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[187894_at] Homeobox protein

Description K03E6.1 /REP_DB=WormBase Gene ID /WP=CE07328 /GEN=lim-6 /SUBMIT=ST.LOUIS /CHR=X /FEA=Sanger Annotation /DEF=Homeobox protein
Cluster 6grp_total > 60      4grp_total > 35      6grp_cgc > 94      6grp_cgc_sub > 04      6grp_total_sub > Hat      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 49
1 2 3 4 range
A 25.3
(-1)
A 		53.8
(3)
A 		10.7
(-3)
A 		18.7
(-1.9)
A 		43
B 6.1
(-3)
A 		14.2
(-2)
A 		6.4
(-3)
A 		54.7
(3)
A 		49
C 19
(-1.6)
A 		54.8
(3)
A 		15.8
(-2)
A 		8.4
(-3)
A 		46
avr 16.8
(-1.8) 		40.9
(3) 		11
(-3) 		27.3
(0.3) 		30

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 47
1 2 3 4 5 6 range
A 6.1
(-2.9)
A 		18.7
(-0.6)
A 		7.1
(-2.7)
A 		5.4
(-3)
A 		9
(-2.3)
A 		38.1
(3)
A 		33
B 29.8
(3)
A 		15.6
(-0.4)
A 		12.2
(-1.2)
A 		27.8
(2.5)
A 		5.5
(-2.8)
A 		4.5
(-3)
A 		25
C 14.7
(-1.7)
A 		11
(-2.1)
A 		41.2
(1.7)
A 		51.2
(3)
A 		5.1
(-2.9)
A 		4.2
(-3)
A 		47
avr 16.9
(-0.1) 		15.1
(-0.6) 		20.2
(0.8) 		28.1
(3) 		6.5
(-3) 		15.6
(-0.5) 		22
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 14
1 2 3 4 range
A 9.2
(1.3)
A 		11.7
(3)
A 		2.8
(-2.9)
A 		2.7
(-3)
A 		9
B 1.9
(-2.8)
A 		3.5
(-1.8)
A 		1.5
(-3)
A 		11.7
(3)
A 		10
C 6.3
(-1)
A 		15.8
(3)
A 		5.5
(-1.3)
A 		1.4
(-3)
A 		14
avr 5.8
(-0.9) 		10.3
(3) 		3.3
(-3) 		5.3
(-1.3) 		7

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 9
1 2 3 4 5 6 range
A 1.1
(-3)
A 		6.7
(1.1)
A 		1.5
(-2.7)
A 		1.4
(-2.8)
A 		2.7
(-1.8)
A 		9.3
(3)
A 		8
B 10.4
(3)
A 		5.2
(-0.6)
A 		3
(-2.1)
A 		7.4
(0.9)
A 		2.2
(-2.7)
A 		1.7
(-3)
A 		9
C 5.4
(-0.4)
A 		3.4
(-1.7)
A 		10.5
(3)
A 		10.3
(2.9)
A 		1.6
(-2.9)
A 		1.4
(-3)
A 		9
avr 5.6
(1.9) 		5.1
(1.1) 		5
(1) 		6.4
(3) 		2.2
(-3) 		4.1
(-0.3) 		4
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 187894_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.18240
Sequence Type Exemplar sequence
Representative Public ID K03E6.1 NCBI
Target Description K03E6.1 /REP_DB=WormBase Gene ID /WP=CE07328 /GEN=lim-6 /SUBMIT=ST.LOUIS /CHR=X /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_075803(9)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_075803 NCBI Caenorhabditis elegans LIM domain family member (lim-6) (lim-6) mRNA, complete cds. 9/11 None
K03E6.1 ENSEMBL cdna:known chromosome:CEL140:X:1074933:1078636:1 gene:K03E6.1 9/11 None
Annotation Notes
Cross Hybridizing mRNA Matched Probes Nature of Assignment Related Probesets by Grade
GENEFINDER00000010597 8/11 Cross Hyb Matching Probes None
SNAP00000010591 4/11 Cross Hyb Matching Probes None
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrX:1074932-1078636(+) 100.0 100.0
Public Domain and Genome References
Gene Title Homeobox protein
Gene Symbol lim-6
Ensembl K03E6.1
Entrez Gene 180459 Entrez gene
SwissProt Q21192 EMBL-EBI
WormBase CE35737 Wormbase
Functional Annotations
Ortholog
ID Title Organism
DROSOPHILA_2:1625864_AT dm
DROSGENOME1:148652_AT dm
DROSGENOME1:148651_AT dm
U133_X3P:HS2AFFX.1.26.S1_3P_AT LIM homeobox transcription factor 1, alpha hs
HG-U133_PLUS_2:1553541_AT LIM homeobox transcription factor 1, alpha hs
HG-U133_PLUS_2:237595_AT LIM homeobox transcription factor 1, alpha hs
HG-U133B:237595_AT LIM homeobox transcription factor 1, alpha hs
HG-U95E:82713_AT LIM homeobox transcription factor 1, alpha hs
U133_X3P:HS.145108.0.S1_3P_AT LIM homeobox transcription factor 1, alpha hs
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 AAC69042 Lim domain family protein 6 [Caenorhabditis elegans] ref|NP_508204.2| LIM domain family member (lim-6) [Caenorhabditis elegans] 1.0E-141
blast CAE63576 Hypothetical protein CBG08064 [Caenorhabditis briggsae] 4.0E-96
blast AAD12189 putative transcription factor LIM-6 [Caenorhabditis elegans] 5.0E-55
Protein Domains
Database ID Description E-Value
scop a.4.1.Homeodomain All alpha proteins; DNA/RNA-binding 3-helical bundle; Homeodomain-like; Homeodomain 3.99999987306209E-19
Pfam IPR001356 EMBL-EBI Homeobox 9.5E-22
Pfam IPR001781 EMBL-EBI Zn-binding protein, LIM 7.7E-16
Pfam IPR001781 EMBL-EBI Zn-binding protein, LIM 2.9E-11
Sequence
Target Sequence 
>C. ELEGANS:187894_AT
tgcgcaatgtttcagctgctgttcctgtcaacgaccatttaatctgggtgatgaatatca
tgtattcgatggagaagtattttgtcggaatgactaccagtccatttgtaattttcaaac
aagtgagtttcactatacccttaccttcacaacttttgcaatttcagtatcaaatccaga
ccctctcatggaagaagtagtacggtcagaaatccaccgaaaaacgccaaaacgaccaag
aacgatcctcaatgctcagcaacggagacagtttaagactgcttttgaaagaagttcaaa
accaagtcgaaaggtcagggagcaactcgcaaatgaaactggcctcagtgttcgtgttgt
gcaagtttggtttcaaaatcagagggcgaagatcaagaagctgaacaagaaagattcgga
ttcaggggatacatttaaacacgggcctggaagtgagggacggagcacggaagacattcg
aagctctgatgatgaggaagagtctgtgataagtaagttgaagagaataggtatagatat
tggcgagttgtggctttaca

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
TGCGCAATGTTTCAGCTGCTGTTCC 642 583 414 Antisense
GTTCCTGTCAACGACCATTTAATCT 124 441 434 Antisense
GACTACCAGTCCATTTGTAATTTTC 532 371 505 Antisense
AGTGAGTTTCACTATACCCTTACCT 140 59 535 Antisense
CCCTTACCTTCACAACTTTTGCAAT 274 259 551 Antisense
TATCAAATCCAGACCCTCTCATGGA 22 657 581 Antisense
CAAGAACGATCCTCAATGCTCAGCA 345 185 650 Antisense
GAAACTGGCCTCAGTGTTCGTGTTG 702 357 748 Antisense
GGGGATACATTTAAACACGGGCCTG 443 497 838 Antisense
GGGACGGAGCACGGAAGACATTCGA 618 493 870 Antisense
GATATTGGCGAGTTGTGGCTTTACA 647 425 949 Antisense
Sequence Source Affymetrix Proprietary Database