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[193268_at] LIM domain containing proteins (2 domains)

Description Y1A5A.1 /REP_DB=WormBase Gene ID /WP=CE20175 /TR=Q9XXT7 /GB=CAA15978.1 /SUBMIT=HINXTON /CHR=3 /FEA=Sanger Annotation /DEF=LIM domain containing proteins (2 domains)
Cluster 6grp_total > 97      4grp_total > 16      6grp_total_sub > Increase      6grp_rule_based > S6      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 77
1 2 3 4 range
A 93.1
(-3)
M 		135.4
(3)
P 		129.3
(2.1)
A 		115.9
(0.2)
A 		42
B 79.7
(-3)
M 		145.1
(2.7)
M 		109.9
(-0.4)
P 		148.2
(3)
A 		69
C 149.4
(2.8)
P 		74.9
(-3)
A 		129.7
(1.3)
P 		151.8
(3)
A 		77
avr 107.4
(-3) 		118.5
(-0.9) 		123
(0) 		138.6
(3) 		31

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 291
1 2 3 4 5 6 range
A 154.2
(-1.6)
A 		98.8
(-2.8)
P 		88
(-3)
P 		162.1
(-1.5)
P 		244.3
(0.2)
P 		376.7
(3)
P 		289
B 113.8
(-2.3)
M 		86.2
(-3)
A 		86.6
(-3)
A 		107.7
(-2.5)
P 		279
(1.6)
P 		337.7
(3)
P 		252
C 93.3
(-3)
A 		117.7
(-2.4)
A 		156.4
(-1.5)
P 		179
(-1)
A 		221.7
(0)
P 		347.4
(3)
P 		254
avr 120.4
(-2.5) 		100.9
(-3) 		110.3
(-2.8) 		149.6
(-1.8) 		248.3
(0.5) 		353.9
(3) 		253
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 33
1 2 3 4 range
A 33.9
(3)
M 		29.4
(1.4)
P 		33.8
(3)
A 		17
(-3)
A 		17
B 25.4
(-3)
M 		35.8
(3)
M 		25.5
(-2.9)
P 		31.6
(0.6)
A 		10
C 49.5
(3)
P 		21.5
(-3)
A 		45.2
(2.1)
P 		25.6
(-2.1)
A 		28
avr 36.3
(3) 		28.9
(-0.8) 		34.8
(2.2) 		24.7
(-3) 		12

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 107
1 2 3 4 5 6 range
A 28.4
(-2.2)
A 		35.1
(-1.7)
P 		19.2
(-3)
P 		41.1
(-1.2)
P 		73.7
(1.5)
P 		91.7
(3)
P 		73
B 39.6
(-1.9)
M 		28.7
(-2.6)
A 		21
(-3)
A 		28.5
(-2.6)
P 		113.4
(2.3)
P 		125.9
(3)
P 		105
C 34.6
(-3)
A 		35.9
(-2.9)
A 		39.8
(-2.6)
P 		36
(-2.9)
A 		71.8
(-0.3)
P 		116.3
(3)
P 		82
avr 34.2
(-2.5) 		33.2
(-2.5) 		26.7
(-3) 		35.2
(-2.4) 		86.3
(1.2) 		111.3
(3) 		85
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 193268_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.6457
Sequence Type Exemplar sequence
Representative Public ID Y1A5A.1 NCBI
Target Description Y1A5A.1 /REP_DB=WormBase Gene ID /WP=CE20175 /TR=Q9XXT7 /GB=CAA15978.1 /SUBMIT=HINXTON /CHR=3 /FEA=Sanger Annotation /DEF=LIM domain containing proteins (2 domains)
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_065400(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_065400 NCBI Caenorhabditis elegans Y1A5A.1 (Y1A5A.1) mRNA, complete cds. 11/11 None
SNAP00000042840 ENSEMBL cdna:SNAP chromosome:CEL140:III:3985649:3986748:-1 11/11 None
GENEFINDER00000042841 ENSEMBL cdna:GeneFinder chromosome:CEL140:III:3985649:3986748:-1 11/11 None
Y1A5A.1 ENSEMBL cdna:known chromosome:CEL140:III:3985590:3986784:-1 gene:Y1A5A.1 11/11 None
Annotation Notes
Cross Hybridizing mRNA Matched Probes Nature of Assignment Related Probesets by Grade
SNAP00000017716 1/11 Cross Hyb Matching Probes None
C47A4.4 1/11 Cross Hyb Matching Probes None
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrIII:3985648-3986784(-) 100.0 100.0
Public Domain and Genome References
Gene Title LIM domain containing proteins (2 domains)
Ensembl Y1A5A.1
Entrez Gene 175515 Entrez gene
SwissProt Q9XXT7 EMBL-EBI
WormBase CE20175 Wormbase
Functional Annotations
Gene Ontology
GO Biological Process (view graph)
ID Description Evidence Links
6118 electron transport inferred from electronic annotation QuickGO AmiGO
GO Molecular Function (view graph)
ID Description Evidence Links
5489 electron transporter activity inferred from electronic annotation QuickGO AmiGO
20037 heme binding inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast CAA15978 Hypothetical protein Y1A5A.1 [Caenorhabditis elegans] ref|NP_497801.1| Y1A5A.1 [Caenorhabditis elegans] 1.0E-119
blast CAA15978 Hypothetical protein Y1A5A.1 [Caenorhabditis elegans] ref|NP_497801.1| Y1A5A.1 [Caenorhabditis elegans] 1.0E-112
blast CAE60105 Hypothetical protein CBG03641 [Caenorhabditis briggsae] 1.0E-80
blast CAE60105 Hypothetical protein CBG03641 [Caenorhabditis briggsae] 2.0E-80
blast XP_653490 paxillin, putative [Entamoeba histolytica HM-1:IMSS] gb|EAL48104.1| paxillin, putative [Entamoeba histolytica HM-1:IMSS] 4.0E-22
Protein Domains
Database ID Description E-Value
Pfam IPR001781 EMBL-EBI Zn-binding protein, LIM 6.2E-13
Pfam IPR001781 EMBL-EBI Zn-binding protein, LIM 7.4E-18
Pfam IPR001781 EMBL-EBI Zn-binding protein, LIM 6.2E-13
Pfam IPR001781 EMBL-EBI Zn-binding protein, LIM 7.4E-18
Sequence
Target Sequence 
>C. ELEGANS:193268_AT
gtgccaatacattccacgttatcatccccaaatgccaacgtgtccactttttgaatcaaa
gtcaatcattactccagtcttctacttcaactgtaaacgaatggatcgtagcattgatcg
tcgtctctgtgggcactgtcaccaatcgattggaagtgaggcacttgtcgccatgaatcg
tctctggcatccggaccacttcacgtgctcatcgtgcaaacgtccgatcaagcagacgtt
ccaggctgccgacaaccacgcctactgtgtccagtgctttgctcaaaagtacaacccgaa
atgtgctggatgcatggaaactctcgtcgacacgtgccttcttgctttggaccgacactg
gcatccacgttgcttcacgtgctcctcgtgcaatcgcccattgccaaatggagaattcta
tctggttgatgataagccgtacgacttggattgtcactgggcaaagcgtctcg

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GTGCCAATACATTCCACGTTATCAT 699 477 84 Antisense
AAATGCCAACGTGTCCACTTTTTGA 670 93 113 Antisense
GTCAATCATTACTCCAGTCTTCTAC 541 463 144 Antisense
TCTGTGGGCACTGTCACCAATCGAT 631 605 209 Antisense
GGCACTTGTCGCCATGAATCGTCTC 477 535 243 Antisense
CCACTTCACGTGCTCATCGTGCAAA 350 273 279 Antisense
TCAAGCAGACGTTCCAGGCTGCCGA 195 631 311 Antisense
CTGTGTCCAGTGCTTTGCTCAAAAG 511 239 348 Antisense
TGGATGCATGGAAACTCTCGTCGAC 232 549 390 Antisense
TCGTGCAATCGCCCATTGCCAAATG 334 603 469 Antisense
GATTGTCACTGGGCAAAGCGTCTCG 209 435 532 Antisense
Sequence Source Affymetrix Proprietary Database