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[193846_at] homeobox protein (even-skipped subfamily)

Description M142.4 /REP_DB=WormBase Gene ID /WP=CE12432 /GEN=vab-7 /TR=SW:Q93899 /GB=CAA97809.1 /SUBMIT=HINXTON /CHR=3 /FEA=Sanger Annotation /DEF=homeobox protein (even-skipped subfamily)
Cluster 6grp_total > 35      4grp_total > 27      6grp_cgc > 34      6grp_cgc_sub > Cu      6grp_total_sub > Cup      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 60
1 2 3 4 range
A 89.6
(-0.5)
A 		110.1
(3)
A 		74.8
(-3)
A 		100
(1.3)
A 		35
B 89.1
(1.4)
A 		95.1
(3)
A 		88
(1.1)
A 		72.5
(-3)
A 		23
C 80.9
(-3)
A 		99.2
(-0.9)
A 		86.9
(-2.3)
A 		132.1
(3)
A 		51
avr 86.5
(-1.9) 		101.5
(3) 		83.2
(-3) 		101.5
(3) 		18

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 92
1 2 3 4 5 6 range
A 93.5
(3)
A 		61.8
(0.9)
A 		52.7
(0.2)
A 		4.5
(-3)
A 		40.7
(-0.6)
A 		57.2
(0.6)
A 		89
B 72.3
(0.9)
A 		96.4
(3)
A 		75.3
(1.1)
M 		57.3
(-0.4)
A 		28.3
(-3)
A 		57.3
(-0.4)
M 		68
C 53.5
(1.3)
A 		45.2
(-0.2)
A 		49.4
(0.6)
A 		63.3
(3)
A 		29
(-3)
A 		46.6
(0.1)
A 		34
avr 73.1
(3) 		67.8
(2.2) 		59.1
(0.9) 		41.7
(-1.7) 		32.7
(-3) 		53.7
(0.1) 		40
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 18
1 2 3 4 range
A 32.6
(3)
A 		23.9
(0.1)
A 		19.5
(-1.4)
A 		14.6
(-3)
A 		18
B 28.4
(3)
A 		23.5
(0.7)
A 		20.4
(-0.7)
A 		15.4
(-3)
A 		13
C 26.8
(0.4)
A 		28.5
(1.7)
A 		30.3
(3)
A 		22.3
(-3)
A 		8
avr 29.3
(3) 		25.3
(1) 		23.4
(0) 		17.4
(-3) 		12

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 31
1 2 3 4 5 6 range
A 17.2
(1.6)
A 		22
(3)
A 		11.5
(-0)
A 		1.1
(-3)
A 		12.3
(0.2)
A 		13.9
(0.7)
A 		21
B 25.2
(1)
A 		32.1
(3)
A 		18.3
(-1)
M 		15.2
(-1.9)
A 		11.5
(-3)
A 		21.4
(-0.1)
M 		21
C 19.8
(3)
A 		13.8
(-0.5)
A 		12.6
(-1.2)
A 		12.7
(-1.1)
A 		9.4
(-3)
A 		15.6
(0.6)
A 		10
avr 20.7
(2.1) 		22.6
(3) 		14.1
(-1) 		9.7
(-3) 		11.1
(-2.3) 		17
(0.4) 		13
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 193846_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.7020
Sequence Type Exemplar sequence
Representative Public ID M142.4 NCBI
Target Description M142.4 /REP_DB=WormBase Gene ID /WP=CE12432 /GEN=vab-7 /TR=SW:Q93899 /GB=CAA97809.1 /SUBMIT=HINXTON /CHR=3 /FEA=Sanger Annotation /DEF=homeobox protein (even-skipped 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_067000(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_067000 NCBI Caenorhabditis elegans Variable ABnormal morphology family member (vab-7) (vab-7) mRNA, complete cds. 11/11 None
GENEFINDER00000000575 ENSEMBL cdna:GeneFinder chromosome:CEL140:III:10921482:10928786:1 11/11 None
M142.4 ENSEMBL cdna:known chromosome:CEL140:III:10920213:10925925:1 gene:M142.4 11/11 None
Annotation Notes
Cross Hybridizing mRNA Matched Probes Nature of Assignment Related Probesets by Grade
SNAP00000000572 6/11 Cross Hyb Matching Probes None
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrIII:10920258-10925885(+) 100.0 100.0
Public Domain and Genome References
Gene Title homeobox protein (even-skipped subfamily)
Gene Symbol vab-7
Ensembl M142.4
Entrez Gene 176521 Entrez gene
SwissProt Q93899 EMBL-EBI
WormBase CE12432 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 AAB37087 Protein kinase protein 31 [Caenorhabditis elegans] ref|NP_498912.3| protein KINase family member (kin-31) [Caenorhabditis elegans] sp|P34265|KIN31_CAEEL Probable tyrosine-protein kinase kin-31 1.0E-146
blast NP_501309 protein KINase family member (kin-26) [Caenorhabditis elegans] gb|AAA82302.1| Protein kinase protein 26 [Caenorhabditis elegans] 1.0E-141
blast G88535 protein B0523.1 [imported] - Caenorhabditis elegans 1.0E-128
blast CAA97809 Hypothetical protein M142.4 [Caenorhabditis elegans] ref|NP_499401.1| Variable ABnormal morphology family member (vab-7) [Caenorhabditis elegans] sp|Q93899|VAB7_CAEEL Homeobox protein vab-7 5.0E-88
blast CAA65441 vab-7 [Caenorhabditis elegans] pir||T43629 hypothetical protein vab-7 - Caenorhabditis elegans (fragment) 5.0E-88
blast CAE71372 Hypothetical protein CBG18276 [Caenorhabditis briggsae] 3.0E-54
Protein Families
Method ID Description E-Value
hanks 2.1.6 CaMK Group; CaMK I Regulated by Ca2+/CaM and close relatives; CamKI 3.0E-62
Protein Domains
Database ID Description E-Value
scop a.4.1.Homeodomain All alpha proteins; DNA/RNA-binding 3-helical bundle; Homeodomain-like; Homeodomain 4.99999984132761E-21
scop a.4.1.Homeodomain All alpha proteins; DNA/RNA-binding 3-helical bundle; Homeodomain-like; Homeodomain 9.99999968265523E-22
Pfam IPR000980 EMBL-EBI SH2 motif 1.4E-5
Pfam IPR001356 EMBL-EBI Homeobox 1.4E-28
Pfam IPR000719 EMBL-EBI Protein kinase 8.9E-53
Pfam IPR001356 EMBL-EBI Homeobox 1.4E-28
Sequence
Target Sequence 
>C. ELEGANS:193846_AT
tgtggtggccgcagcggcagcagcagcagccgccggacgtcatcatccgtatgataaccg
agacgacggtcaaatgcggaggtatcgaacggctttttcacgagaacagattgggaggct
tgagagggaattcgcaaaggaaaactatgttagcaggaagacacgtggcgagttggcggc
agagttgaatcttccagaaggtacaattaaggtatggttccaaaatcgtcgaatgaaaga
taaacggcaacgagtcggtggtctcgcgtggccctttcctccacaaatggctgcctacat
gttaaacccatttgcatatgaaatgtggatgaaaacagctgccgcctcacaattcggagc
cacgggtcccggaaatggagcttatgggaataatggatcaagcacatctccatcagcagc
tggatctcttccattccttccaccattaggttttccatcatttttatcacaaaattcaac
aaaatctccatcttctccacattcagacgattcc

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
TGTGGTGGCCGCAGCGGCAGCAGCA 166 555 141 Antisense
GGAGGTATCGAACGGCTTTTTCACG 86 497 218 Antisense
GAAGACACGTGGCGAGTTGGCGGCA 512 331 297 Antisense
GTTGGCGGCAGAGTTGAATCTTCCA 515 435 312 Antisense
AACGGCAACGAGTCGGTGGTCTCGC 120 143 383 Antisense
GGCTGCCTACATGTTAAACCCATTT 90 521 429 Antisense
TTCGGAGCCACGGGTCCCGGAAATG 308 33 493 Antisense
TTCCTTCCACCATTAGGTTTTCCAT 438 695 574 Antisense
AGGTTTTCCATCATTTTTATCACAA 265 57 588 Antisense
ATTCAACAAAATCTCCATCTTCTCC 391 11 614 Antisense
ATCTTCTCCACATTCAGACGATTCC 576 31 630 Antisense
Sequence Source Affymetrix Proprietary Database