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[173754_at]

Description C56732_rc /REP_DB=TREMBL Accession /5_PRIME_EXT_ID=C39E6.3 /5_PRIME_EXT_DB=WormBase Gene ID /GB=C56732 /WB_GENE_ID=C39E6.3 /WP=CE06939 /CHR=X /FEA=Genomic Cluster /DEF=homeobox protein; C.elegans cDNA clone yk276h9 : 3prime end, single read.
Cluster 6grp_high1_10_10 > 37      6grp_total > 38      4grp_total > 31      6grp_cgc > 08      6grp_cgc_sub > Cu      6grp_total_sub > Cup      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 161
1 2 3 4 range
A 177.1
(3)
P 		57.9
(-3)
A 		82.9
(-1.7)
A 		120.5
(0.2)
A 		119
B 199.3
(3)
P 		45.8
(-3)
M 		52.8
(-2.7)
A 		98.7
(-0.9)
M 		154
C 193.7
(3)
P 		49.1
(-2.6)
A 		38.1
(-3)
A 		127.9
(0.5)
P 		156
avr 190
(3) 		50.9
(-3) 		57.9
(-2.7) 		115.7
(-0.2) 		139

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 124
1 2 3 4 5 6 range
A 105.3
(3)
P 		46.6
(-3)
P 		81.6
(0.6)
P 		60.4
(-1.6)
P 		68.8
(-0.7)
A 		99.2
(2.4)
A 		59
B 126.1
(3)
P 		101.7
(1.4)
A 		36.2
(-3)
A 		41.3
(-2.7)
A 		63.5
(-1.2)
P 		88.3
(0.5)
P 		90
C 153.2
(3)
P 		72.7
(-0.9)
P 		28.9
(-3)
A 		94.1
(0.1)
A 		99.7
(0.4)
A 		98.6
(0.4)
P 		124
avr 128.2
(3) 		73.7
(-1.1) 		48.9
(-3) 		65.3
(-1.8) 		77.3
(-0.9) 		95.4
(0.5) 		79
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 53
1 2 3 4 range
A 64.5
(3)
P 		12.6
(-3)
A 		21.7
(-1.9)
A 		17.6
(-2.4)
A 		52
B 63.5
(3)
P 		11.3
(-3)
M 		12.2
(-2.9)
A 		21
(-1.9)
M 		52
C 64.1
(3)
P 		14.1
(-2.9)
A 		13.3
(-3)
A 		21.6
(-2)
P 		51
avr 64
(3) 		12.7
(-3) 		15.7
(-2.6) 		20.1
(-2.1) 		51

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 49
1 2 3 4 5 6 range
A 19.4
(-0.2)
P 		16.6
(-2.1)
P 		17.8
(-1.3)
P 		15.3
(-3)
P 		20.8
(0.7)
A 		24.2
(3)
A 		9
B 43.9
(3)
P 		33.9
(1.3)
A 		8.8
(-3)
A 		10.9
(-2.6)
A 		25.8
(-0.1)
P 		32.9
(1.1)
P 		35
C 56.8
(3)
P 		22.2
(-1.2)
P 		7.4
(-3)
A 		18.9
(-1.6)
A 		32.3
(0)
A 		33
(0.1)
P 		49
avr 40
(3) 		24.2
(-0.3) 		11.3
(-3) 		15
(-2.2) 		26.3
(0.1) 		30
(0.9) 		29
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 173754_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.25763
Sequence Type Exemplar sequence
Representative Public ID C56732 NCBI
Target Description C56732_rc /REP_DB=TREMBL Accession /5_PRIME_EXT_ID=C39E6.3 /5_PRIME_EXT_DB=WormBase Gene ID /GB=C56732 /WB_GENE_ID=C39E6.3 /WP=CE06939 /CHR=X /FEA=Genomic Cluster /DEF=homeobox protein; C.elegans cDNA clone yk276h9 : 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_076414(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_076414 NCBI Caenorhabditis elegans Mesodermal Lineage Specification family member (mls-2) (mls-2) mRNA, complete cds. 11/11 None
C39E6.4 ENSEMBL cdna:known chromosome:CEL140:X:4758840:4761580:-1 gene:C39E6.4 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
chrX:4758851-4759805(-) 100.0 100.0
Public Domain and Genome References
Gene Title
Gene Symbol mls-2
Ensembl C39E6.4
Entrez Gene 180751 Entrez gene
SwissProt Q18533 EMBL-EBI
WormBase CE30891 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
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
Protein Similarities
Method ID Description E-Value
blast AAM51525 Mesodermal lineage specification protein 2 [Caenorhabditis elegans] ref|NP_508815.2| Mesodermal Lineage Specification family member (mls-2) [Caenorhabditis elegans] 1.0E-154
blast T29739 hypothetical protein C39E6.3 - Caenorhabditis elegans 2.0E-75
blast T29740 hypothetical protein C39E6.4 - Caenorhabditis elegans 2.0E-69
Protein Domains
Database ID Description E-Value
scop a.4.1.Homeodomain All alpha proteins; DNA/RNA-binding 3-helical bundle; Homeodomain-like; Homeodomain 9.99999988726602E-27
Pfam IPR001356 EMBL-EBI Homeobox 1.8E-27
Sequence
Target Sequence 
>C. ELEGANS:173754_AT
gcgcagaacatgtgaacaccttattactaatttagactcaccccctgtgcaattcaactc
aacctcaacacatttttcatctcatcactgactctatctcttcacacttgatttttgatt
catcgcccttcgtatatattttatttttcataccctatatgtttattatgtgtca

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GCGCAGAACATGTGAACACCTTATT 180 285 617 Antisense
ACATGTGAACACCTTATTACTAATT 52 105 624 Antisense
TATTACTAATTTAGACTCACCCCCT 264 663 638 Antisense
CTGTGCAATTCAACTCAACCTCAAC 34 241 661 Antisense
TTTCATCTCATCACTGACTCTATCT 207 673 691 Antisense
ACTCTATCTCTTCACACTTGATTTT 102 101 707 Antisense
CTTGATTTTTGATTCATCGCCCTTC 219 219 723 Antisense
GATTCATCGCCCTTCGTATATATTT 395 431 733 Antisense
ATCGCCCTTCGTATATATTTTATTT 682 37 738 Antisense
ATTTTATTTTTCATACCCTATATGT 117 15 754 Antisense
TACCCTATATGTTTATTATGTGTCA 486 649 767 Antisense
Sequence Source Affymetrix Proprietary Database