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[192019_at] homeobox protein

Description F33D11.4 /REP_DB=WormBase Gene ID /WP=CE09894 /GEN=ceh-12 /TR=Q9TZZ7 /GB=AAB96698.1 /SUBMIT=ST.LOUIS /CHR=1 /FEA=Sanger Annotation /DEF=homeobox protein
Cluster 6grp_total > 0      4grp_total > 43      6grp_total_sub > Hat      6grp_cgc > 53      6grp_cgc_sub > 02      6grp_rule_based > S2      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 82
1 2 3 4 range
A 5.7
(-3)
A 		26.7
(3)
A 		8.3
(-2.3)
A 		13.9
(-0.7)
A 		21
B 5.3
(-3)
A 		84.9
(3)
A 		33.7
(-0.9)
A 		29.7
(-1.2)
A 		80
C 2.8
(-3)
A 		67.5
(3)
A 		6.2
(-2.7)
A 		27.6
(-0.7)
A 		65
avr 4.6
(-3) 		59.7
(3) 		16.1
(-1.7) 		23.7
(-0.9) 		55

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 36
1 2 3 4 5 6 range
A 8.8
(-2.3)
A 		36.8
(3)
A 		9.2
(-2.2)
A 		7.2
(-2.6)
A 		4.9
(-3)
A 		8.5
(-2.3)
A 		32
B 2.4
(-3)
A 		38.4
(3)
A 		5.3
(-2.5)
A 		9.7
(-1.8)
A 		7.7
(-2.1)
A 		4.7
(-2.6)
A 		36
C 2.1
(-3)
A 		29.8
(3)
A 		7.2
(-1.9)
A 		8.5
(-1.6)
A 		2
(-3)
A 		4.8
(-2.4)
A 		28
avr 4.4
(-3) 		35
(3) 		7.2
(-2.5) 		8.5
(-2.2) 		4.9
(-2.9) 		6
(-2.7) 		31
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 20
1 2 3 4 range
A 2.1
(-2.8)
A 		5.8
(3)
A 		2.2
(-2.7)
A 		2
(-3)
A 		4
B 1.7
(-3)
A 		21
(3)
A 		7.8
(-1.1)
A 		6.3
(-1.6)
A 		19
C 0.9
(-3)
A 		19.4
(3)
A 		2.2
(-2.6)
A 		4.7
(-1.8)
A 		19
avr 1.6
(-3) 		15.4
(3) 		4.1
(-1.9) 		4.3
(-1.8) 		14

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 12
1 2 3 4 5 6 range
A 1.6
(-2.9)
A 		13.1
(3)
A 		2
(-2.7)
A 		1.8
(-2.8)
A 		1.5
(-3)
A 		2.1
(-2.7)
A 		12
B 0.8
(-3)
A 		12.8
(3)
A 		1.3
(-2.8)
A 		2.6
(-2.1)
A 		3.1
(-1.9)
A 		1.8
(-2.5)
A 		12
C 0.8
(-2.9)
A 		9.1
(3)
A 		1.8
(-2.2)
A 		1.7
(-2.3)
A 		0.7
(-3)
A 		1.6
(-2.4)
A 		8
avr 1.1
(-3) 		11.7
(3) 		1.7
(-2.7) 		2
(-2.5) 		1.8
(-2.6) 		1.8
(-2.6) 		11
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 192019_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.516
Sequence Type Exemplar sequence
Representative Public ID F33D11.4 NCBI
Target Description F33D11.4 /REP_DB=WormBase Gene ID /WP=CE09894 /GEN=ceh-12 /TR=Q9TZZ7 /GB=AAB96698.1 /SUBMIT=ST.LOUIS /CHR=1 /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_059292(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_059292 NCBI Caenorhabditis elegans C.Elegans Homeobox family member (ceh-12) (ceh-12) mRNA, complete cds. 11/11 None
GENEFINDER00000028972 ENSEMBL cdna:GeneFinder chromosome:CEL140:I:5848425:5849969:1 10/11 None
F33D11.4 ENSEMBL cdna:known chromosome:CEL140:I:5848425:5850022:1 gene:F33D11.4 11/11 None
Annotation Notes
Cross Hybridizing mRNA Matched Probes Nature of Assignment Related Probesets by Grade
SNAP00000028949 6/11 Cross Hyb Matching Probes None
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrI:5848424-5850022(+) 100.0 100.0
Public Domain and Genome References
Gene Title homeobox protein
Gene Symbol ceh-12
Ensembl F33D11.4
Entrez Gene 172255 Entrez gene
SwissProt P17487 EMBL-EBI
WormBase CE09894 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 AAB96698 C.elegans homeobox protein 12 [Caenorhabditis elegans] ref|NP_491693.1| C.Elegans Homeobox family member (ceh-12) [Caenorhabditis elegans] sp|P17487|HM12_CAEEL Homeobox protein ceh-12 1.0E-72
blast AAB96698 C.elegans homeobox protein 12 [Caenorhabditis elegans] ref|NP_491693.1| C.Elegans Homeobox family member (ceh-12) [Caenorhabditis elegans] sp|P17487|HM12_CAEEL Homeobox protein ceh-12 4.0E-63
blast CAE60417 Hypothetical protein CBG04023 [Caenorhabditis briggsae] 5.0E-51
blast CAE60417 Hypothetical protein CBG04023 [Caenorhabditis briggsae] 2.0E-41
blast AAF50503 CG8254-PA [Drosophila melanogaster] ref|NP_648164.1| CG8254-PA [Drosophila melanogaster] gb|AAL89903.1| RE39081p [Drosophila melanogaster] 2.0E-18
blast AAF50503 CG8254-PA [Drosophila melanogaster] ref|NP_648164.1| CG8254-PA [Drosophila melanogaster] gb|AAL89903.1| RE39081p [Drosophila melanogaster] 3.0E-11
Protein Domains
Database ID Description E-Value
scop a.4.1.Homeodomain All alpha proteins; DNA/RNA-binding 3-helical bundle; Homeodomain-like; Homeodomain 6.99999997202938E-12
scop a.4.1.Homeodomain All alpha proteins; DNA/RNA-binding 3-helical bundle; Homeodomain-like; Homeodomain 9.99999968265523E-20
Pfam IPR001356 EMBL-EBI Homeobox 3.8E-30
Pfam IPR001356 EMBL-EBI Homeobox 1.8E-15
Sequence
Target Sequence 
>C. ELEGANS:192019_AT
gatgttttcctcaatagattctcttcttaaaatctcaacttcttctcaaaatgaagatca
aaaattagagagtcacccctcccctccatcacaaattccaaattattcaaccagctgctc
tgaggaattaatgaaaatggcggcaaaagcagcccaatttgctgctcaagcctcgctgga
gaactcattttccagttctacttctcccacatcaactgttactccactttctgcatacac
gtcactggttcagccggtccttcctttgatctacgatcatttagcattaacatattcagt
aaatgcatggcaagcatggggaaagatgagaagaccacgaaccgcattcagcagtgaaca
attagttcaattagagaaacaattctcagataatcgatatttgagtagaccaagaagata
tcaattggcacaacaattatctctttcagagactcagatcaaaatctggttccaaaatcg
tcgaatgaaaaacaaacgttgcccatcttca

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GATGTTTTCCTCAATAGATTCTCTT 53 411 15 Antisense
CTTCTTAAAATCTCAACTTCTTCTC 676 219 37 Antisense
CCCCTCCATCACAAATTCCAAATTA 469 261 95 Antisense
CCAAATTATTCAACCAGCTGCTCTG 591 275 112 Antisense
GCAGCCCAATTTGCTGCTCAAGCCT 488 311 163 Antisense
CTCAAGCCTCGCTGGAGAACTCATT 581 227 179 Antisense
AACTCATTTTCCAGTTCTACTTCTC 389 141 196 Antisense
TTTCTGCATACACGTCACTGGTTCA 228 671 242 Antisense
TGAGAAGACCACGAACCGCATTCAG 396 545 341 Antisense
TTGGCACAACAATTATCTCTTTCAG 295 709 439 Antisense
GAAAAACAAACGTTGCCCATCTTCA 574 353 501 Antisense
Sequence Source Affymetrix Proprietary Database