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[189546_s_at] homeobox protein

Description F17A9.6 /REP_DB=WormBase Gene ID /WP=CE27970 /TR=O16218 /GB=AAB65283.2 /SUBMIT=ST.LOUIS /CHR=5 /FEA=Sanger Annotation /DEF=homeobox protein
Cluster 6grp_total > 79      4grp_total > 39      6grp_cgc > 59      6grp_cgc_sub > Da      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 49
1 2 3 4 range
A 8.3
(-1.2)
A 		5.8
(-3)
A 		9.5
(-0.4)
A 		14.3
(3)
A 		9
B 54.5
(3)
A 		29.2
(-0.9)
A 		25.9
(-1.4)
A 		15.2
(-3)
A 		39
C 51.4
(3)
A 		36.7
(-0.7)
A 		27.5
(-3)
A 		50
(2.6)
A 		24
avr 38.1
(3) 		23.9
(-2) 		21
(-3) 		26.5
(-1.1) 		17

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 101
1 2 3 4 5 6 range
A 47.7
(-0.3)
A 		9.2
(-3)
A 		17.3
(-2.4)
A 		13
(-2.7)
A 		59.7
(0.6)
P 		93.8
(3)
P 		85
B 22.9
(-1.8)
A 		23.1
(-1.8)
A 		8.8
(-2.7)
A 		3.6
(-3)
A 		70.5
(1.3)
P 		97.2
(3)
P 		94
C 19.4
(-2.4)
A 		28.6
(-1.8)
A 		34.4
(-1.4)
A 		9.4
(-3)
A 		56
(-0.1)
P 		104.6
(3)
P 		95
avr 30
(-1.6) 		20.3
(-2.2) 		20.2
(-2.2) 		8.7
(-3) 		62.1
(0.6) 		98.5
(3) 		90
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 16
1 2 3 4 range
A 3
(3)
A 		1.3
(-3)
A 		2.5
(1.2)
A 		2.1
(-0.2)
A 		2
B 17.4
(3)
A 		7.2
(-1.3)
A 		6
(-1.8)
A 		3.2
(-3)
A 		14
C 17
(3)
A 		10.5
(-1.5)
A 		9.6
(-2.2)
A 		8.4
(-3)
A 		9
avr 12.5
(3) 		6.3
(-1.7) 		6
(-1.9) 		4.6
(-3) 		8

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 35
1 2 3 4 5 6 range
A 8.8
(-1.3)
A 		3.3
(-3)
A 		3.8
(-2.8)
A 		3.3
(-3)
A 		18
(1.5)
P 		22.8
(3)
P 		20
B 8
(-1.8)
A 		7.7
(-1.9)
A 		2.1
(-2.8)
A 		1
(-3)
A 		28.6
(1.7)
P 		36.2
(3)
P 		35
C 7.2
(-2)
A 		8.7
(-1.8)
A 		8.8
(-1.7)
A 		1.9
(-3)
A 		18.1
(-0.1)
P 		35
(3)
P 		33
avr 8
(-1.8) 		6.6
(-2.1) 		4.9
(-2.4) 		2.1
(-3) 		21.6
(1) 		31.3
(3) 		29
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 189546_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.11770
Sequence Type Exemplar sequence
Representative Public ID F17A9.6 NCBI
Target Description F17A9.6 /REP_DB=WormBase Gene ID /WP=CE27970 /TR=O16218 /GB=AAB65283.2 /SUBMIT=ST.LOUIS /CHR=5 /FEA=Sanger Annotation /DEF=homeobox 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_072180(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_072180 NCBI Caenorhabditis elegans F17A9.6 (F17A9.6) mRNA, complete cds. 11/11 None
GENEFINDER00000021130 ENSEMBL cdna:GeneFinder chromosome:CEL140:V:6120661:6122795:-1 11/11 None
F17A9.6 ENSEMBL cdna:known chromosome:CEL140:V:6120992:6122795:-1 gene:F17A9.6 11/11 None
Annotation Notes
Cross Hybridizing mRNA Matched Probes Nature of Assignment Related Probesets by Grade
SNAP00000021124 3/11 Cross Hyb Matching Probes None
SNAP00000021125 6/11 Cross Hyb Matching Probes None
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrV:6121106-6122795(-) 94.67 100.0
Public Domain and Genome References
Gene Title homeobox protein
Gene Symbol ceh-49
Ensembl F17A9.6
Entrez Gene 179001 Entrez gene
SwissProt O16218 EMBL-EBI
WormBase CE27970 Wormbase
Functional Annotations
Gene Ontology
GO Biological Process (view graph)
ID Description Evidence Links
6355 regulation of transcription, DNA-dependent inferred from electronic annotation QuickGO AmiGO
GO Cellular Component (view graph)
ID Description Evidence Links
5634 nucleus inferred from electronic annotation QuickGO AmiGO
GO Molecular Function (view graph)
ID Description Evidence Links
3677 DNA binding inferred from electronic annotation QuickGO AmiGO
3700 transcription factor activity inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast AAB65283 Hypothetical protein F17A9.6 [Caenorhabditis elegans] ref|NP_504581.1| F17A9.6 [Caenorhabditis elegans] 1.0E-174
blast AAB65283 Hypothetical protein F17A9.6 [Caenorhabditis elegans] ref|NP_504581.1| F17A9.6 [Caenorhabditis elegans] 1.0E-128
blast CAE68199 Hypothetical protein CBG13865 [Caenorhabditis briggsae] 1.0E-20
blast CAE63442 Hypothetical protein CBG07897 [Caenorhabditis briggsae] 1.0E-19
blast CAE68199 Hypothetical protein CBG13865 [Caenorhabditis briggsae] 1.0E-12
blast CAE63442 Hypothetical protein CBG07897 [Caenorhabditis briggsae] 9.0E-12
Protein Domains
Database ID Description E-Value
scop a.4.1.Homeodomain All alpha proteins; DNA/RNA-binding 3-helical bundle; Homeodomain-like; Homeodomain 6.99999975040555E-4
Pfam IPR001356 EMBL-EBI Homeobox 5.0E-4
Pfam IPR003350 EMBL-EBI Homeodomain protein CUT 9.9E-16
Pfam IPR003350 EMBL-EBI Homeodomain protein CUT 9.9E-16
Sequence
Target Sequence 
>C. ELEGANS:189546_S_AT
agacaagaagctgtatctccctcatcgagtaactctgaacagtcaaagtacagcaagcag
gaagctcttgcgatgcttgataatccaacaatcataaaagagattgacttcgatttaaaa
gatctctgtgataagatgtttgtcttcttttccgaaaacaagaggcatattgaaatttcg
aaaccaatgaaccaaacaaatttcgcggagcacattctcaacagaactcaaggatcgttg
tccgaactgctgaatcatccaaaaccatgggacgcagtttccatgggaagaacggtctac
cagagaatgttcaattggctggaaatgtctgaggatgatcgcgcagagatttggaagctt
gatttgaagaaggagaaggctgacaagacaacaaaaactccgcgagcacgatgtttgctg
tcgcaggatcaaaaaagccaactcagcatctttttcgagaccaatccccgtccagactcg
ctggaaatgaagcaactgggaagtactctcaatctttgcaaaagcacgatcatcaattat
ttcacga

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
AGACAAGAAGCTGTATCTCCCTCAT 569 71 430 Antisense
TCTCCCTCATCGAGTAACTCTGAAC 451 611 445 Antisense
GCAGGAAGCTCTTGCGATGCTTGAT 310 311 486 Antisense
TAAGATGTTTGTCTTCTTTTCCGAA 404 637 561 Antisense
AGAACTCAAGGATCGTTGTCCGAAC 629 71 652 Antisense
TTGTCCGAACTGCTGAATCATCCAA 335 709 667 Antisense
AAAACTCCGCGAGCACGATGTTTGC 137 131 823 Antisense
GCACGATGTTTGCTGTCGCAGGATC 166 315 835 Antisense
GCCAACTCAGCATCTTTTTCGAGAC 66 279 866 Antisense
TGGGAAGTACTCTCAATCTTTGCAA 209 555 926 Antisense
AGCACGATCATCAATTATTTCACGA 467 77 952 Antisense
Sequence Source Affymetrix Proprietary Database