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[173313_s_at] dna binding protein

Description CEK098E4R_rc /REP_DB=TREMBL Accession /GB=D72399 /FEA=Transcript Cluster /DEF=C.elegans cDNA clone yk98e4 : 3prime end, single read.
Cluster 6grp_high1_10_10 > 69      4grp_highest_8_8 > 43      4grp_high_8_8 > 32      6grp_total > 79      4grp_total > 55      6grp_high1_sub > Cu      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 371
1 2 3 4 range
A 563.1
(3)
P 		192.4
(-3)
P 		253.9
(-2)
P 		224.2
(-2.5)
P 		371
B 418.9
(3)
P 		199.4
(-3)
P 		270
(-1.1)
P 		258.8
(-1.4)
P 		220
C 458.1
(3)
P 		221.9
(-3)
P 		302.5
(-1)
P 		263
(-2)
P 		236
avr 480
(3) 		204.6
(-3) 		275.5
(-1.5) 		248.7
(-2) 		275

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 286
1 2 3 4 5 6 range
A 294.5
(-3)
P 		348.2
(-1.5)
P 		313.2
(-2.5)
P 		335.5
(-1.9)
P 		296.8
(-2.9)
A 		508.6
(3)
P 		214
B 353.2
(-0.4)
P 		365.6
(0.4)
P 		410.3
(3)
P 		308.8
(-3)
P 		395.5
(2.1)
P 		354.1
(-0.3)
P 		102
C 423
(2.3)
P 		451.1
(3)
P 		263.5
(-1.9)
P 		222.6
(-3)
P 		389.8
(1.4)
P 		441.5
(2.7)
P 		229
avr 356.9
(-0.2) 		388.3
(1.1) 		329
(-1.4) 		289
(-3) 		360.7
(-0) 		434.7
(3) 		146
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 172
1 2 3 4 range
A 205
(3)
P 		41.8
(-2.7)
P 		66.4
(-1.8)
P 		32.8
(-3)
P 		172
B 133.6
(3)
P 		49.2
(-3)
P 		62.6
(-2)
P 		55.2
(-2.6)
P 		84
C 151.7
(3)
P 		63.8
(-1.9)
P 		105.4
(0.4)
P 		44.3
(-3)
P 		107
avr 163.4
(3) 		51.6
(-2.6) 		78.1
(-1.3) 		44.1
(-3) 		119

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 116
1 2 3 4 5 6 range
A 54.3
(-3)
P 		123.8
(3)
P 		68.2
(-1.8)
P 		85.1
(-0.3)
P 		89.6
(0)
A 		123.8
(3)
P 		70
B 122.9
(0.1)
P 		121.7
(0)
P 		99.6
(-1.6)
P 		81.8
(-3)
P 		160.7
(3)
P 		132
(0.8)
P 		79
C 156.8
(3)
P 		137.6
(2)
P 		67.1
(-1.8)
P 		44.8
(-3)
P 		126.1
(1.4)
P 		147.8
(2.5)
P 		112
avr 111.3
(0.8) 		127.7
(2.4) 		78.3
(-2.3) 		70.6
(-3) 		125.5
(2.2) 		134.5
(3) 		64
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 173313_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.28000
Sequence Type Exemplar sequence
Representative Public ID CEK098E4R NCBI
Target Description CEK098E4R_rc /REP_DB=TREMBL Accession /GB=D72399 /FEA=Transcript Cluster /DEF=C.elegans cDNA clone yk98e4 : 3prime end, single read.
Cluster Evidence This cluster is supported by a Transcript Cluster.
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_062355(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_062355 NCBI Caenorhabditis elegans C01F1.1 (C01F1.1) mRNA, complete cds. 11/11 A 
SNAP00000028117 ENSEMBL cdna:SNAP chromosome:CEL140:II:4301601:4305148:1 11/11 None
GENEFINDER00000028121 ENSEMBL cdna:GeneFinder chromosome:CEL140:II:4301601:4305148:1 11/11 None
C01F1.1 ENSEMBL cdna:known chromosome:CEL140:II:4301599:4305269:1 gene:C01F1.1 11/11 A 
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
chrII:4303978-4305247(+) 99.01 99.01
Public Domain and Genome References
Gene Title dna binding protein
Ensembl C01F1.1
Entrez Gene 173764 Entrez gene
SwissProt Q17558 EMBL-EBI
WormBase CE06742 Wormbase
Functional Annotations
Ortholog
ID Title Organism
CANINE:1604381_AT similar to Transcription initiation factor IIF alpha subunit (TFIIF-alpha) (Transcription initiation factor RAP74) (General transcription factor IIF polypeptide 1 74 kDa subunit protein) cfa
CANINE_2:CFA.257.1.S1_S_AT similar to Transcription initiation factor IIF alpha subunit (TFIIF-alpha) (Transcription initiation factor RAP74) (General transcription factor IIF polypeptide 1 74 kDa subunit protein) cfa
CANINE_2:CFAAFFX.28544.1.S1_S_AT similar to Transcription initiation factor IIF alpha subunit (TFIIF-alpha) (Transcription initiation factor RAP74) (General transcription factor IIF polypeptide 1 74 kDa subunit protein) cfa
DROSOPHILA_2:1640495_AT Transcription factor IIF dm
DROSGENOME1:154355_AT Transcription factor IIF dm
HG-U133_PLUS_2:202355_S_AT general transcription factor IIF, polypeptide 1, 74kDa hs
HG-U133A:202355_S_AT general transcription factor IIF, polypeptide 1, 74kDa hs
HG-FOCUS:202355_S_AT general transcription factor IIF, polypeptide 1, 74kDa hs
HG-U133A_2:202355_S_AT general transcription factor IIF, polypeptide 1, 74kDa hs
HG-U133_PLUS_2:202356_S_AT general transcription factor IIF, polypeptide 1, 74kDa hs
HG-U133A:202356_S_AT general transcription factor IIF, polypeptide 1, 74kDa hs
HG-U133A_2:202356_S_AT general transcription factor IIF, polypeptide 1, 74kDa hs
HG-U133A_2:202354_S_AT general transcription factor IIF, polypeptide 1, 74kDa hs
HG-U133_PLUS_2:202354_S_AT general transcription factor IIF, polypeptide 1, 74kDa hs
HG-U133A:202354_S_AT general transcription factor IIF, polypeptide 1, 74kDa hs
HU35KSUBC:RC_AA115477_S_AT general transcription factor IIF, polypeptide 1, 74kDa hs
HUGENEFL:X64037_AT general transcription factor IIF, polypeptide 1, 74kDa hs
U133_X3P:G12652738_3P_A_AT general transcription factor IIF, polypeptide 1, 74kDa hs
U133_X3P:HS.68257.0.S1_3P_A_AT general transcription factor IIF, polypeptide 1, 74kDa hs
HG-U95AV2:36826_AT general transcription factor IIF, polypeptide 1, 74kDa hs
HG-U95E:71100_AT general transcription factor IIF, polypeptide 1, 74kDa hs
MU11KSUBA:AA154593_S_AT general transcription factor IIF, polypeptide 1 mm
MU11KSUBB:MSA.17602.0_S_AT general transcription factor IIF, polypeptide 1 mm
MU11KSUBB:MSA.30961.0_S_AT general transcription factor IIF, polypeptide 1 mm
MU11KSUBB:MSA.7111.0_S_AT general transcription factor IIF, polypeptide 1 mm
MG-U74AV2:103762_AT general transcription factor IIF, polypeptide 1 mm
MG-U74BV2:108354_AT general transcription factor IIF, polypeptide 1 mm
MOE430A:1417698_AT general transcription factor IIF, polypeptide 1 mm
MOUSE430A_2:1417698_AT general transcription factor IIF, polypeptide 1 mm
MOUSE430_2:1417698_AT general transcription factor IIF, polypeptide 1 mm
MOE430A:1417699_AT general transcription factor IIF, polypeptide 1 mm
MOUSE430A_2:1417699_AT general transcription factor IIF, polypeptide 1 mm
MOUSE430_2:1417699_AT general transcription factor IIF, polypeptide 1 mm
MU19KSUBA:TC24695_AT General transcription factor IIF, polypeptide 1, mRNA (cDNA clone MGC:36237 IMAGE:5026448) mm
RG-U34B:RC_AA955573_AT general transcription factor IIF, polypeptide 1, 74kDa rn
RG-U34B:RC_AA955573_G_AT general transcription factor IIF, polypeptide 1, 74kDa rn
RG-U34B:RC_AI012037_AT general transcription factor IIF, polypeptide 1, 74kDa rn
RAE230B:1385567_AT general transcription factor IIF, polypeptide 1, 74kDa rn
RAT230_2:1385567_AT general transcription factor IIF, polypeptide 1, 74kDa rn
RAE230B:1383627_A_AT general transcription factor IIF, polypeptide 1, 74kDa rn
RAT230_2:1383627_A_AT general transcription factor IIF, polypeptide 1, 74kDa rn
RAE230B:1393106_X_AT general transcription factor IIF, polypeptide 1, 74kDa rn
RAT230_2:1393106_X_AT general transcription factor IIF, polypeptide 1, 74kDa rn
Gene Ontology
GO Biological Process (view graph)
ID Description Evidence Links
45941 positive regulation of transcription 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
16563 transcriptional activator activity inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast AAB00717 Hypothetical protein C01F1.1 [Caenorhabditis elegans] ref|NP_494756.1| C01F1.1 [Caenorhabditis elegans] 0.0
blast CAE60114 Hypothetical protein CBG03654 [Caenorhabditis briggsae] 0.0
blast CAA78999 transcription factor IIF subunit [Xenopus laevis] gb|AAH70569.1| LOC398325 protein [Xenopus laevis] sp|Q04870|T2FA_XENLA Transcription initiation factor IIF alpha subunit (TFIIF-alpha) (Transcription initiation factor RAP74) 5.0E-40
Protein Domains
Database ID Description E-Value
Pfam IPR008851 EMBL-EBI Transcription initiation factor IIF, alpha subunit 1.0E-126
Pfam IPR008851 EMBL-EBI Transcription initiation factor IIF, alpha subunit 4.0E-41
Sequence
Target Sequence 
>C. ELEGANS:173313_S_AT
ggataatcttggtccgagtgatgcgnnnnnngcgaaaccggctgttaaatttgaggaagg
actcaatgaggaaactgttcgcagatatttgcgtcgtaaaccgcatacaacgaaggaact
cctccacacaatgagcggaaaatgcggaaatatgagcaaatctgaaatggtaacccaact
ggcttcaattctgaaagcaatcganccgaatcaatctcgannnnnnnnnnnnnnnnnnnn
nntactcttcttctcacttgtcaacactatc

BLASTn GenBank NR
Note: "n"'s represent regions that are not probed by the probe sequences.
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GGATAATCTTGGTCCGAGTGATGCG 384 511 42 Antisense
GCGAAACCGGCTGTTAAATTTGAGG 625 219 73 Antisense
GGCTGTTAAATTTGAGGAAGGACTC 203 505 81 Antisense
GACTCAATGAGGAAACTGTTCGCAG 1 375 101 Antisense
ACTGTTCGCAGATATTTGCGTCGTA 574 97 115 Antisense
TTGCGTCGTAAACCGCATACAACGA 385 695 130 Antisense
CATACAACGAAGGAACTCCTCCACA 166 213 145 Antisense
GAGCAAATCTGAAATGGTAACCCAA 30 391 195 Antisense
GGTAACCCAACTGGCTTCAATTCTG 58 505 210 Antisense
AACCCAACTGGCTTCAATTCTGAAA 81 145 213 Antisense
CTTCTTCTCACTTGTCAACACTATC 269 221 288 Antisense
Sequence Source Affymetrix Proprietary Database