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[172067_x_at] LIM domain containing proteins (2 domains), homeobox protein (lim subfamily)

Description g1620740 /REP_DB=GenBank Identifier /GB=U72211.1 /PROTEIN_GB=AAB97099.1 /CHR=X /FEA=Mapped Transcript /DEF=putative transcription factor TTX-3
Cluster 6grp_total > 07      4grp_total > 39      6grp_cgc > 11      6grp_cgc_sub > De      6grp_total_sub > Decrease      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 173
1 2 3 4 range
A 142.5
(3)
M 		23.9
(-2.8)
A 		19.4
(-3)
A 		98.8
(0.9)
A 		123
B 126.8
(3)
A 		99.3
(1.6)
A 		6.5
(-3)
A 		77.6
(0.5)
A 		120
C 179.2
(3)
M 		11.8
(-3)
A 		68.6
(-1)
A 		64.4
(-1.1)
A 		167
avr 149.5
(3) 		45
(-2.3) 		31.5
(-3) 		80.3
(-0.5) 		118

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 105
1 2 3 4 5 6 range
A 67.8
(0.3)
A 		22.2
(-3)
A 		105.4
(3)
A 		46.5
(-1.2)
A 		48.2
(-1.1)
A 		65.5
(0.1)
A 		83
B 107.5
(3)
A 		23.6
(-2)
A 		53
(-0.2)
A 		54.5
(-0.1)
A 		6.2
(-3)
A 		57.8
(0.1)
A 		101
C 99.8
(2.9)
A 		101.2
(3)
A 		20.4
(-1.9)
A 		4.7
(-2.9)
A 		58.7
(0.4)
A 		2.5
(-3)
A 		99
avr 91.7
(3) 		49
(-1.5) 		59.6
(-0.4) 		35.2
(-3) 		37.7
(-2.7) 		41.9
(-2.3) 		57
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 58
1 2 3 4 range
A 51.9
(3)
M 		5.2
(-3)
A 		5.1
(-3)
A 		14.5
(-1.8)
A 		47
B 40.4
(3)
A 		24.5
(0.5)
A 		1.5
(-3)
A 		16.5
(-0.7)
A 		39
C 59.3
(3)
M 		3.4
(-3)
A 		23.9
(-0.8)
A 		10.9
(-2.2)
A 		56
avr 50.5
(3) 		11
(-2.9) 		10.2
(-3) 		14
(-2.4) 		40

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 37
1 2 3 4 5 6 range
A 12.5
(-1.2)
A 		7.9
(-3)
A 		22.9
(3)
A 		11.8
(-1.4)
A 		14.5
(-0.4)
A 		16
(0.2)
A 		15
B 37.4
(3)
A 		7.8
(-2.1)
A 		12.9
(-1.2)
A 		14.4
(-1)
A 		2.5
(-3)
A 		21.5
(0.3)
A 		35
C 37
(3)
A 		30.9
(2)
A 		5.2
(-2.3)
A 		0.9
(-3)
A 		19
(0)
A 		0.8
(-3)
A 		36
avr 29
(3) 		15.5
(-1.1) 		13.7
(-1.6) 		9
(-3) 		12
(-2.1) 		12.8
(-1.9) 		20
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 172067_x_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.19987
Sequence Type Exemplar sequence
Representative Public ID 1620740 NCBI
Target Description g1620740 /REP_DB=GenBank Identifier /GB=U72211.1 /PROTEIN_GB=AAB97099.1 /CHR=X /FEA=Mapped Transcript /DEF=putative transcription factor TTX-3
Cluster Evidence This cluster is supported by a Mapped Transcript.
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 7/11 Cross Hyb Matching Probes None
GENEFINDER00000010976 7/11 Cross Hyb Matching Probes None
GENEFINDER00000010980 3/11 Cross Hyb Matching Probes None
SNAP00000010973 3/11 Cross Hyb Matching Probes None
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrX:11764587-11769299(-) 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:172067_X_AT
attacacaatgtctccgcaaggtcatttatattgtcatgctcattacaatgcagttcgtt
caacggtgttatgcgaagaggcggcagtagctacggtacctgctgttgtggctccgccgc
caccgccaccgacgacaacaacagcaccaccaccagcggcaccggaacaaccacccaggg
aggcatcgacggaagcggaagcgtctaccgatgaagatggaaatggtagcggaagccaac
gatcgaaacgcatgcggacatcatttaaacatcaccagctacgtgctatgaaaacatact
ttgcccttaaccataacccagatgctaaagacttgaagcagctagccgctaaaacaaatt
tgacaaaaagggttctgcaggtttggtttcaaaatgctcgtgcaaaataccgtcgagagc
ttcacgatggtggccgaagttctagtccactttgtgtctctgccccattggcatcaatgg
atatgaatccgccactctcttcttcatcatccggacactcaacagatggataccagctca
acacacca

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
ATTACACAATGTCTCCGCAAGGTCA 333 11 644 Antisense
CAGTAGCTACGGTACCTGCTGTTGT 560 207 728 Antisense
ACAACCACCCAGGGAGGCATCGACG 525 111 810 Antisense
GCCAACGATCGAAACGCATGCGGAC 603 277 878 Antisense
AAACATCACCAGCTACGTGCTATGA 348 129 910 Antisense
TGAAAACATACTTTGCCCTTAACCA 512 573 932 Antisense
GTCGAGAGCTTCACGATGGTGGCCG 554 473 1055 Antisense
AGTTCTAGTCCACTTTGTGTCTCTG 187 65 1081 Antisense
AATGGATATGAATCCGCCACTCTCT 202 163 1119 Antisense
TTCATCATCCGGACACTCAACAGAT 206 689 1146 Antisense
AGATGGATACCAGCTCAACACACCA 597 67 1167 Antisense
Sequence Source GenBank