[Home] | [Total List]

[190539_s_at] Brachyury

Description T07C4.6 /REP_DB=WormBase Gene ID /WP=CE00636 /GEN=tbx-9 /TR=SW:Q22289 /GB=CAA82575.1 /SUBMIT=HINXTON /CHR=3 /FEA=Sanger Annotation /DEF=Brachyury
Cluster 6grp_total > 78      4grp_total > 18      6grp_cgc > 49      6grp_cgc_sub > Da      6grp_total_sub > Increase      6grp_rule_based > S6      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 42
1 2 3 4 range
A 5.6
(-3)
A 		27
(0.4)
A 		23.8
(-0.1)
A 		43.9
(3)
A 		38
B 35.7
(3)
A 		9.6
(-1.6)
A 		32.8
(2.5)
A 		1.5
(-3)
A 		34
C 12
(-1.6)
A 		29.4
(1.1)
A 		2.5
(-3)
A 		41.9
(3)
P 		39
avr 17.8
(-3) 		22
(-0.8) 		19.7
(-2) 		29.1
(3) 		11

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 189
1 2 3 4 5 6 range
A 81
(-0.5)
A 		19.5
(-2.6)
A 		8.8
(-3)
A 		10
(-3)
A 		95.6
(0)
P 		181.5
(3)
P 		173
B 12.3
(-2.7)
A 		7.1
(-2.8)
A 		15.4
(-2.6)
A 		1.7
(-3)
A 		53.8
(-1.3)
P 		190.7
(3)
P 		189
C 23.9
(-2.3)
A 		7.6
(-3)
A 		23.7
(-2.3)
A 		71.3
(-0.3)
A 		48.8
(-1.3)
P 		151
(3)
P 		143
avr 39.1
(-2) 		11.4
(-3) 		16
(-2.8) 		27.7
(-2.4) 		66.1
(-1) 		174.4
(3) 		163
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 11
1 2 3 4 range
A 2.1
(-3)
A 		5.9
(2.3)
A 		6.2
(2.7)
A 		6.4
(3)
A 		4
B 11.4
(3)
A 		2.4
(-1.9)
A 		7.6
(0.9)
A 		0.3
(-3)
A 		11
C 4
(-0.6)
A 		8.5
(3)
A 		0.9
(-3)
A 		7.1
(1.9)
P 		8
avr 5.8
(3) 		5.6
(2) 		4.9
(-1.5) 		4.6
(-3) 		1

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 71
1 2 3 4 5 6 range
A 14.9
(-1.2)
A 		6.9
(-2.3)
A 		1.9
(-3)
A 		2.5
(-2.9)
A 		28.8
(0.8)
P 		44.2
(3)
P 		42
B 4.3
(-2.7)
A 		2.4
(-2.8)
A 		3.7
(-2.7)
A 		0.4
(-3)
A 		21.9
(-1.2)
P 		71.1
(3)
P 		71
C 8.9
(-2.2)
A 		2.3
(-3)
A 		6
(-2.5)
A 		14.3
(-1.5)
A 		15.8
(-1.3)
P 		50.5
(3)
P 		48
avr 9.4
(-2.4) 		3.9
(-3) 		3.9
(-3) 		5.7
(-2.8) 		22.2
(-0.9) 		55.3
(3) 		51
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 190539_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.7074
Sequence Type Exemplar sequence
Representative Public ID T07C4.6 NCBI
Target Description T07C4.6 /REP_DB=WormBase Gene ID /WP=CE00636 /GEN=tbx-9 /TR=SW:Q22289 /GB=CAA82575.1 /SUBMIT=HINXTON /CHR=3 /FEA=Sanger Annotation /DEF=Brachyury
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_066885(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_066885 NCBI Caenorhabditis elegans T07C4.6 (Brachyury) mRNA, complete cds. 11/11 None
SNAP00000030157 ENSEMBL cdna:SNAP chromosome:CEL140:III:10339951:10341737:-1 11/11 None
GENEFINDER00000030170 ENSEMBL cdna:GeneFinder chromosome:CEL140:III:10339951:10346222:-1 11/11 None
T07C4.6.2 ENSEMBL cdna:known chromosome:CEL140:III:10339870:10341740:-1 gene:T07C4.6 11/11 None
T07C4.6.1 ENSEMBL cdna:known chromosome:CEL140:III:10339875:10341744:-1 gene:T07C4.6 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
chrIII:10339946-10343714(-) 97.71 100.0
Public Domain and Genome References
Gene Title Brachyury
Gene Symbol tbx-9
Ensembl T07C4.6
Entrez Gene 176449 Entrez gene
SwissProt Q22289 EMBL-EBI
WormBase CE36892 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
3700 transcription factor activity inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast CAA82575 Hypothetical protein T07C4.6 [Caenorhabditis elegans] ref|NP_499286.2| T07C4.6 [Caenorhabditis elegans] dbj|BAC66463.1| T-box transcription factor TBX-9 [Caenorhabditis elegans] sp|Q22289|TBX9_CAEEL T-box transcription factor tbx-9 1.0E-130
blast CAA82578 Hypothetical protein T07C4.2 [Caenorhabditis elegans] ref|NP_499287.2| T07C4.2 [Caenorhabditis elegans] dbj|BAD14918.1| T-box transcription factor TBX-8 [Caenorhabditis elegans] sp|Q22292|TBX8_CAEEL T-box transcription factor tbx-8 1.0E-68
blast S41015 transcription factor tbx8 - Caenorhabditis elegans 1.0E-68
Protein Domains
Database ID Description E-Value
Pfam IPR001699 EMBL-EBI Transcription factor, T-box 1.0E-126
Pfam IPR001699 EMBL-EBI Transcription factor, T-box 1.0E-126
Sequence
Target Sequence 
>C. ELEGANS:190539_S_AT
gatgtggcatgctgatggagttcggaagggaagtgactggatgtggagttcgatttgctt
tgatcgtgtgaaaatctccaactattcagagtccaacaacgcttcaatgatttacctcaa
cagcatgcacaagtacattccagtgctgacaatctacgagtctccatcggagagcccttt
ctgcgtcccacaatcctcaaaccaaatcgtcgccaccgccaaattccctcataccgagtt
tattgcagtaacggcttaccagaaccaaaaaatcaccgacttgaaaatcaagcacaacag
ttttgccaaaggtttccgtgacgggaacttgagtcgcaagagaagatcaccatcatattc
cgacggcagcaactcacagtccccatcgccaaaatccagatcaccaccggaggtcgcacc
tcttcagtcgatgcctccaatcaacccatttcttttttattttccccatatgttatctga
aaatcttccagtccaatttccatt

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GATGTGGCATGCTGATGGAGTTCGG 327 407 528 Antisense
GGATGTGGAGTTCGATTTGCTTTGA 569 513 566 Antisense
TTCAGAGTCCAACAACGCTTCAATG 512 681 612 Antisense
AATGATTTACCTCAACAGCATGCAC 181 165 633 Antisense
GCTGACAATCTACGAGTCTCCATCG 192 295 672 Antisense
CACAATCCTCAAACCAAATCGTCGC 418 193 716 Antisense
CCAAATTCCCTCATACCGAGTTTAT 414 275 746 Antisense
AAGATCACCATCATATTCCGACGGC 423 155 870 Antisense
AAAATCCAGATCACCACCGGAGGTC 484 131 918 Antisense
TTTATTTTCCCCATATGTTATCTGA 321 675 983 Antisense
AAAATCTTCCAGTCCAATTTCCATT 478 133 1007 Antisense
Sequence Source Affymetrix Proprietary Database