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[175280_at] LIM domain containing proteins (2 domains), homeobox protein (lim subfamily)

Description AV185518_rc /REP_DB=TREMBL Accession /GB=AV185518 /CHR=1 /FEA=Genomic Cluster /DEF=Caenorhabditis elegans cDNA clone:yk679c8 : 3prime end, single read.
Cluster 6grp_high1_10_10 > 19      4grp_high_8_8 > 32      6grp_total > 29      4grp_total > 47      6grp_cgc > 02      4grp_rule_based > L1      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 435
1 2 3 4 range
A 530.4
(3)
P 		229.6
(-1.9)
P 		164.5
(-3)
A 		201
(-2.4)
P 		366
B 591.3
(3)
P 		199.8
(-3)
A 		204.2
(-2.9)
M 		306.6
(-1.4)
P 		392
C 599.8
(3)
P 		276.6
(-2.8)
P 		278.7
(-2.7)
P 		263.7
(-3)
P 		336
avr 573.8
(3) 		235.3
(-2.7) 		215.8
(-3) 		257.1
(-2.3) 		358

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 314
1 2 3 4 5 6 range
A 462.4
(3)
P 		369.2
(0.4)
P 		247.9
(-3)
P 		256.9
(-2.7)
P 		438
(2.3)
P 		272.2
(-2.3)
P 		215
B 549.8
(3)
P 		389.3
(-0.5)
P 		276.4
(-3)
P 		432.7
(0.4)
P 		418.1
(0.1)
P 		348.7
(-1.4)
P 		273
C 455.9
(3)
P 		355.4
(0.3)
P 		236.3
(-3)
A 		276.4
(-1.9)
M 		375
(0.8)
P 		364
(0.5)
P 		220
avr 489.4
(3) 		371.3
(-0) 		253.5
(-3) 		322
(-1.3) 		410.4
(1) 		328.3
(-1.1) 		236
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 169
1 2 3 4 range
A 193.1
(3)
P 		49.8
(-2.3)
P 		43
(-2.5)
A 		29.4
(-3)
P 		164
B 188.5
(3)
P 		49.3
(-2.9)
A 		47.3
(-3)
M 		65.3
(-2.2)
P 		141
C 198.6
(3)
P 		79.5
(-1.6)
P 		97.1
(-1)
P 		44.5
(-3)
P 		154
avr 193.4
(3) 		59.5
(-2.5) 		62.5
(-2.3) 		46.4
(-3) 		147

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 137
1 2 3 4 5 6 range
A 85.2
(-0.6)
P 		131.3
(2.9)
P 		54
(-3)
P 		65.1
(-2.1)
P 		132.2
(3)
P 		66.3
(-2.1)
P 		78
B 191.3
(3)
P 		129.6
(0)
P 		67.1
(-3)
P 		114.6
(-0.7)
P 		169.9
(2)
P 		130
(0)
P 		124
C 169
(3)
P 		108.5
(-0.2)
P 		60.1
(-2.8)
A 		55.6
(-3)
M 		121.4
(0.5)
P 		121.9
(0.5)
P 		113
avr 148.5
(3) 		123.1
(1.3) 		60.4
(-3) 		78.4
(-1.8) 		141.2
(2.5) 		106.1
(0.1) 		88
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 175280_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.20243
Sequence Type Exemplar sequence
Representative Public ID AV185518 NCBI
Target Description AV185518_rc /REP_DB=TREMBL Accession /GB=AV185518 /CHR=1 /FEA=Genomic Cluster /DEF=Caenorhabditis elegans cDNA clone:yk679c8 : 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_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
ZC247.3 ENSEMBL cdna:known chromosome:CEL140:I:10256410:10263441:1 gene:ZC247.3 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
chrI:10262885-10263309(+) 100.0 100.0
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
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
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
Sequence
Target Sequence 
>C. ELEGANS:175280_AT
ctcccaacaaatcccacatacaggagtattccacgttcgtgtagtttttcttcctcgcat
tattttaaattctcaaaaagcactcacttaaacattttccacaccgatttccaaatgcaa
caaaatcaacgaattcctctcattcat

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
CTCCCAACAAATCCCACATACAGGA 380 233 132 Antisense
AATCCCACATACAGGAGTATTCCAC 588 165 141 Antisense
ACAGGAGTATTCCACGTTCGTGTAG 571 105 151 Antisense
TATTCCACGTTCGTGTAGTTTTTCT 495 663 158 Antisense
TTTCTTCCTCGCATTATTTTAAATT 35 673 178 Antisense
TCCTCGCATTATTTTAAATTCTCAA 464 593 183 Antisense
ATTCTCAAAAAGCACTCACTTAAAC 241 11 200 Antisense
GCACTCACTTAAACATTTTCCACAC 558 315 211 Antisense
TTTTCCACACCGATTTCCAAATGCA 573 673 226 Antisense
TCCACACCGATTTCCAAATGCAACA 368 587 229 Antisense
AAATCAACGAATTCCTCTCATTCAT 244 117 254 Antisense
Sequence Source Affymetrix Proprietary Database