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[192609_at] homeobox protein (msh subfamily)

Description R07B1.1 /REP_DB=WormBase Gene ID /WP=CE01626 /TR=SW:Q09604 /GB=CAA88539.1 /SUBMIT=HINXTON /CHR=X /FEA=Sanger Annotation /DEF=homeobox protein (msh subfamily)
Cluster 6grp_total > 09      4grp_total > 43      6grp_cgc > 0      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 56
1 2 3 4 range
A 30
(2)
A 		8.8
(-2.1)
A 		4.4
(-3)
A 		35.1
(3)
A 		31
B 19.4
(-2)
A 		60.3
(3)
A 		37.8
(0.3)
A 		10.9
(-3)
A 		49
C 15.1
(0)
A 		25.1
(3)
A 		5.1
(-3)
A 		6.4
(-2.6)
A 		20
avr 21.5
(-0.8) 		31.4
(3) 		15.8
(-3) 		17.5
(-2.3) 		16

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 41
1 2 3 4 5 6 range
A 43
(3)
A 		4.3
(-2.7)
A 		3.5
(-2.8)
A 		16.9
(-0.8)
A 		16.9
(-0.8)
A 		2.3
(-3)
A 		41
B 40
(3)
A 		24.5
(0.2)
A 		15.2
(-1.4)
A 		6.4
(-3)
A 		17.8
(-1)
A 		32.1
(1.6)
A 		34
C 41.6
(3)
A 		7.9
(-2.2)
A 		8.2
(-2.2)
A 		40.3
(2.8)
A 		11.1
(-1.7)
A 		2.9
(-3)
A 		39
avr 41.5
(3) 		12.2
(-2.4) 		9
(-3) 		21.2
(-0.7) 		15.3
(-1.8) 		12.4
(-2.4) 		33
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 14
1 2 3 4 range
A 10.9
(3)
A 		1.9
(-2.6)
A 		1.2
(-3)
A 		5.1
(-0.6)
A 		10
B 6.2
(-1.1)
A 		14.9
(3)
A 		8.8
(0.1)
A 		2.3
(-3)
A 		13
C 5
(0.8)
A 		7.2
(3)
A 		1.8
(-2.3)
A 		1.1
(-3)
A 		6
avr 7.4
(2.3) 		8
(3) 		3.9
(-1.7) 		2.8
(-3) 		5

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 15
1 2 3 4 5 6 range
A 7.9
(3)
A 		1.5
(-2.3)
A 		0.8
(-2.8)
A 		4.3
(0)
A 		5.1
(0.7)
A 		0.6
(-3)
A 		7
B 13.9
(3)
A 		8.1
(0.1)
A 		3.7
(-2)
A 		1.7
(-3)
A 		7.3
(-0.2)
A 		12
(2.1)
A 		12
C 15.4
(3)
A 		2.4
(-2.4)
A 		2.1
(-2.5)
A 		8.1
(-0)
A 		3.6
(-1.9)
A 		1
(-3)
A 		14
avr 12.4
(3) 		4
(-1.9) 		2.2
(-3) 		4.7
(-1.5) 		5.3
(-1.2) 		4.5
(-1.6) 		10
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 192609_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.16270
Sequence Type Exemplar sequence
Representative Public ID R07B1.1 NCBI
Target Description R07B1.1 /REP_DB=WormBase Gene ID /WP=CE01626 /TR=SW:Q09604 /GB=CAA88539.1 /SUBMIT=HINXTON /CHR=X /FEA=Sanger Annotation /DEF=homeobox protein (msh subfamily)
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_077247(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_077247 NCBI Caenorhabditis elegans Variable ABnormal morphology family member (vab-15) (vab-15) mRNA, complete cds. 11/11 A 
SNAP00000020684 ENSEMBL cdna:SNAP chromosome:CEL140:X:9847222:9847917:1 9/11 None
GENEFINDER00000020702 ENSEMBL cdna:GeneFinder chromosome:CEL140:X:9847222:9849044:1 11/11 None
R07B1.1 ENSEMBL cdna:known chromosome:CEL140:X:9847208:9849664:1 gene:R07B1.1 11/11 None
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:9847221-9849044(+) 100.0 100.0
Public Domain and Genome References
Gene Title homeobox protein (msh subfamily)
Gene Symbol vab-15
Ensembl R07B1.1
Entrez Gene 181197 Entrez gene
SwissProt Q09604 EMBL-EBI
WormBase CE01626 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 CAA88539 Hypothetical protein R07B1.1 [Caenorhabditis elegans] ref|NP_509648.1| Variable ABnormal morphology family member (vab-15) [Caenorhabditis elegans] gb|AAF88063.1| VAB-15 [Caenorhabditis elegans] sp|Q09604|VAB15_CAEEL Homeobox protein vab-15 2.0E-95
blast CAA88539 Hypothetical protein R07B1.1 [Caenorhabditis elegans] ref|NP_509648.1| Variable ABnormal morphology family member (vab-15) [Caenorhabditis elegans] gb|AAF88063.1| VAB-15 [Caenorhabditis elegans] sp|Q09604|VAB15_CAEEL Homeobox protein vab-15 3.0E-76
blast CAE58718 Hypothetical protein CBG01903 [Caenorhabditis briggsae] 8.0E-76
blast CAE58718 Hypothetical protein CBG01903 [Caenorhabditis briggsae] 3.0E-63
blast CAA10201 Msx protein [Branchiostoma floridae] 6.0E-33
Protein Domains
Database ID Description E-Value
scop a.4.1.Homeodomain All alpha proteins; DNA/RNA-binding 3-helical bundle; Homeodomain-like; Homeodomain 9.9999998245167E-15
scop a.4.1.Homeodomain All alpha proteins; DNA/RNA-binding 3-helical bundle; Homeodomain-like; Homeodomain 3.00000003404354E-18
Pfam IPR001356 EMBL-EBI Homeobox 1.4E-28
Pfam IPR001356 EMBL-EBI Homeobox 3.1E-20
Sequence
Target Sequence 
>C. ELEGANS:192609_AT
attacgccaaaaactcctatgctaataccaggattacatcctatgactccatacttcggc
gctcaattggatcctgtgatgatatatttcgctcagaccggaaaccggctgccaatagta
agctccgacagttcacctgaatcctgtgcctcgtctccactgtctatgcaacattcactt
caatggctatcatctcagcgagaagattcaccaactagcgatgacgccaagattcaaata
gggctttccaagtgcatgttaaggaaacacaagaacaatagaaagccacgtaccccattc
tctactcaacaacttatttctttggaaagaaagtttcaatcaaaacagtacctgtcaatt
gcggaaagagcagagtttagcgcatcattgcaattgacagagacacaagtcaaaatttgg
ttccagaatcgaagggctaaatcaaaaagactacaggaagctgaagtggaaaaagtgaag
tttgcacaggccagtgcttacgcagcagctgcagttggcggagcaccagatcca

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
ATTACGCCAAAAACTCCTATGCTAA 297 13 121 Antisense
TACATCCTATGACTCCATACTTCGG 467 639 155 Antisense
ATACTTCGGCGCTCAATTGGATCCT 432 23 171 Antisense
CGCTCAGACCGGAAACCGGCTGCCA 275 255 210 Antisense
AATAGTAAGCTCCGACAGTTCACCT 451 173 234 Antisense
GACAGTTCACCTGAATCCTGTGCCT 306 369 247 Antisense
CCACTGTCTATGCAACATTCACTTC 570 273 277 Antisense
GATTCACCAACTAGCGATGACGCCA 418 431 325 Antisense
CATTCTCTACTCAACAACTTATTTC 292 217 416 Antisense
TGCACAGGCCAGTGCTTACGCAGCA 345 577 603 Antisense
TGCAGTTGGCGGAGCACCAGATCCA 283 577 630 Antisense
Sequence Source Affymetrix Proprietary Database