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[174235_at] LIM domain

Description C54498_rc /REP_DB=TREMBL Accession /GB=C54498 /CHR=2 /FEA=Genomic Cluster /DEF=C.elegans cDNA clone yk359f3 : 3prime end, single read.
Cluster 6grp_highest_10_10 > 33      6grp_high1_10_10 > 10      4grp_highest_8_8 > 24      4grp_high_8_8 > 51      6grp_highest_nonorm > 32      6grp_total > 13      4grp_total > 52      6grp_highest_sub > 02      6grp_cgc > 40      6grp_total_sub > Decrease      4grp_rule_based > L2      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 773
1 2 3 4 range
A 1291.2
(3)
P 		1019
(0.6)
P 		1187.4
(2.1)
P 		622.1
(-3)
P 		669
B 1182.7
(1.9)
P 		1321.9
(3)
P 		1034.3
(0.6)
P 		591.1
(-3)
P 		731
C 1198.8
(1.8)
P 		1359.4
(3)
P 		1355.7
(3)
P 		586.7
(-3)
P 		773
avr 1224.2
(2.9) 		1233.4
(3) 		1192.5
(2.6) 		600
(-3) 		633

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 871
1 2 3 4 5 6 range
A 1595.1
(3)
P 		1584.9
(2.9)
P 		1487.4
(2.2)
P 		1585.3
(2.9)
P 		1044
(-1.2)
P 		815
(-3)
P 		780
B 1613.9
(2.7)
P 		1652.2
(3)
P 		1410.3
(1.2)
P 		1454.6
(1.5)
P 		942.1
(-2.4)
P 		857.1
(-3)
P 		795
C 1365.9
(0.7)
P 		1667.5
(2.9)
P 		1255
(-0.1)
P 		1686
(3)
P 		848.5
(-3)
P 		910.9
(-2.6)
P 		838
avr 1525
(2.1) 		1634.9
(3) 		1384.2
(1.1) 		1575.3
(2.5) 		944.9
(-2.3) 		861
(-3) 		774
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 381
1 2 3 4 range
A 470.1
(3)
P 		221.2
(-0.9)
P 		310.4
(0.5)
P 		91.1
(-3)
P 		379
B 377.2
(3)
P 		326.5
(1.8)
P 		239.7
(-0.3)
P 		126
(-3)
P 		251
C 396.8
(1.8)
P 		390.8
(1.7)
P 		472.5
(3)
P 		98.9
(-3)
P 		374
avr 414.7
(3) 		312.8
(1) 		340.9
(1.6) 		105.3
(-3) 		309

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 365
1 2 3 4 5 6 range
A 294.1
(-1.4)
P 		563.7
(3)
P 		323.9
(-0.9)
P 		402.1
(0.3)
P 		315
(-1.1)
P 		198.4
(-3)
P 		365
B 561.6
(3)
P 		549.9
(2.7)
P 		342.5
(-2.4)
P 		385.3
(-1.4)
P 		382.8
(-1.4)
P 		319.6
(-3)
P 		242
C 506.3
(2.9)
P 		508.8
(3)
P 		319.4
(-1.9)
P 		339.1
(-1.3)
P 		274.6
(-3)
P 		304.9
(-2.2)
P 		234
avr 454
(1) 		540.8
(3) 		328.6
(-1.8) 		375.5
(-0.7) 		324.1
(-1.9) 		274.3
(-3) 		267
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 174235_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.20475
Sequence Type Exemplar sequence
Representative Public ID C54498 NCBI
Target Description C54498_rc /REP_DB=TREMBL Accession /GB=C54498 /CHR=2 /FEA=Genomic Cluster /DEF=C.elegans cDNA clone yk359f3 : 3prime end, single read.
Cluster Evidence This cluster is supported by a Genomic Cluster.
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_063296(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_063296 NCBI Caenorhabditis elegans Lim and Transglutaminase Domain family member (ltd-1) (ltd-1) mRNA, complete cds. 11/11 A 
K02C4.4 ENSEMBL cdna:known chromosome:CEL140:II:8088348:8092675:-1 gene:K02C4.4 11/11 A 
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
chrII:8088417-8088707(-) 100.0 100.0
Public Domain and Genome References
Gene Title LIM domain
Gene Symbol ltd-1
Ensembl K02C4.4
Entrez Gene 174301 Entrez gene
SwissProt Q09577 EMBL-EBI
WormBase CE32687 Wormbase
Functional Annotations
Ortholog
ID Title Organism
DROSOPHILA_2:1623227_S_AT Hillarin dm
DROSGENOME1:147557_AT Hillarin dm
DROSGENOME1:147556_AT Hillarin dm
Gene Ontology
GO Biological Process (view graph)
ID Description Evidence Links
910 cytokinesis inferred from sequence similarity QuickGO AmiGO
GO Cellular Component (view graph)
ID Description Evidence Links
5911 intercellular junction inferred from direct assay QuickGO AmiGO
5737 cytoplasm inferred from direct assay QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast CAA87787 Hypothetical protein K02C4.4 [Caenorhabditis elegans] ref|NP_495697.2| Lim and Transglutaminase Domain family member (ltd-1) [Caenorhabditis elegans] gb|AAN09795.1| lim and transglutaminase domain protein [Caenorhabditis elegans] 0.0
blast CAE57723 Hypothetical protein CBG00733 [Caenorhabditis briggsae] 0.0
blast EAA10341 ENSANGP00000002507 [Anopheles gambiae str. PEST] ref|XP_315127.2| ENSANGP00000002507 [Anopheles gambiae str. PEST] 0.0
Protein Domains
Database ID Description E-Value
scop a.2.7.Methicillin resistance protein FemA probable tRNA-binding arm All alpha proteins; Long alpha-hairpin; tRNA-binding arm; Methicillin resistance protein FemA probable tRNA-binding arm 6.09999990463257
Pfam IPR001781 EMBL-EBI Zn-binding protein, LIM 2.3E-6
Sequence
Target Sequence 
>C. ELEGANS:174235_AT
gagagtattgttcttgtccctcaaatgttgccattcattctttttgagagaaagaaacgg
acctgcagggtattccaattgtccttagttatctcattattaatctaattttctctgaat
atgttctgatgaatctgtgcgtctttgatgtttcattggcacacacgggtttatctttga
aactgaaattcctgatgatacaatcccgagttctgttatttctcttttgtgtcacacac

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GAGAGTATTGTTCTTGTCCCTCAAA 528 389 31 Antisense
GTCCCTCAAATGTTGCCATTCATTC 595 475 46 Antisense
GAAACGGACCTGCAGGGTATTCCAA 378 355 84 Antisense
GGTATTCCAATTGTCCTTAGTTATC 142 505 99 Antisense
ATTGTCCTTAGTTATCTCATTATTA 361 5 108 Antisense
ATGTTCTGATGAATCTGTGCGTCTT 467 47 151 Antisense
TGTGCGTCTTTGATGTTTCATTGGC 290 557 166 Antisense
TTGGCACACACGGGTTTATCTTTGA 508 705 186 Antisense
GAAATTCCTGATGATACAATCCCGA 491 363 215 Antisense
TACAATCCCGAGTTCTGTTATTTCT 486 641 229 Antisense
GTTATTTCTCTTTTGTGTCACACAC 611 447 245 Antisense
Sequence Source Affymetrix Proprietary Database