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[193715_at] transcription initiation factor IIA gamma chain

Description Y111B2A.13 /REP_DB=WormBase Gene ID /WP=CE26630 /TR=Q9NEX2 /GB=CAC35842.1 /SUBMIT=HINXTON /CHR=3 /FEA=Sanger Annotation /DEF=transcription initiation factor IIA gamma chain
Cluster 6grp_highest_10_10 > 16      6grp_high1_10_10 > 61      4grp_highest_8_8 > 31      4grp_high_8_8 > 13      6grp_highest_nonorm > 43      6grp_total > 61      4grp_total > 11      6grp_highest_sub > 03_04      6grp_high1_sub > 04      6grp_total_sub > Hat      6grp_rule_based > S4      4grp_rule_based > L4      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 715
1 2 3 4 range
A 820.5
(-2.5)
P 		858.4
(-2.2)
P 		767.5
(-3)
P 		1415.1
(3)
P 		648
B 952
(-0.8)
P 		861.6
(-1.8)
P 		757.9
(-3)
P 		1287.4
(3)
P 		530
C 920.2
(-2.6)
P 		902.5
(-2.7)
P 		876.7
(-3)
P 		1473
(3)
P 		596
avr 897.6
(-2) 		874.2
(-2.3) 		800.7
(-3) 		1391.8
(3) 		591

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 1230
1 2 3 4 5 6 range
A 932.4
(-1.6)
P 		1059.4
(-1)
P 		1880.9
(3)
P 		1837.2
(2.8)
P 		947
(-1.6)
P 		651.4
(-3)
P 		1230
B 1125.1
(-0.3)
P 		1298.3
(1.1)
P 		1521.6
(2.9)
P 		1530.1
(3)
P 		1259.7
(0.8)
P 		786.2
(-3)
P 		744
C 1215.6
(0.3)
P 		1218.1
(0.3)
P 		1253.1
(0.6)
P 		1619.5
(3)
P 		1200.3
(0.2)
P 		717.2
(-3)
P 		902
avr 1091
(-0.6) 		1191.9
(0) 		1551.9
(2.3) 		1662.3
(3) 		1135.7
(-0.3) 		718.3
(-3) 		944
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 130
1 2 3 4 range
A 298.7
(3)
P 		186.3
(-3)
P 		200.6
(-2.2)
P 		207.1
(-1.9)
P 		112
B 303.6
(3)
P 		212.8
(-1.3)
P 		175.6
(-3)
P 		274.4
(1.6)
P 		128
C 304.6
(2.9)
P 		259.5
(-1.8)
P 		305.6
(3)
P 		248.4
(-3)
P 		57
avr 302.3
(3) 		219.5
(-3) 		227.3
(-2.4) 		243.3
(-1.3) 		83

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 353
1 2 3 4 5 6 range
A 171.9
(-2.7)
P 		376.8
(1.3)
P 		409.6
(1.9)
P 		466
(3)
P 		285.8
(-0.5)
P 		158.6
(-3)
P 		307
B 391.5
(-0.3)
P 		432.2
(0.8)
P 		369.5
(-0.9)
P 		405.3
(0.1)
P 		511.8
(3)
P 		293.2
(-3)
P 		219
C 450.6
(3)
P 		371.7
(0.8)
P 		318.9
(-0.8)
P 		325.7
(-0.6)
P 		388.4
(1.2)
P 		240.1
(-3)
P 		211
avr 338
(0.8) 		393.6
(2.8) 		366
(1.8) 		399
(3) 		395.3
(2.9) 		230.6
(-3) 		168
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 193715_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.6744
Sequence Type Exemplar sequence
Representative Public ID Y111B2A.13 NCBI
Target Description Y111B2A.13 /REP_DB=WormBase Gene ID /WP=CE26630 /TR=Q9NEX2 /GB=CAC35842.1 /SUBMIT=HINXTON /CHR=3 /FEA=Sanger Annotation /DEF=transcription initiation factor IIA gamma chain
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_067243(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_067243 NCBI Caenorhabditis elegans Y111B2A.13 (Y111B2A.13) mRNA, complete cds. 11/11 None
Y111B2A.13 ENSEMBL cdna:known chromosome:CEL140:III:12624641:12625763:1 gene:Y111B2A.13 11/11 None
Annotation Notes
Cross Hybridizing mRNA Matched Probes Nature of Assignment Related Probesets by Grade
SNAP00000006161 6/11 Cross Hyb Matching Probes None
GENEFINDER00000006268 6/11 Cross Hyb Matching Probes None
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrIII:12624644-12625458(+) 100.0 100.0
Public Domain and Genome References
Gene Title transcription initiation factor IIA gamma chain
Ensembl Y111B2A.13
Entrez Gene 176682 Entrez gene
SwissProt Q9NEX2 EMBL-EBI
WormBase CE26630 Wormbase
Functional Annotations
Ortholog
ID Title Organism
ATGENOME1:18612_S_AT transcription initiation factor IIA gamma chain / TFIIA-gamma (TFIIA-S) at
ATH1-121501:254162_AT transcription initiation factor IIA gamma chain / TFIIA-gamma (TFIIA-S) at
CANINE:1587668_AT similar to general transcription factor Iia 2 cfa
CANINE_2:CFA.9946.1.S1_AT similar to general transcription factor Iia 2 cfa
CANINE_2:CFA.9946.2.S1_S_AT similar to general transcription factor Iia 2 cfa
DROSOPHILA_2:1632370_AT Transcription-factor-IIA-S dm
DROSGENOME1:143708_AT Transcription-factor-IIA-S dm
HG-U95AV2:869_AT general transcription factor IIA, 2, 12kDa hs
HC-G110:869_AT general transcription factor IIA, 2, 12kDa hs
HG-U133A:202678_AT general transcription factor IIA, 2, 12kDa hs
HG-U133_PLUS_2:202678_AT general transcription factor IIA, 2, 12kDa hs
HG-FOCUS:202678_AT general transcription factor IIA, 2, 12kDa hs
HG-U133A_2:202678_AT general transcription factor IIA, 2, 12kDa hs
HUGENEFL:U14193_AT general transcription factor IIA, 2, 12kDa hs
U133_X3P:G4758485_3P_S_AT general transcription factor IIA, 2, 12kDa hs
HG-U95AV2:37010_AT general transcription factor IIA, 2, 12kDa hs
HG-U133_PLUS_2:230376_AT General transcription factor IIA, 2, 12kDa hs
HG-U133B:230376_AT General transcription factor IIA, 2, 12kDa hs
HG-U133_PLUS_2:243985_AT General transcription factor IIA, 2, 12kDa hs
HG-U133B:243985_AT General transcription factor IIA, 2, 12kDa hs
HG-U95C:64672_AT General transcription factor IIA, 2, 12kDa hs
HU35KSUBC:RC_C21215_AT General transcription factor IIA, 2, 12kDa hs
U133_X3P:HS.279528.0.A1_3P_AT General transcription factor IIA, 2, 12kDa hs
U133_X3P:HS.44324.0.A1_3P_AT General transcription factor IIA, 2, 12kDa hs
RG-U34A:RC_AI012534_AT general transcription factor IIa 2 rn
RG-U34C:R47046_AT general transcription factor IIa 2 rn
RAE230A:1387775_AT general transcription factor IIa 2 rn
RAT230_2:1387775_AT general transcription factor IIa 2 rn
YEAST_2:1779551_AT TFIIA small subunit; involved in transcriptional activation, acts as antirepressor or as coactivator; homologous to smallest subunit of human and Drosophila TFIIA Sc
Gene Ontology
GO Biological Process (view graph)
ID Description Evidence Links
6367 transcription initiation from RNA polymerase II promoter inferred from electronic annotation QuickGO AmiGO
GO Cellular Component (view graph)
ID Description Evidence Links
5672 transcription factor TFIIA 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 CAC35842 Hypothetical protein Y111B2A.13 [Caenorhabditis elegans] ref|NP_499644.1| Y111B2A.13 [Caenorhabditis elegans] sp|Q9NEX2|T2AG_CAEEL Probable transcription initiation factor IIA gamma chain (TFIIA P12 subunit) (TFIIA-12) (TFIIAS) (TFIIA-gamma) 1.0E-60
blast CAE72838 Hypothetical protein CBG20129 [Caenorhabditis briggsae] 1.0E-48
blast BAE38203.1 unnamed protein product [Mus musculus] 7.0E-25
Protein Domains
Database ID Description E-Value
Pfam IPR003194 EMBL-EBI Transcription initiation factor IIA, gamma subunit 2.1E-11
Pfam IPR003194 EMBL-EBI Transcription initiation factor IIA, gamma subunit 2.8E-15
Sequence
Target Sequence 
>C. ELEGANS:193715_AT
tacaacattgggacaggcccttcagaaaacgctggatgattttgtcggcgatcaaatgat
acctgatagcttatcgaagaaaattatggattctttcgacaaatcaatcaataaaattct
tccgcataaggcgaagaataaggtgaatttccgtgctgacaaacttcgagcctatcggta
ttgtgacaatgtttggacattcatcgtcgaacaaattgatctacgcgatgcagttgaggg
cgggacagtggatcgattgaaaatcgtggcctgtgacgg

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
TACAACATTGGGACAGGCCCTTCAG 614 641 45 Antisense
GACAGGCCCTTCAGAAAACGCTGGA 575 337 56 Antisense
ACGCTGGATGATTTTGTCGGCGATC 278 91 73 Antisense
AATAAAATTCTTCCGCATAAGGCGA 510 169 154 Antisense
GAATAAGGTGAATTTCCGTGCTGAC 518 315 180 Antisense
TCCGTGCTGACAAACTTCGAGCCTA 450 595 194 Antisense
TCGAGCCTATCGGTATTGTGACAAT 16 603 210 Antisense
AACAAATTGATCTACGCGATGCAGT 675 133 254 Antisense
GCGATGCAGTTGAGGGCGGGACAGT 438 289 269 Antisense
AGGGCGGGACAGTGGATCGATTGAA 221 57 281 Antisense
GATTGAAAATCGTGGCCTGTGACGG 251 427 299 Antisense
Sequence Source Affymetrix Proprietary Database