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[194029_s_at] Approximately 25 cadherin-repeats, 3 EGF domains and one Laminin G domain

Description F25F2.2 /REP_DB=WormBase Gene ID /WP=CE00961 /TR=Q19319 /GB=CAA84339.1 /SUBMIT=HINXTON /CHR=3 /FEA=Sanger Annotation /DEF=Approximately 25 cadherin-repeats, 3 EGF domains and one Laminin G domain
Cluster 6grp_highest_10_10 > 52      6grp_high1_10_10 > 25      4grp_highest_8_8 > 50      4grp_high_8_8 > 33      6grp_highest_nonorm > 40      6grp_total > 26      4grp_total > 46      6grp_highest_sub > 01_02      6grp_cgc > 14      6grp_high1_sub > 01_02      6grp_cgc_sub > Cu      6grp_total_sub > Cup      4grp_rule_based > L1      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 1164
1 2 3 4 range
A 1441.5
(3)
P 		536.6
(-2.1)
P 		422.1
(-2.7)
P 		374.6
(-3)
P 		1067
B 1221.8
(3)
P 		510.9
(-1.5)
P 		339.8
(-2.6)
P 		277.9
(-3)
P 		944
C 1297.6
(3)
P 		502.2
(-2.4)
P 		405.7
(-3)
P 		420.9
(-2.9)
P 		892
avr 1320.3
(3) 		516.6
(-2) 		389.2
(-2.8) 		357.8
(-3) 		963

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 742
1 2 3 4 5 6 range
A 940
(3)
P 		944.1
(3)
P 		407
(-3)
P 		531.9
(-1.6)
P 		532.9
(-1.6)
P 		568.3
(-1.2)
P 		537
B 1085.7
(3)
P 		833.6
(1)
P 		433.7
(-2.3)
P 		600.2
(-0.9)
P 		343.4
(-3)
P 		645.8
(-0.6)
P 		742
C 788.9
(1.4)
P 		941
(3)
P 		691.8
(0.4)
P 		603.7
(-0.6)
P 		372.6
(-3)
P 		525.1
(-1.4)
P 		568
avr 938.2
(3) 		906.2
(2.6) 		510.8
(-1.9) 		578.6
(-1.1) 		416.3
(-3) 		579.7
(-1.1) 		522
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 470
1 2 3 4 range
A 524.9
(3)
P 		116.5
(-2.2)
P 		110.3
(-2.3)
P 		54.8
(-3)
P 		470
B 389.6
(3)
P 		126.2
(-1.8)
P 		78.7
(-2.6)
P 		59.2
(-3)
P 		330
C 429.5
(3)
P 		144.4
(-1.8)
P 		141.4
(-1.8)
P 		71
(-3)
P 		359
avr 448
(3) 		129
(-2) 		110.1
(-2.2) 		61.7
(-3) 		386

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 289
1 2 3 4 5 6 range
A 173.3
(-0.9)
P 		335.8
(3)
P 		88.6
(-3)
P 		134.9
(-1.9)
P 		160.8
(-1.2)
P 		138.4
(-1.8)
P 		247
B 377.8
(3)
P 		277.5
(0.8)
P 		105.3
(-3)
P 		159
(-1.8)
P 		139.5
(-2.2)
P 		240.8
(-0)
P 		273
C 292.4
(3)
P 		287.1
(2.8)
P 		176.1
(-1.1)
P 		121.4
(-3)
P 		120.6
(-3)
P 		175.8
(-1.1)
P 		172
avr 281.2
(2.4) 		300.1
(3) 		123.3
(-3) 		138.4
(-2.5) 		140.3
(-2.4) 		185
(-0.9) 		177
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 194029_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.7932
Sequence Type Exemplar sequence
Representative Public ID F25F2.2 NCBI
Target Description F25F2.2 /REP_DB=WormBase Gene ID /WP=CE00961 /TR=Q19319 /GB=CAA84339.1 /SUBMIT=HINXTON /CHR=3 /FEA=Sanger Annotation /DEF=Approximately 25 cadherin-repeats, 3 EGF domains and one Laminin G domain
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_065516(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_065516 NCBI Caenorhabditis elegans CaDHerin family member (cdh-4) (cdh-4) mRNA, complete cds. 11/11 None
SNAP00000031335 ENSEMBL cdna:SNAP chromosome:CEL140:III:4533591:4536626:1 11/11 None
GENEFINDER00000031345 ENSEMBL cdna:GeneFinder chromosome:CEL140:III:4533779:4536626:1 11/11 None
F25F2.2 ENSEMBL cdna:known chromosome:CEL140:III:4520424:4536954:1 gene:F25F2.2 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:4520423-4536626(+) 100.0 100.0
Public Domain and Genome References
Gene Title Approximately 25 cadherin-repeats, 3 EGF domains and one Laminin G domain
Gene Symbol cdh-4
Ensembl F25F2.2
Entrez Gene 175590 Entrez gene
SwissProt Q19319 EMBL-EBI
WormBase CE00961 Wormbase
Functional Annotations
Ortholog
ID Title Organism
CANINE:1605067_AT similar to FAT tumor suppressor 1 precursor cfa
CANINE:1604935_S_AT similar to FAT tumor suppressor 1 precursor cfa
CANINE_2:CFA.1833.1.S1_S_AT similar to FAT tumor suppressor 1 precursor cfa
CANINE_2:CFA.1956.1.S1_S_AT similar to FAT tumor suppressor 1 precursor cfa
CANINE_2:CFAAFFX.11837.1.S1_S_AT similar to FAT tumor suppressor 1 precursor cfa
CANINE_2:CFAAFFX.11854.1.S1_S_AT similar to FAT tumor suppressor 1 precursor cfa
CANINE_2:CFAAFFX.11855.1.S1_S_AT similar to FAT tumor suppressor 1 precursor cfa
DROSOPHILA_2:1627761_AT dm
DROSGENOME1:153251_AT dm
CHICKEN:GGA.9480.1.S1_AT FAT tumor suppressor homolog 1 (Drosophila) gga
CHICKEN:GGAAFFX.24226.1.S1_AT FAT tumor suppressor homolog 1 (Drosophila) gga
HU35KSUBA:X87241_AT FAT tumor suppressor homolog 1 (Drosophila) hs
HUGENEFL:X87241_AT FAT tumor suppressor homolog 1 (Drosophila) hs
HG-U133A_2:201579_AT FAT tumor suppressor homolog 1 (Drosophila) hs
HG-U133A:201579_AT FAT tumor suppressor homolog 1 (Drosophila) hs
HG-U133_PLUS_2:201579_AT FAT tumor suppressor homolog 1 (Drosophila) hs
HG-FOCUS:201579_AT FAT tumor suppressor homolog 1 (Drosophila) hs
HU35KSUBD:RC_N93969_AT FAT tumor suppressor homolog 1 (Drosophila) hs
U133_X3P:G4885228_3P_AT FAT tumor suppressor homolog 1 (Drosophila) hs
HG-U95AV2:40454_AT FAT tumor suppressor homolog 1 (Drosophila) hs
U133_X3P:HS2.385669.1.S1_3P_AT FAT tumor suppressor homolog 1 (Drosophila) hs
HG-U133_PLUS_2:1562937_AT FAT tumor suppressor homolog 1 (Drosophila) hs
HG-U95E:73600_AT FAT tumor suppressor homolog 1 (Drosophila) hs
MU19KSUBA:TC16289_AT FATH protein (Fath) mm
MU19KSUBB:TC34469_AT FATH protein (Fath) mm
MU19KSUBB:TC34469_G_AT FATH protein (Fath) mm
Gene Ontology
GO Biological Process (view graph)
ID Description Evidence Links
7155 cell adhesion inferred from electronic annotation QuickGO AmiGO
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
5198 structural molecule activity inferred from electronic annotation QuickGO AmiGO
5509 calcium ion binding inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast CAA84721 Hypothetical protein F25F2.2 [Caenorhabditis elegans] emb|CAA84661.1| Hypothetical protein F25F2.2 [Caenorhabditis elegans] emb|CAA84339.1| Hypothetical protein F25F2.2 [Caenorhabditis elegans] ref|NP_497917.1| CaDHerin family member (cdh-4) [Caenorhabditis elegans] 0.0
blast CAE71193 Hypothetical protein CBG18050 [Caenorhabditis briggsae] 0.0
blast AAZ66056 CG7749-PB, isoform B [Drosophila melanogaster] gb|AAF49078.2| CG7749-PA, isoform A [Drosophila melanogaster] ref|NP_649171.2| CG7749-PA [Drosophila melanogaster] sp|Q9VW71|FAT2_DROME Putative fat-like cadherin-related tumor suppressor homolog precursor 0.0
Protein Domains
Database ID Description E-Value
Pfam IPR001791 EMBL-EBI Laminin G 6.4E-14
Pfam IPR006209 EMBL-EBI EGF-like domain 3.4E-5
Pfam IPR006209 EMBL-EBI EGF-like domain 1.3E-7
Pfam IPR006209 EMBL-EBI EGF-like domain 1.6E-5
Pfam IPR002126 EMBL-EBI Cadherin 3.2E-8
Pfam IPR002126 EMBL-EBI Cadherin 3.1E-7
Pfam IPR002126 EMBL-EBI Cadherin 1.2E-18
Pfam IPR002126 EMBL-EBI Cadherin 8.9E-12
Pfam IPR002126 EMBL-EBI Cadherin 1.3E-9
Pfam IPR002126 EMBL-EBI Cadherin 5.0E-17
Pfam IPR002126 EMBL-EBI Cadherin 3.8E-7
Pfam IPR002126 EMBL-EBI Cadherin 4.1E-5
Pfam IPR002126 EMBL-EBI Cadherin 4.1E-14
Pfam IPR002126 EMBL-EBI Cadherin 5.4E-19
Pfam IPR002126 EMBL-EBI Cadherin 2.2E-4
Pfam IPR002126 EMBL-EBI Cadherin 2.3E-15
Pfam IPR002126 EMBL-EBI Cadherin 2.2E-16
Pfam IPR002126 EMBL-EBI Cadherin 1.0E-6
Pfam IPR002126 EMBL-EBI Cadherin 4.5E-21
Pfam IPR002126 EMBL-EBI Cadherin 3.2E-9
Pfam IPR002126 EMBL-EBI Cadherin 2.5E-16
Pfam IPR002126 EMBL-EBI Cadherin 1.2E-15
Pfam IPR002126 EMBL-EBI Cadherin 3.4E-8
Pfam IPR002126 EMBL-EBI Cadherin 5.4E-7
Pfam IPR002126 EMBL-EBI Cadherin 5.4E-7
Pfam IPR001791 EMBL-EBI Laminin G 6.4E-14
Pfam IPR006209 EMBL-EBI EGF-like domain 3.4E-5
Pfam IPR006209 EMBL-EBI EGF-like domain 1.3E-7
Pfam IPR006209 EMBL-EBI EGF-like domain 1.6E-5
Pfam IPR002126 EMBL-EBI Cadherin 5.4E-7
Pfam IPR001791 EMBL-EBI Laminin G 6.4E-14
Pfam IPR006209 EMBL-EBI EGF-like domain 3.4E-5
Pfam IPR006209 EMBL-EBI EGF-like domain 1.3E-7
Pfam IPR006209 EMBL-EBI EGF-like domain 1.6E-5
Trans Membrane
ID Number Of Domains Domain Boundaries
NP_497917.1 1 4052-4074
F25F2.2 1 4052-4074
SNAP00000031335 1 709-731
GENEFINDER00000031345 1 646-668
Sequence
Target Sequence 
>C. ELEGANS:194029_S_AT
aacatcgtctgtaaccacatctcatcgtccaatggttcaagttaaaccatattcttctga
tatccgtgactcaagatctccatctgcgtgcggaagttcaaagggaactcgaagagatcc
attgccatcggacaaattccggagagtagacgaaactgcaaatagaattcgtcattccga
taggaaagatccacgtggagatgtactctcatctttgagagattcatcagatgaatggat
gggaattgatgatcgaattgattcttcattgaaatactcccgtgctgcagctggtaccgt
tattgttggtgacaccgagctgatgccagtgatcaatgataacgactatatgacgatgaa
accacgaaaggacaagaacttcgaacgagagaaacctccagctattcctgctcatgcgac
tccgctcgaatctgtactcaaattgggtagctcttcaagtggagaagaggctccacgaaa
tgcattatacgacgatccgatctcat

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
AACATCGTCTGTAACCACATCTCAT 566 137 12375 Antisense
CACATCTCATCGTCCAATGGTTCAA 540 193 12390 Antisense
TATCCGTGACTCAAGATCTCCATCT 213 659 12435 Antisense
TCTCCATCTGCGTGCGGAAGTTCAA 126 611 12451 Antisense
GAACTCGAAGAGATCCATTGCCATC 252 349 12479 Antisense
GCTGCAGCTGGTACCGTTATTGTTG 442 297 12658 Antisense
GTGACACCGAGCTGATGCCAGTGAT 456 481 12683 Antisense
GAGAGAAACCTCCAGCTATTCCTGC 137 389 12761 Antisense
TCCGCTCGAATCTGTACTCAAATTG 209 597 12795 Antisense
GAGGCTCCACGAAATGCATTATACG 651 405 12841 Antisense
GCATTATACGACGATCCGATCTCAT 663 307 12856 Antisense
Sequence Source Affymetrix Proprietary Database