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[192210_at] transcription factor

Description W03F9.5 /REP_DB=WormBase Gene ID /WP=CE27396 /GEN=ttb-1 /TR=O16991 /GB=AAG24202.2 /SUBMIT=ST.LOUIS /CHR=5 /FEA=Sanger Annotation /DEF=transcription factor
Cluster 6grp_total > 78      4grp_total > 37      6grp_cgc > 59      6grp_cgc_sub > Da      6grp_total_sub > Increase      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 164
1 2 3 4 range
A 168.1
(0.4)
P 		240.3
(3)
A 		76
(-3)
A 		131
(-1)
A 		164
B 217.7
(3)
P 		157.8
(-3)
A 		174.9
(-1.3)
P 		202.9
(1.5)
A 		60
C 193.2
(3)
P 		121.3
(-1.6)
A 		100.2
(-3)
A 		175.9
(1.9)
A 		93
avr 193
(3) 		173.1
(1.4) 		117
(-3) 		169.9
(1.2) 		76

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 191
1 2 3 4 5 6 range
A 113.1
(-3)
A 		149.4
(0.1)
A 		164.3
(1.3)
A 		149.6
(0.1)
A 		161
(1.1)
A 		184
(3)
P 		71
B 137.3
(-2.1)
A 		128.4
(-2.8)
A 		125.1
(-3)
P 		159.5
(-0.6)
A 		161
(-0.5)
P 		210.4
(3)
P 		85
C 122.4
(0.7)
P 		114.7
(0.5)
A 		104.4
(0.1)
A 		19.9
(-3)
A 		144.1
(1.5)
P 		184
(3)
P 		164
avr 124.3
(-1.9) 		130.8
(-1.5) 		131.3
(-1.4) 		109.7
(-3) 		155.4
(0.3) 		192.8
(3) 		83
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 50
1 2 3 4 range
A 61.2
(3)
P 		52.2
(1.7)
A 		19.9
(-2.9)
A 		19.2
(-3)
A 		42
B 69.4
(3)
P 		39
(-3)
A 		40.5
(-2.7)
P 		43.2
(-2.2)
A 		30
C 64
(3)
P 		34.9
(-2.1)
A 		34.9
(-2.1)
A 		29.7
(-3)
A 		34
avr 64.9
(3) 		42
(-1) 		31.8
(-2.8) 		30.7
(-3) 		34

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 75
1 2 3 4 5 6 range
A 20.9
(-3)
A 		53.1
(3)
A 		35.8
(-0.2)
A 		37.9
(0.2)
A 		48.6
(2.2)
A 		44.8
(1.5)
P 		32
B 47.8
(-0.8)
A 		42.7
(-1.5)
A 		30.4
(-3)
P 		42.2
(-1.5)
A 		65.4
(1.4)
P 		78.5
(3)
P 		48
C 45.4
(1.3)
P 		35
(0.2)
A 		26.6
(-0.6)
A 		4
(-3)
A 		46.6
(1.4)
P 		61.6
(3)
P 		58
avr 38
(-1.2) 		43.6
(-0.2) 		30.9
(-2.5) 		28
(-3) 		53.5
(1.6) 		61.6
(3) 		34
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 192210_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.15054
Sequence Type Exemplar sequence
Representative Public ID W03F9.5 NCBI
Target Description W03F9.5 /REP_DB=WormBase Gene ID /WP=CE27396 /GEN=ttb-1 /TR=O16991 /GB=AAG24202.2 /SUBMIT=ST.LOUIS /CHR=5 /FEA=Sanger Annotation /DEF=transcription factor
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_070745(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_070745 NCBI Caenorhabditis elegans TFII(two)B (general transcription factor) family member (ttb-1) (ttb-1) mRNA, complete cds. 11/11 A 
W03F9.5.3 ENSEMBL cdna:known chromosome:CEL140:V:156648:166691:1 gene:W03F9.5 11/11 A 
W03F9.5.1 ENSEMBL cdna:known chromosome:CEL140:V:156653:166691:1 gene:W03F9.5 11/11 A 
W03F9.5.2 ENSEMBL cdna:known chromosome:CEL140:V:156653:166672:1 gene:W03F9.5 11/11 A 
W03F9.5.4 ENSEMBL cdna:known chromosome:CEL140:V:156656:166687:1 gene:W03F9.5 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
chrV:156658-157186(+) 100.0 100.0
Public Domain and Genome References
Gene Title transcription factor
Gene Symbol ttb-1
Ensembl W03F9.5
Entrez Gene 178544 Entrez gene
SwissProt O16991 EMBL-EBI
WormBase CE27396 Wormbase
Functional Annotations
Ortholog
ID Title Organism
ATGENOME1:17129_AT transcription initiation factor IIB-1 / general transcription factor TFIIB-1 (TFIIB1) at
ATH1-121501:245114_AT transcription initiation factor IIB-1 / general transcription factor TFIIB-1 (TFIIB1) at
CANINE:1586810_AT similar to general transcription factor IIB cfa
CANINE_2:CFA.1947.1.A1_S_AT similar to general transcription factor IIB cfa
DROSOPHILA_2:1634172_AT Transcription factor IIB dm
DROSGENOME1:143536_AT Transcription factor IIB dm
CHICKEN:GGA.10024.1.S1_AT similar to Transcription initiation factor IIB (General transcription factor TFIIB) (RNA polymerase II alpha initiation factor) gga
HG-U95AV2:1070_AT general transcription factor IIB hs
HC-G110:1070_AT general transcription factor IIB hs
HG-U133_PLUS_2:208066_S_AT general transcription factor IIB hs
HG-U133A:208066_S_AT general transcription factor IIB hs
HG-FOCUS:208066_S_AT general transcription factor IIB hs
HG-U133A_2:208066_S_AT general transcription factor IIB hs
HU35KSUBD:RC_H60184_F_AT general transcription factor IIB hs
HUGENEFL:M76766_AT general transcription factor IIB hs
U133_X3P:G13435384_3P_S_AT general transcription factor IIB hs
HG-U95AV2:37380_AT general transcription factor IIB hs
HG-U95AV2:37381_G_AT general transcription factor IIB hs
MU11KSUBB:MSA.4224.0_S_AT general transcription factor IIB mm
MG-U74AV2:160225_AT general transcription factor IIB mm
MOE430A:1451135_AT general transcription factor IIB mm
MOUSE430A_2:1451135_AT general transcription factor IIB mm
MOUSE430_2:1451135_AT general transcription factor IIB mm
MOUSE430_2:1438066_AT General transcription factor IIB (Gtf2b), mRNA mm
MOE430B:1438066_AT General transcription factor IIB (Gtf2b), mRNA mm
MU11KSUBB:MSA.34879.0_S_AT General transcription factor IIB (Gtf2b), mRNA mm
MU19KSUBA:TC19574_AT General transcription factor IIB (Gtf2b), mRNA mm
MU19KSUBC:TC41121_AT General transcription factor IIB (Gtf2b), mRNA mm
RG-U34A:X65948_AT general transcription factor IIB rn
RAE230A:1368220_AT general transcription factor IIB rn
RAT230_2:1368220_AT general transcription factor IIB rn
YEAST_2:1772750_AT Transcription factor TFIIB, a general transcription factor required for transcription initiation and start site selection by RNA polymerase II Sc
Gene Ontology
GO Biological Process (view graph)
ID Description Evidence Links
6355 regulation of transcription, DNA-dependent inferred from electronic annotation QuickGO AmiGO
6367 transcription initiation from RNA polymerase II promoter inferred from electronic annotation QuickGO AmiGO
GO Cellular Component (view graph)
ID Description Evidence Links
5634 nucleus inferred from electronic annotation QuickGO AmiGO
5667 transcription factor complex inferred from electronic annotation QuickGO AmiGO
GO Molecular Function (view graph)
ID Description Evidence Links
3702 RNA polymerase II transcription factor activity inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast NP_503146 TFII(two)B (general transcription factor) family member (ttb-1) [Caenorhabditis elegans] gb|AAG24202.2| Tfii(two)b (general transcription factor) protein 1 [Caenorhabditis elegans] sp|O16991|TF2B_CAEEL Transcription initiation factor IIB (General transcription factor TFIIB) 1.0E-154
blast CAE62359 Hypothetical protein CBG06439 [Caenorhabditis briggsae] 1.0E-149
Protein Domains
Database ID Description E-Value
Pfam IPR000812 EMBL-EBI Transcription factor TFIIB 1.3E-26
Pfam IPR000812 EMBL-EBI Transcription factor TFIIB 5.8E-24
Sequence
Target Sequence 
>C. ELEGANS:192210_AT
cgatccatccagacgtgcatttgatcgaagatcaccgtgccggggatctggtctgtccgg
cgtgcggcttggtcgtcggtgatcgtctggtcgacgtcggaaccgaatggcgttcatttt
ccaacgaacgtagtggaaatgacccatctcgtgtcggagcaccggaaaatccgctgctca
gcggcggagatttgagcacaactatcgccgtgggctttggcggctccgacagtgataata
gtttggcgaatgctcaaagaaagtcaatgaacaatacggatcgtcaaatgaccgccgcga
tgagccttattagggaaatgagcgagagaattcacttgccaaga

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
CGATCCATCCAGACGTGCATTTGAT 400 249 35 Antisense
GATCGAAGATCACCGTGCCGGGGAT 495 417 57 Antisense
TGCCGGGGATCTGGTCTGTCCGGCG 161 585 72 Antisense
GTGATCGTCTGGTCGACGTCGGAAC 195 483 113 Antisense
TGGAAATGACCCATCTCGTGTCGGA 353 547 168 Antisense
AGCACCGGAAAATCCGCTGCTCAGC 507 73 192 Antisense
CACAACTATCGCCGTGGGCTTTGGC 60 195 231 Antisense
TTGGCGGCTCCGACAGTGATAATAG 172 707 251 Antisense
TACGGATCGTCAAATGACCGCCGCG 360 647 309 Antisense
CCGCCGCGATGAGCCTTATTAGGGA 309 263 326 Antisense
GAGCGAGAGAATTCACTTGCCAAGA 304 387 354 Antisense
Sequence Source Affymetrix Proprietary Database