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[191102_at] LIM-homeodomain

Description ZC64.4 /REP_DB=WormBase Gene ID /WP=CE25675 /GEN=lim-4 /TR=Q23380 /GB=AAA80428.1 /SUBMIT=ST.LOUIS /CHR=X /FEA=Sanger Annotation /DEF=LIM-homeodomain
Cluster 6grp_total > 26      4grp_total > 23      6grp_cgc > 24      6grp_cgc_sub > Cu      6grp_total_sub > Cup      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 228
1 2 3 4 range
A 205.5
(3)
P 		25.3
(-2.9)
A 		23.1
(-3)
A 		145.4
(1)
P 		182
B 238.7
(3)
P 		13.3
(-3)
A 		24.3
(-2.7)
A 		164.5
(1)
P 		225
C 228
(3)
P 		10.6
(-3)
A 		33.6
(-2.4)
A 		130.8
(0.3)
A 		217
avr 224.1
(3) 		16.4
(-3) 		27
(-2.7) 		146.9
(0.8) 		208

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 147
1 2 3 4 5 6 range
A 175.5
(3)
P 		130
(0.7)
P 		61.5
(-2.8)
A 		113.5
(-0.2)
P 		58.2
(-3)
A 		107.4
(-0.5)
A 		117
B 145.9
(3)
P 		113.3
(0.9)
P 		120.6
(1.4)
A 		80.1
(-1.2)
A 		51.6
(-3)
A 		96.7
(-0.1)
A 		94
C 148.8
(3)
P 		130.6
(2.1)
P 		88.9
(0)
P 		78.3
(-0.5)
A 		29
(-3)
A 		54.9
(-1.7)
A 		120
avr 156.7
(3) 		124.6
(1.3) 		90.3
(-0.6) 		90.6
(-0.6) 		46.3
(-3) 		86.3
(-0.8) 		110
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 73
1 2 3 4 range
A 74.8
(3)
P 		5.5
(-3)
A 		6
(-3)
A 		21.3
(-1.6)
P 		69
B 76.1
(3)
P 		3.3
(-3)
A 		5.6
(-2.8)
A 		35.1
(-0.4)
P 		73
C 75.5
(3)
P 		3
(-3)
A 		11.7
(-2.3)
A 		22.1
(-1.4)
A 		73
avr 75.5
(3) 		3.9
(-3) 		7.8
(-2.7) 		26.2
(-1.1) 		72

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 46
1 2 3 4 5 6 range
A 32.3
(0.5)
P 		46.2
(3)
P 		13.4
(-3)
A 		28.8
(-0.2)
P 		17.6
(-2.2)
A 		26.1
(-0.7)
A 		33
B 50.8
(3)
P 		37.7
(0.4)
P 		29.3
(-1.3)
A 		21.2
(-3)
A 		21
(-3)
A 		36
(0)
A 		30
C 55.2
(3)
P 		39.9
(1)
P 		22.6
(-1.3)
P 		15.8
(-2.2)
A 		9.4
(-3)
A 		18.4
(-1.8)
A 		46
avr 46.1
(3) 		41.3
(2) 		21.8
(-1.8) 		21.9
(-1.8) 		16
(-3) 		26.8
(-0.8) 		30
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 191102_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.18062
Sequence Type Exemplar sequence
Representative Public ID ZC64.4 NCBI
Target Description ZC64.4 /REP_DB=WormBase Gene ID /WP=CE25675 /GEN=lim-4 /TR=Q23380 /GB=AAA80428.1 /SUBMIT=ST.LOUIS /CHR=X /FEA=Sanger Annotation /DEF=LIM-homeodomain
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_076268(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_076268 NCBI Caenorhabditis elegans ZC64.4 (LIM-homeodomain) mRNA, complete cds. 11/11 None
SNAP00000028302 ENSEMBL cdna:SNAP chromosome:CEL140:X:3869674:3871627:-1 10/11 None
GENEFINDER00000028305 ENSEMBL cdna:GeneFinder chromosome:CEL140:X:3869733:3873526:-1 11/11 None
ZC64.4 ENSEMBL cdna:known chromosome:CEL140:X:3869733:3873275:-1 gene:ZC64.4 11/11 None
Annotation Notes
There are no noteworthy cross hybridizing mRNAs found for this probe set.
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrX:3869733-3873276(-) 100.0 100.0
Public Domain and Genome References
Gene Title LIM-homeodomain
Gene Symbol lim-4
Ensembl ZC64.4
Entrez Gene 180672 Entrez gene
SwissProt Q23380 EMBL-EBI
WormBase CE25675 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
6355 regulation of transcription, DNA-dependent inferred from direct assay QuickGO AmiGO
GO Cellular Component (view graph)
ID Description Evidence Links
5634 nucleus inferred from electronic annotation QuickGO AmiGO
5623 cell inferred from direct assay 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
3700 transcription factor activity inferred from sequence similarity QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast AAA80428 Lim domain family protein 4 [Caenorhabditis elegans] ref|NP_508669.1| ZC64.4 [Caenorhabditis elegans] gb|AAB17273.1| putative transcription factor LIM-4 [Caenorhabditis elegans] 0.0
blast CAE68493 Hypothetical protein CBG14299 [Caenorhabditis briggsae] 1.0E-125
blast AAA80428 Lim domain family protein 4 [Caenorhabditis elegans] ref|NP_508669.1| ZC64.4 [Caenorhabditis elegans] gb|AAB17273.1| putative transcription factor LIM-4 [Caenorhabditis elegans] 4.0E-89
blast CAE68493 Hypothetical protein CBG14299 [Caenorhabditis briggsae] 2.0E-73
blast EAL31062 GA10520-PA [Drosophila pseudoobscura] 4.0E-58
Protein Domains
Database ID Description E-Value
scop a.4.1.Homeodomain All alpha proteins; DNA/RNA-binding 3-helical bundle; Homeodomain-like; Homeodomain 1.99999993653105E-19
scop a.4.1.Homeodomain All alpha proteins; DNA/RNA-binding 3-helical bundle; Homeodomain-like; Homeodomain 8.9999997143897E-22
Pfam IPR001356 EMBL-EBI Homeobox 1.0E-22
Pfam IPR001781 EMBL-EBI Zn-binding protein, LIM 3.5E-16
Pfam IPR001781 EMBL-EBI Zn-binding protein, LIM 1.1E-21
Pfam IPR001781 EMBL-EBI Zn-binding protein, LIM 1.1E-21
Pfam IPR001356 EMBL-EBI Homeobox 1.0E-22
Pfam IPR001356 EMBL-EBI Homeobox 1.0E-22
Pfam IPR001781 EMBL-EBI Zn-binding protein, LIM 3.5E-16
Pfam IPR001781 EMBL-EBI Zn-binding protein, LIM 1.1E-21
Sequence
Target Sequence 
>C. ELEGANS:191102_AT
tatttccgaacgcatgtcacatcaaccgcttccagttgcagagaacttggacccaagtgt
gcatcttgcgatcgtactattcaggcgactgattgggtacgaagagcaagaaactatgta
taccatcttgcgtgtttttcgtgcaaccagtgcaaaagacaattgagtacaggggaagaa
tacgcacttcaagagggcaatcttctctgcaaacagcactttttggaacttgttgaagga
gacagtggggtgtctagtcagaaagctaagactaaaagggttcggaccacttttgcggaa
gatcaattatcggttcttcagacatatttcaaccgggacagtaatccggatggtgctgat
ttggaaaagattgcctccatgacaggactgagtaaaagagtgacccaggtgtggttccag
aattcacgagctcgtcaaaagaaatggcatcaaaaatccgaaggtgacaatggagatagc
cagaggtcatctgtggggccttccagtcctagtcaaaaatcg

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
TATTTCCGAACGCATGTCACATCAA 524 661 457 Antisense
CATCAACCGCTTCCAGTTGCAGAGA 517 211 476 Antisense
GGACCCAAGTGTGCATCTTGCGATC 1 525 505 Antisense
GCGATCGTACTATTCAGGCGACTGA 32 291 524 Antisense
ATACCATCTTGCGTGTTTTTCGTGC 518 21 576 Antisense
GAGGGCAATCTTCTCTGCAAACAGC 59 403 649 Antisense
GTTCGGACCACTTTTGCGGAAGATC 47 443 736 Antisense
GATTGCCTCCATGACAGGACTGAGT 550 433 825 Antisense
GAGTGACCCAGGTGTGGTTCCAGAA 324 401 854 Antisense
AGCCAGAGGTCATCTGTGGGGCCTT 194 85 934 Antisense
GCCTTCCAGTCCTAGTCAAAAATCG 374 279 954 Antisense
Sequence Source Affymetrix Proprietary Database