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[182023_at]

Description C39E6.4 /REP_DB=WormBase Gene ID /WP=CE06940 /TR=Q18533 /GB=AAA93418.1 /SUBMIT=ST.LOUIS /CHR=X /FEA=Sanger Annotation
Cluster 6grp_total > 18      4grp_total > 29      6grp_cgc > 02      6grp_total_sub > Decrease      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 71
1 2 3 4 range
A 40.2
(0.8)
A 		44.9
(2.2)
A 		26.6
(-3)
A 		47.8
(3)
A 		21
B 68.8
(2.2)
P 		44.1
(0.1)
A 		7.3
(-3)
A 		77.8
(3)
A 		71
C 53.3
(3)
P 		31.7
(-3)
A 		32.5
(-2.8)
A 		47.8
(1.5)
P 		22
avr 54.1
(2.4) 		40.2
(0) 		22.1
(-3) 		57.8
(3) 		36

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 72
1 2 3 4 5 6 range
A 74.5
(3)
P 		46.9
(0.7)
A 		14.8
(-2.1)
A 		3.8
(-3)
A 		71.9
(2.8)
A 		28.7
(-0.9)
A 		71
B 75.5
(3)
P 		33.7
(-0.7)
A 		6.9
(-3)
A 		26.8
(-1.3)
A 		17.2
(-2.1)
A 		45.3
(0.4)
P 		69
C 54.8
(1.5)
A 		47.9
(0.9)
A 		18.4
(-1.7)
A 		72.2
(3)
A 		4.2
(-3)
A 		21.4
(-1.5)
A 		68
avr 68.3
(3) 		42.8
(0.2) 		13.4
(-3) 		34.3
(-0.7) 		31.1
(-1.1) 		31.8
(-1) 		55
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 20
1 2 3 4 range
A 14.6
(3)
A 		9.8
(-0.7)
A 		6.9
(-3)
A 		7
(-2.9)
A 		8
B 21.9
(3)
P 		10.9
(-0.3)
A 		1.7
(-3)
A 		16.6
(1.4)
A 		20
C 17.6
(3)
P 		9.1
(-2.4)
A 		11.3
(-1)
A 		8.1
(-3)
P 		10
avr 18
(3) 		9.9
(-1.3) 		6.6
(-3) 		10.6
(-0.9) 		11

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 25
1 2 3 4 5 6 range
A 13.7
(0.7)
P 		16.7
(1.6)
A 		3.2
(-2.4)
A 		1
(-3)
A 		21.7
(3)
A 		7
(-1.3)
A 		21
B 26.3
(3)
P 		11.2
(-0.7)
A 		1.7
(-3)
A 		7.1
(-1.7)
A 		7
(-1.7)
A 		16.9
(0.7)
P 		25
C 20.3
(3)
A 		14.6
(1.2)
A 		4.7
(-2)
A 		14.5
(1.2)
A 		1.4
(-3)
A 		7.2
(-1.2)
A 		19
avr 20.1
(3) 		14.2
(0.9) 		3.2
(-3) 		7.5
(-1.5) 		10
(-0.6) 		10.4
(-0.4) 		17
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 182023_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.16624
Sequence Type Exemplar sequence
Representative Public ID C39E6.4 NCBI
Target Description C39E6.4 /REP_DB=WormBase Gene ID /WP=CE06940 /TR=Q18533 /GB=AAA93418.1 /SUBMIT=ST.LOUIS /CHR=X /FEA=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 
SNAP00000034199 ENSEMBL cdna:SNAP chromosome:CEL140:X:4761093:4761580:-1 11/11 None
GENEFINDER00000034204 ENSEMBL cdna:GeneFinder chromosome:CEL140:X:4761093:4761580:-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:4761093-4761581(-) 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 1.0E-71
blast AAM51525 Mesodermal lineage specification protein 2 [Caenorhabditis elegans] ref|NP_508815.2| Mesodermal Lineage Specification family member (mls-2) [Caenorhabditis elegans] 2.0E-70
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:182023_AT
gccgacttcagttatgaatctccctattgatatgacgacaatgagctcgcaagaacgtct
cgaaaaaatgtcacaacttccaaagattgaactgatggaggaagaagaggaagaagagat
gaagccaagttcagataataagattaaattcaatatttctgagttgctggaagatgacag
aaaaccaactacacaaagttccccgtcggcatcttcagaggatagcaccaatgaaattga
gcaaacggcgtttaatttcaattttgatccaaaaatgaatccgatttctgccctcctgca
acttcagcaaactttcttgaacgtcggcaatcaacaaaacatgatctcaccacttaccat
gttcccattctttggacttccgactgctcaactaatgca

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GCCGACTTCAGTTATGAATCTCCCT 284 285 15 Antisense
GAATCTCCCTATTGATATGACGACA 415 329 30 Antisense
ATGAGCTCGCAAGAACGTCTCGAAA 485 45 55 Antisense
AATTCAATATTTCTGAGTTGCTGGA 528 173 161 Antisense
GATGACAGAAAACCAACTACACAAA 491 403 187 Antisense
CCCGTCGGCATCTTCAGAGGATAGC 73 261 216 Antisense
CCTCCTGCAACTTCAGCAAACTTTC 112 267 306 Antisense
GCAAACTTTCTTGAACGTCGGCAAT 107 317 321 Antisense
AAAACATGATCTCACCACTTACCAT 555 129 350 Antisense
ACCATGTTCCCATTCTTTGGACTTC 631 85 370 Antisense
GACTTCCGACTGCTCAACTAATGCA 578 371 389 Antisense
Sequence Source Affymetrix Proprietary Database