6026 Antisense
GCTCGCGGAGCCAAATGGACTCGGG 517 299 6218 Antisense
GTATCAATCAACTCATCGGTCACAG 428 453 6259 Antisense
GGCCCAATACGACATACGACTCGCT 252 543 6335 Antisense
TATACGCACGCGTCGAGGATGTCCT 523 657 6374 Antisense
CACCCGGACCAATCAGTCTAACGAC 62 201 6401 Antisense
GTCTAACGACCCCAAATCAACATTC 81 471 6416 Antisense
Sequence Source Affymetrix Proprietary Database