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[194088_at] LIM domain containing proteins (2 domains), homeobox protein (lim subfamily)

Description ZC247.3 /REP_DB=WormBase Gene ID /WP=CE15150 /GEN=lin-11 /TR=SW:P20154 /GB=CAB02310.1 /SUBMIT=HINXTON /CHR=1 /FEA=Sanger Annotation /DEF=LIM domain containing proteins (2 domains), homeobox protein (lim subfamily)
Cluster 6grp_total > 05      4grp_total > 38      6grp_cgc > 02      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 260
1 2 3 4 range
A 293.1
(3)
P 		214.9
(0.2)
A 		124.6
(-3)
A 		166.9
(-1.5)
A 		169
B 305.6
(3)
P 		184
(-0.3)
A 		87
(-3)
A 		188.5
(-0.2)
A 		219
C 347.4
(3)
P 		152.8
(-2.5)
A 		135.8
(-3)
A 		194.9
(-1.3)
A 		212
avr 315.4
(3) 		183.9
(-1) 		115.8
(-3) 		183.4
(-1) 		200

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 203
1 2 3 4 5 6 range
A 308.5
(3)
A 		216.2
(-0.4)
M 		145.7
(-3)
A 		214.8
(-0.5)
P 		222.7
(-0.2)
A 		179.7
(-1.7)
A 		163
B 330.8
(3)
P 		265.2
(0.9)
A 		154.1
(-2.5)
A 		183.3
(-1.6)
M 		196.4
(-1.2)
P 		138.9
(-3)
A 		192
C 287
(3)
P 		208.6
(0)
A 		210.7
(0.1)
A 		192.6
(-0.6)
A 		241.5
(1.3)
A 		128.2
(-3)
A 		159
avr 308.8
(3) 		230
(0) 		170.2
(-2.2) 		196.9
(-1.2) 		220.2
(-0.3) 		148.9
(-3) 		160
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 95
1 2 3 4 range
A 106.7
(3)
P 		46.6
(-1.4)
A 		32.6
(-2.4)
A 		24.4
(-3)
A 		82
B 97.5
(3)
P 		45.4
(-1)
A 		20.2
(-3)
A 		40.2
(-1.4)
A 		77
C 115
(3)
P 		43.9
(-2.2)
A 		47.3
(-1.9)
A 		32.9
(-3)
A 		82
avr 106.4
(3) 		45.3
(-2) 		33.4
(-2.9) 		32.5
(-3) 		74

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 83
1 2 3 4 5 6 range
A 56.9
(0.3)
A 		76.9
(3)
M 		31.7
(-3)
A 		54.5
(0)
P 		67.2
(1.7)
A 		43.8
(-1.4)
A 		45
B 115.1
(3)
P 		88.3
(0.9)
A 		37.4
(-3)
A 		48.6
(-2.1)
M 		79.8
(0.3)
P 		51.8
(-1.9)
A 		78
C 106.4
(3)
P 		63.6
(-0.8)
A 		53.6
(-1.7)
A 		38.7
(-3)
A 		78.1
(0.5)
A 		42.9
(-2.6)
A 		68
avr 92.8
(3) 		76.3
(1.1) 		40.9
(-3) 		47.3
(-2.3) 		75
(0.9) 		46.2
(-2.4) 		52
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 194088_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.1051
Sequence Type Exemplar sequence
Representative Public ID ZC247.3 NCBI
Target Description ZC247.3 /REP_DB=WormBase Gene ID /WP=CE15150 /GEN=lin-11 /TR=SW:P20154 /GB=CAB02310.1 /SUBMIT=HINXTON /CHR=1 /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_060295(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_060295 NCBI Caenorhabditis elegans abnormal cell LINeage family member (lin-11) (lin-11) mRNA, complete cds. 11/11 None
GENEFINDER00000007178 ENSEMBL cdna:GeneFinder chromosome:CEL140:I:10253652:10263192:1 11/11 None
ZC247.3 ENSEMBL cdna:known chromosome:CEL140:I:10256410:10263441:1 gene:ZC247.3 11/11 A 
Annotation Notes
Cross Hybridizing mRNA Matched Probes Nature of Assignment Related Probesets by Grade
SNAP00000007175 3/11 Cross Hyb Matching Probes None
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrI:10256391-10263123(+) 98.6 100.0
Public Domain and Genome References
Gene Title LIM domain containing proteins (2 domains), homeobox protein (lim subfamily)
Gene Symbol lin-11
Ensembl ZC247.3
Entrez Gene 172893 Entrez gene
SwissProt P20154 EMBL-EBI
WormBase CE15150 Wormbase
Functional Annotations
Ortholog
ID Title Organism
CANINE_2:CFAAFFX.27322.1.S1_AT similar to LIM homeobox protein 1 cfa
DROSOPHILA_2:1633262_S_AT Saccharomyces cerevisiae UAS construct a of Tsuji dm
DROSOPHILA_2:1629733_AT Saccharomyces cerevisiae UAS construct a of Tsuji dm
DROSGENOME1:144715_AT Saccharomyces cerevisiae UAS construct a of Tsuji dm
DROSGENOME1:144141_AT Saccharomyces cerevisiae UAS construct a of Tsuji dm
CHICKEN:GGA.789.1.S1_AT LIM homeobox 1 gga
HG-U133_PLUS_2:206230_AT LIM homeobox 1 hs
HG-U133A:206230_AT LIM homeobox 1 hs
HG-FOCUS:206230_AT LIM homeobox 1 hs
HG-U133A_2:206230_AT LIM homeobox 1 hs
U133_X3P:G5031866_3P_AT LIM homeobox 1 hs
HG-U95AV2:35388_AT LIM homeobox 1 hs
HG-U95D:72976_AT LIM homeobox 1 hs
HG-U95D:91336_AT LIM homeobox 1 hs
MG-U74AV2:92961_AT LIM homeobox protein 1 mm
MU11KSUBB:Z27410_S_AT LIM homeobox protein 1 mm
MOE430A:1450428_AT LIM homeobox protein 1 mm
MOUSE430A_2:1450428_AT LIM homeobox protein 1 mm
MOUSE430_2:1450428_AT LIM homeobox protein 1 mm
MOE430A:1421951_AT LIM homeobox protein 1 mm
MOUSE430A_2:1421951_AT LIM homeobox protein 1 mm
MOUSE430_2:1421951_AT LIM homeobox protein 1 mm
RG-U34A:S71523_AT LIM homeobox protein 1 rn
RAE230A:1377206_AT LIM homeobox protein 1 rn
RAT230_2:1377206_AT LIM homeobox protein 1 rn
RAE230A:1389982_AT LIM homeobox protein 1 rn
RAT230_2:1389982_AT LIM homeobox protein 1 rn
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
3700 transcription factor activity inferred from sequence similarity QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast CAB02310 Hypothetical protein ZC247.3 [Caenorhabditis elegans] ref|NP_492696.1| abnormal cell LINeage family member (lin-11) [Caenorhabditis elegans] sp|P20154|LIN11_CAEEL Abnormal cell lineage protein 11 (Protein lin-11) 0.0
blast CAA38240 lin-11 protein [Caenorhabditis elegans] prf||1608206A lin-11 gene 0.0
blast CAE66862 Hypothetical protein CBG12236 [Caenorhabditis briggsae] 0.0
blast CAE66862 Hypothetical protein CBG12236 [Caenorhabditis briggsae] 1.0E-168
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-21
scop a.4.1.Homeodomain All alpha proteins; DNA/RNA-binding 3-helical bundle; Homeodomain-like; Homeodomain 9.99999968265523E-22
Pfam IPR001356 EMBL-EBI Homeobox 1.7E-25
Pfam IPR001781 EMBL-EBI Zn-binding protein, LIM 1.7E-22
Pfam IPR001781 EMBL-EBI Zn-binding protein, LIM 3.7E-24
Pfam IPR001356 EMBL-EBI Homeobox 1.7E-25
Pfam IPR001781 EMBL-EBI Zn-binding protein, LIM 1.7E-22
Pfam IPR001781 EMBL-EBI Zn-binding protein, LIM 6.4E-15
Sequence
Target Sequence 
>C. ELEGANS:194088_AT
ggatgcttgtgatgaggtcggactcgatgatggagaaggcgattgtgggaaggacaattc
agatgactcgaattctgcgaaaaggcgtggccctcgaacgacaattaaagcaaaacaact
tgaaaccttaaaaaacgcgttcgccgcaacacccaaaccaactcgacatatccgtgaaca
acttgccgccgagacaggactcaacatgagagtcattcaggtgtggtttcaaaaccgccg
aagcaaggaacgaagaatgaaacaacttcgttttggaggatatcgtcaatcccgaagacc
acgccgtgacgatattgtagatatgttcccgaatgaccaacaattctacccaccacctcc
accatcaaatgttcaattcttttgtgacccatacacaacttctcccaacaatccagaaac
cattcaaatggctccacaatttgcagttccaa

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GGATGCTTGTGATGAGGTCGGACTC 358 511 651 Antisense
TTCTGCGAAAAGGCGTGGCCCTCGA 542 687 723 Antisense
ACCCAAACCAACTCGACATATCCGT 641 35 801 Antisense
ACATATCCGTGAACAACTTGCCGCC 462 105 816 Antisense
GAGAGTCATTCAGGTGTGGTTTCAA 523 395 858 Antisense
GATATCGTCAATCCCGAAGACCACG 528 425 929 Antisense
AGACCACGCCGTGACGATATTGTAG 165 69 946 Antisense
CGAATGACCAACAATTCTACCCACC 297 253 980 Antisense
CCACCTCCACCATCAAATGTTCAAT 58 275 1003 Antisense
TTGTGACCCATACACAACTTCTCCC 440 703 1032 Antisense
ATGGCTCCACAATTTGCAGTTCCAA 547 53 1078 Antisense
Sequence Source Affymetrix Proprietary Database