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[190326_at] cadherin-type repeat

Description F59C12.1 /REP_DB=WormBase Gene ID /WP=CE04682 /TR=Q21035 /GB=AAK29708.1 /SUBMIT=ST.LOUIS /CHR=X /FEA=Sanger Annotation /DEF=cadherin-type repeat
Cluster 6grp_total > 26      4grp_total > 42      6grp_cgc > 14      6grp_cgc_sub > Cu      6grp_total_sub > Cup      4grp_rule_based > L2      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 142
1 2 3 4 range
A 11.5
(-2.7)
A 		103.3
(3)
A 		51.7
(-0.2)
A 		6.2
(-3)
A 		97
B 10.4
(-3)
A 		130
(3)
A 		53.6
(-0.8)
A 		11.2
(-3)
A 		120
C 36.3
(-1.8)
A 		148.1
(3)
A 		61.5
(-0.7)
A 		9
(-3)
A 		139
avr 19.4
(-2.5) 		127.1
(3) 		55.6
(-0.6) 		8.8
(-3) 		118

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 114
1 2 3 4 5 6 range
A 70
(0.7)
A 		104.8
(3)
A 		41.5
(-1.2)
A 		65.4
(0.4)
A 		29
(-2)
A 		14.1
(-3)
A 		91
B 77.6
(2.8)
A 		80
(3)
A 		27.3
(-2.3)
A 		61.2
(1.1)
A 		19.8
(-3)
A 		48
(-0.2)
A 		60
C 118.4
(3)
A 		50
(-0.6)
A 		4.6
(-3)
A 		22.3
(-2.1)
A 		37.7
(-1.3)
A 		56.4
(-0.3)
A 		114
avr 88.7
(3) 		78.3
(2) 		24.5
(-3) 		49.6
(-0.7) 		28.8
(-2.6) 		39.5
(-1.6) 		64
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 42
1 2 3 4 range
A 4.2
(-2.1)
A 		22.4
(3)
A 		13.5
(0.5)
A 		0.9
(-3)
A 		22
B 3.3
(-2.8)
A 		32.1
(3)
A 		12.4
(-1)
A 		2.4
(-3)
A 		30
C 12
(-1.5)
A 		42.6
(3)
A 		21.4
(-0.1)
A 		1.5
(-3)
A 		41
avr 6.5
(-2) 		32.4
(3) 		15.8
(-0.2) 		1.6
(-3) 		31

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 43
1 2 3 4 5 6 range
A 12.9
(-1.3)
A 		37.3
(3)
A 		9
(-2)
A 		16.6
(-0.7)
A 		8.8
(-2)
A 		3.4
(-3)
A 		34
B 27
(3)
A 		26.6
(2.9)
A 		6.6
(-3)
A 		16.2
(-0.2)
A 		8
(-2.6)
A 		17.9
(0.3)
A 		20
C 43.9
(3)
A 		15.3
(-1)
A 		1.2
(-3)
A 		4.5
(-2.5)
A 		12.2
(-1.5)
A 		18.9
(-0.5)
A 		43
avr 27.9
(3) 		26.4
(2.6) 		5.6
(-3) 		12.4
(-1.2) 		9.7
(-1.9) 		13.4
(-0.9) 		22
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 190326_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.17423
Sequence Type Exemplar sequence
Representative Public ID F59C12.1 NCBI
Target Description F59C12.1 /REP_DB=WormBase Gene ID /WP=CE04682 /TR=Q21035 /GB=AAK29708.1 /SUBMIT=ST.LOUIS /CHR=X /FEA=Sanger Annotation /DEF=cadherin-type repeat
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_078284(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_078284 NCBI Caenorhabditis elegans CaDHerin family member (cdh-9) (cdh-9) mRNA, complete cds. 11/11 None
GENEFINDER00000016447 ENSEMBL cdna:GeneFinder chromosome:CEL140:X:16595153:16601825:1 11/11 None
SNAP00000016443 ENSEMBL cdna:SNAP chromosome:CEL140:X:16596020:16601825:1 11/11 None
F59C12.1 ENSEMBL cdna:known chromosome:CEL140:X:16595153:16601955:1 gene:F59C12.1 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
chrX:16595863-16601050(+) 93.82 100.0
Public Domain and Genome References
Gene Title cadherin-type repeat
Gene Symbol cdh-9
Ensembl F59C12.1
Entrez Gene 186608 Entrez gene
SwissProt Q21035 EMBL-EBI
WormBase CE38081 Wormbase
Functional Annotations
Ortholog
ID Title Organism
DROSOPHILA_2:1639044_AT dm
DROSGENOME1:150563_AT dm
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 AAK29708 Cadherin family protein 9 [Caenorhabditis elegans] ref|NP_510685.2| CaDHerin family member (cdh-9) [Caenorhabditis elegans] 0.0
blast CAE69958 Hypothetical protein CBG16348 [Caenorhabditis briggsae] 0.0
blast CAE69984 Hypothetical protein CBG16382 [Caenorhabditis briggsae] 0.0
Protein Domains
Database ID Description E-Value
Pfam IPR002126 EMBL-EBI Cadherin 2.9E-15
Pfam IPR002126 EMBL-EBI Cadherin 2.9E-15
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_510685.2 1 519-541
F59C12.1 1 519-541
GENEFINDER00000016447 1 519-541
SNAP00000016443 1 484-506
Sequence
Target Sequence 
>C. ELEGANS:190326_AT
aaatgtcgtgctccgtaagaaactcgagaagcccgaaacattgaatgttaccgcgagtga
tggagaaaatgttgtctctaccgctctccacttgatgacagccaattcggaagaatcgtg
tcgatcgccgattaagttcgaaaagttcgaatataaaatgacaattgggaaattgaatgt
gttgggagtagtgaatgccacctcacggacaggaacaaagatcacctacattttaatgaa
catgaataatgattttgaaatcgacaccaatggagtcgtgaagcttcttcccaaagcacg
tcttcagtgcaaagtttgtgagctgattgtagtggcaaaatcgggaactcaaatggcaat
caccaagattaacgtggataatccagcatttgttcttcactcgaccaccgctttaacttt
attgattcttatcattttatgtctgatcttcacgatgcttgctatcctcgtgtgtcggaa
gttttgtgaaaaatggaagacgggccatcggagatcgagcatttgttggctcaatgggac
aactgatactggcatttcta

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
AAATGTCGTGCTCCGTAAGAAACTC 147 121 1215 Antisense
GTTGGGAGTAGTGAATGCCACCTCA 445 295 1395 Antisense
AATGCCACCTCACGGACAGGAACAA 557 165 1408 Antisense
TGGAGTCGTGAAGCTTCTTCCCAAA 658 549 1485 Antisense
TCTTCCCAAAGCACGTCTTCAGTGC 567 615 1500 Antisense
TCGGGAACTCAAATGGCAATCACCA 511 605 1555 Antisense
TCGACCACCGCTTTAACTTTATTGA 253 603 1615 Antisense
TGTCTGATCTTCACGATGCTTGCTA 419 557 1654 Antisense
CTTGCTATCCTCGTGTGTCGGAAGT 64 219 1672 Antisense
AGACGGGCCATCGGAGATCGAGCAT 495 71 1712 Antisense
GGGACAACTGATACTGGCATTTCTA 574 493 1750 Antisense
Sequence Source Affymetrix Proprietary Database