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[189498_s_at]

Description C39E6.3 /REP_DB=WormBase Gene ID /WP=CE06939 /TR=Q18532 /GB=AAA93417.1 /SUBMIT=ST.LOUIS /CHR=X /FEA=Sanger Annotation /DEF=homeobox protein
Cluster 6grp_high1_10_10 > 38      6grp_total > 37      4grp_total > 38      6grp_cgc > 0      6grp_high1_sub > Cu      6grp_total_sub > Cup      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 111
1 2 3 4 range
A 147.1
(3)
P 		47.2
(-2.4)
A 		36.6
(-3)
A 		51.5
(-2.2)
A 		111
B 121.1
(3)
P 		83.1
(-1)
P 		63.4
(-3)
A 		68.2
(-2.5)
A 		58
C 104.2
(-0)
P 		87.5
(-1.5)
M 		70.2
(-3)
A 		138.3
(3)
P 		68
avr 124.1
(3) 		72.6
(-1.6) 		56.7
(-3) 		86
(-0.4) 		67

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 181
1 2 3 4 5 6 range
A 202.2
(3)
P 		97.7
(-1.4)
A 		62.8
(-2.9)
P 		133.9
(0.1)
P 		60.4
(-3)
M 		101.9
(-1.2)
P 		142
B 132.6
(3)
P 		67.9
(-2.3)
P 		83.5
(-1)
A 		66.4
(-2.5)
A 		59.8
(-3)
P 		105.5
(0.8)
P 		73
C 106.8
(2.2)
P 		94.2
(1.4)
P 		21.3
(-3)
A 		120.6
(3)
P 		60.6
(-0.6)
A 		109.2
(2.3)
P 		99
avr 147.2
(3) 		86.6
(-1) 		55.9
(-3) 		107
(0.4) 		60.3
(-2.7) 		105.5
(0.3) 		91
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 46
1 2 3 4 range
A 53.6
(3)
P 		10.2
(-2.6)
A 		9.6
(-2.7)
A 		7.5
(-3)
A 		46
B 38.6
(3)
P 		20.5
(-1.5)
P 		14.7
(-3)
A 		14.5
(-3)
A 		24
C 34.5
(3)
P 		25.2
(-2)
M 		24.5
(-2.4)
A 		23.3
(-3)
P 		11
avr 42.2
(3) 		18.6
(-2.2) 		16.3
(-2.7) 		15.1
(-3) 		27

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 41
1 2 3 4 5 6 range
A 37.3
(3)
P 		34.7
(2.3)
A 		13.7
(-3)
P 		34
(2.2)
P 		18.2
(-1.9)
M 		24.8
(-0.2)
P 		24
B 46.1
(3)
P 		22.6
(-1.9)
P 		20.3
(-2.4)
A 		17.6
(-3)
A 		24.3
(-1.6)
P 		39.4
(1.6)
P 		29
C 39.6
(3)
P 		28.8
(1.1)
P 		5.4
(-3)
A 		24.2
(0.3)
P 		19.6
(-0.5)
A 		36.6
(2.5)
P 		34
avr 41
(3) 		28.7
(0.4) 		13.1
(-3) 		25.3
(-0.4) 		20.7
(-1.4) 		33.6
(1.4) 		28
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 189498_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.16497
Sequence Type Exemplar sequence
Representative Public ID C39E6.3 NCBI
Target Description C39E6.3 /REP_DB=WormBase Gene ID /WP=CE06939 /TR=Q18532 /GB=AAA93417.1 /SUBMIT=ST.LOUIS /CHR=X /FEA=Sanger Annotation /DEF=homeobox protein
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_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 A 
SNAP00000034198 ENSEMBL cdna:SNAP chromosome:CEL140:X:4759041:4759803:-1 11/11 None
GENEFINDER00000034201 ENSEMBL cdna:GeneFinder chromosome:CEL140:X:4759041:4759803:-1 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:4759041-4759804(-) 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 3.0E-79
blast AAM51525 Mesodermal lineage specification protein 2 [Caenorhabditis elegans] ref|NP_508815.2| Mesodermal Lineage Specification family member (mls-2) [Caenorhabditis elegans] 6.0E-76
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 6.99999976701182E-26
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
Pfam IPR001356 EMBL-EBI Homeobox 1.8E-27
Sequence
Target Sequence 
>C. ELEGANS:189498_S_AT
gatggggagaccagggattccactggtggcagcccgctggagtctgacgcagaagatgac
gatgatattggccgtggaagcgatgatgaagccaactctagcgatccatcacaaaataga
aagaagaaaaccagaaccgtcttcagcaggagtcaggtgtcccaattggaaatgatgttc
gaatgcaaaagatatttgagcagtcaagagagatcaaatttagcacagaagctgcacttg
acggagacccaagtgaaaatttggttccaaaatcgacgaaacaagttcaagagacaagct
cagactgatgacacgaacatttccctgcagatgcatagagctaatgtgttttcgattcca
gcaaccacagctcttacatctccaatccttacgatcccaacgaccagtgctggtgtgaac
atgagaaatatgatttcatctccaatggatgcttctgcaactgccgccgcgcggtttctt
ttcggttttggtacacttcaggcacagcaaaact

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GATGGGGAGACCAGGGATTCCACTG 242 405 85 Antisense
CCCGCTGGAGTCTGACGCAGAAGAT 296 261 117 Antisense
ATGAAGCCAACTCTAGCGATCCATC 609 43 170 Antisense
CAGAACCGTCTTCAGCAGGAGTCAG 388 201 216 Antisense
GCAGGAGTCAGGTGTCCCAATTGGA 444 309 230 Antisense
CAGAAGCTGCACTTGACGGAGACCC 269 205 310 Antisense
ATGACACGAACATTTCCCTGCAGAT 215 45 392 Antisense
GATCCCAACGACCAGTGCTGGTGTG 432 417 477 Antisense
CAATGGATGCTTCTGCAACTGCCGC 58 183 527 Antisense
TCTTTTCGGTTTTGGTACACTTCAG 212 615 561 Antisense
GGTACACTTCAGGCACAGCAAAACT 118 503 574 Antisense
Sequence Source Affymetrix Proprietary Database