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[194096_s_at] LIM domain containing proteins (2 domains), homeobox protein (lim subfamily)

Description C40H5.5 /REP_DB=WormBase Gene ID /WP=CE27107 /GEN=ttx-3 /TR=Q9U3M5 /GB=CAB03956.3 /SUBMIT=HINXTON /CHR=X /FEA=Sanger Annotation /DEF=LIM domain containing proteins (2 domains), homeobox protein (lim subfamily)
Cluster 6grp_total > 18      4grp_total > 39      6grp_cgc > 01      6grp_total_sub > Decrease      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 133
1 2 3 4 range
A 85.2
(3)
A 		22.5
(-2.2)
A 		13.5
(-3)
A 		31.3
(-1.5)
A 		72
B 146.2
(3)
P 		14
(-3)
A 		24.1
(-2.5)
A 		79.5
(-0)
A 		132
C 141.8
(3)
A 		32.8
(-3)
A 		59.6
(-1.5)
A 		60
(-1.5)
A 		109
avr 124.4
(3) 		23.1
(-3) 		32.4
(-2.4) 		56.9
(-1) 		101

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 135
1 2 3 4 5 6 range
A 148.1
(3)
A 		23.5
(-2.9)
A 		56
(-1.3)
A 		20.9
(-3)
A 		32.2
(-2.5)
A 		36.6
(-2.3)
A 		127
B 134.9
(3)
A 		56.8
(-0.9)
A 		17.9
(-2.8)
A 		28.2
(-2.3)
A 		44.2
(-1.5)
A 		13.5
(-3)
A 		121
C 103
(3)
A 		25.4
(-2.7)
A 		22
(-3)
A 		41.5
(-1.6)
A 		73.7
(0.8)
A 		26
(-2.7)
A 		81
avr 128.7
(3) 		35.2
(-2.4) 		32
(-2.6) 		30.2
(-2.7) 		50
(-1.6) 		25.4
(-3) 		103
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 44
1 2 3 4 range
A 31
(3)
A 		4.9
(-2.7)
A 		3.5
(-3)
A 		4.6
(-2.8)
A 		28
B 46.6
(3)
P 		3.4
(-3)
A 		5.6
(-2.7)
A 		16.9
(-1.1)
A 		43
C 46.9
(3)
A 		9.4
(-3)
A 		20.8
(-1.2)
A 		10.1
(-2.9)
A 		38
avr 41.5
(3) 		5.9
(-3) 		10
(-2.3) 		10.5
(-2.2) 		36

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 43
1 2 3 4 5 6 range
A 27.3
(3)
A 		8.3
(-2.2)
A 		12.2
(-1.1)
A 		5.3
(-3)
A 		9.7
(-1.8)
A 		8.9
(-2)
A 		22
B 46.9
(3)
A 		18.9
(-0.9)
A 		4.3
(-3)
A 		7.5
(-2.5)
A 		18
(-1.1)
A 		5
(-2.9)
A 		43
C 38.2
(3)
A 		7.7
(-2.6)
A 		5.6
(-3)
A 		8.4
(-2.5)
A 		23.9
(0.4)
A 		8.7
(-2.4)
A 		33
avr 37.5
(3) 		11.6
(-2.1) 		7.4
(-2.9) 		7.1
(-3) 		17.2
(-1) 		7.5
(-2.9) 		30
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 194096_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.16013
Sequence Type Exemplar sequence
Representative Public ID C40H5.5 NCBI
Target Description C40H5.5 /REP_DB=WormBase Gene ID /WP=CE27107 /GEN=ttx-3 /TR=Q9U3M5 /GB=CAB03956.3 /SUBMIT=HINXTON /CHR=X /FEA=Sanger Annotation /DEF=LIM domain containing proteins (2 domains), homeobox protein (lim subfamily)
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_077569(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_077569 NCBI Caenorhabditis elegans abnormal ThermoTaXis family member (ttx-3) (ttx-3) mRNA, complete cds. 11/11 A 
C40H5.5 ENSEMBL cdna:known chromosome:CEL140:X:11764402:11769299:-1 gene:C40H5.5 11/11 A 
Annotation Notes
Cross Hybridizing mRNA Matched Probes Nature of Assignment Related Probesets by Grade
SNAP00000010972 8/11 Cross Hyb Matching Probes None
GENEFINDER00000010976 8/11 Cross Hyb Matching Probes None
GENEFINDER00000010980 2/11 Cross Hyb Matching Probes None
SNAP00000010973 2/11 Cross Hyb Matching Probes None
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrX:11764587-11769343(-) 100.0 100.0
Public Domain and Genome References
Gene Title LIM domain containing proteins (2 domains), homeobox protein (lim subfamily)
Gene Symbol ttx-3
Ensembl C40H5.5
Entrez Gene 181357 Entrez gene
SwissProt Q94156 EMBL-EBI
WormBase CE27107 Wormbase
Functional Annotations
Ortholog
ID Title Organism
DROSOPHILA_2:1639498_A_AT apterous dm
DROSOPHILA_2:1624412_AT apterous dm
DROSGENOME1:141640_AT apterous dm
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 CAB03956 Hypothetical protein C40H5.5 [Caenorhabditis elegans] ref|NP_509970.1| abnormal ThermoTaXis family member (ttx-3) [Caenorhabditis elegans] gb|AAB97099.1| putative transcription factor TTX-3 [Caenorhabditis elegans] 0.0
blast CAE57336 Hypothetical protein CBG00265 [Caenorhabditis briggsae] 1.0E-124
blast AAD22008 LIM homeobox protein 9 [Mus musculus] 6.0E-43
Protein Domains
Database ID Description E-Value
scop a.4.1.Homeodomain All alpha proteins; DNA/RNA-binding 3-helical bundle; Homeodomain-like; Homeodomain 4.00000012549758E-22
Pfam IPR001781 EMBL-EBI Zn-binding protein, LIM 1.2E-11
Pfam IPR001781 EMBL-EBI Zn-binding protein, LIM 1.0E-9
Pfam IPR001356 EMBL-EBI Homeobox 3.3E-24
Sequence
Target Sequence 
>C. ELEGANS:194096_S_AT
cagtagctacggtacctgctgttgtggctccgccgccaccgccaccgacgacaacaacag
caccaccaccagcggcaccggaacaaccacccagggaggcatcgacggaagcggaagcgt
ctaccgatgaagatggaaatggtagcggaagccaacgatcgaaacgcatgcggacatcat
ttaaacatcaccagctacgtgctatgaaaacatactttgcccttaaccataacccagatg
ctaaagacttgaagcagctagccgctaaaacaaatttgacaaaaagggttctgcaggttt
ggtttcaaaatgctcgtgcaaaataccgtcgagagcttcacgatggtggccgaagttcta
gtccactttgtgtctctgccccattggcatcaatggatatgaatccgccactctcttctt
catcatccggacactcaacagatggataccagctcaacacacca

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
CAGTAGCTACGGTACCTGCTGTTGT 559 207 758 Antisense
ACAACCACCCAGGGAGGCATCGACG 524 111 840 Antisense
GCCAACGATCGAAACGCATGCGGAC 602 277 908 Antisense
AAACATCACCAGCTACGTGCTATGA 347 129 940 Antisense
TGAAAACATACTTTGCCCTTAACCA 511 573 962 Antisense
GTCGAGAGCTTCACGATGGTGGCCG 553 473 1085 Antisense
AGTTCTAGTCCACTTTGTGTCTCTG 186 65 1111 Antisense
GTCTCTGCCCCATTGGCATCAATGG 687 469 1129 Antisense
AATGGATATGAATCCGCCACTCTCT 201 163 1149 Antisense
TTCATCATCCGGACACTCAACAGAT 205 689 1176 Antisense
AGATGGATACCAGCTCAACACACCA 596 67 1197 Antisense
Sequence Source Affymetrix Proprietary Database