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[183088_at]

Description Y39B6A.I /REP_DB=WormBase Gene ID /WP=CE21669 /TR=Q9NEI3 /GB=CAB61066.2 /SUBMIT=HINXTON /CHR=5 /FEA=Sanger Annotation
Cluster 6grp_highest_10_10 > 57      6grp_high1_10_10 > 74      4grp_highest_8_8 > 01      4grp_high_8_8 > 45      6grp_highest_nonorm > 73      6grp_total > 64      4grp_total > 50      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 297
1 2 3 4 range
A 560
(-2.6)
P 		823.3
(3)
P 		547.6
(-2.9)
P 		542.8
(-3)
P 		281
B 575
(-1.7)
P 		637.1
(-0.1)
P 		751.5
(3)
P 		526.7
(-3)
P 		225
C 615.3
(-1)
P 		640.6
(3)
P 		614.4
(-1.2)
P 		603.1
(-3)
P 		38
avr 583.4
(-1.9) 		700.3
(3) 		637.8
(0.4) 		557.5
(-3) 		143

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 284
1 2 3 4 5 6 range
A 565.4
(-0.9)
P 		651.2
(2.4)
P 		511.7
(-3)
P 		631.7
(1.6)
P 		588.6
(-0)
P 		667
(3)
P 		155
B 490.7
(-2.6)
P 		479.1
(-3)
P 		672.7
(3)
P 		522.1
(-1.7)
P 		590.4
(0.4)
P 		589.2
(0.4)
P 		194
C 654.3
(0.4)
P 		508.2
(-3)
P 		762.9
(3)
P 		558.1
(-1.8)
P 		685
(1.2)
P 		657.5
(0.5)
P 		255
avr 570.1
(-1.6) 		546.2
(-3) 		649.1
(3) 		570.6
(-1.6) 		621.3
(1.4) 		637.9
(2.3) 		103
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 135
1 2 3 4 range
A 203.9
(3)
P 		178.7
(1.8)
P 		143.2
(0.1)
P 		79.5
(-3)
P 		124
B 183.4
(3)
P 		157.4
(0.8)
P 		174.1
(2.2)
P 		112.2
(-3)
P 		71
C 203.7
(2.4)
P 		184.2
(1.4)
P 		214.1
(3)
P 		101.7
(-3)
P 		112
avr 197
(3) 		173.4
(1.6) 		177.1
(1.8) 		97.8
(-3) 		99

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 138
1 2 3 4 5 6 range
A 104.2
(-3)
P 		231.6
(3)
P 		111.4
(-2.7)
P 		160.2
(-0.4)
P 		177.6
(0.5)
P 		162.4
(-0.3)
P 		127
B 170.7
(-1.1)
P 		159.5
(-1.7)
P 		163.4
(-1.5)
P 		138.3
(-3)
P 		239.9
(3)
P 		219.7
(1.8)
P 		102
C 242.5
(3)
P 		155.1
(-1)
P 		194.2
(0.8)
P 		112.2
(-3)
P 		221.7
(2)
P 		220.1
(2)
P 		130
avr 172.5
(-0.2) 		182.1
(0.6) 		156.3
(-1.5) 		136.9
(-3) 		213.1
(3) 		200.7
(2) 		76
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 183088_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.19449
Sequence Type Exemplar sequence
Representative Public ID Y39B6A.I NCBI
Target Description Y39B6A.I /REP_DB=WormBase Gene ID /WP=CE21669 /TR=Q9NEI3 /GB=CAB61066.2 /SUBMIT=HINXTON /CHR=5 /FEA=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_171571(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_171571 NCBI Caenorhabditis elegans Y39B6A.36 (Y39B6A.36) mRNA, complete cds. 11/11 None
SNAP00000030529 ENSEMBL cdna:SNAP chromosome:CEL140:V:18984527:19000682:1 11/11 None
GENEFINDER00000030712 ENSEMBL cdna:GeneFinder chromosome:CEL140:V:18996517:19000682:1 11/11 None
Y39B6A.36 ENSEMBL cdna:known chromosome:CEL140:V:18996512:19000768:1 gene:Y39B6A.36 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:18996516-18998241(+) 91.63 100.0
Public Domain and Genome References
Gene Title
Ensembl Y39B6A.36
Entrez Gene 180243 Entrez gene
SwissProt Q8MYM8 EMBL-EBI
WormBase CE29873 Wormbase
Functional Annotations
Ortholog
ID Title Organism
CANINE:1590114_S_AT similar to general transcription factor IIF, polypeptide 2 cfa
CANINE_2:CFA.2841.1.A1_AT similar to general transcription factor IIF, polypeptide 2 cfa
CANINE_2:CFAAFFX.19982.1.S1_S_AT similar to general transcription factor IIF, polypeptide 2 cfa
CANINE_2:CFAAFFX.7755.1.S1_AT similar to general transcription factor IIF, polypeptide 2 cfa
DROSOPHILA_2:1633349_AT Transcription factor TFIIF dm
DROSGENOME1:142514_AT Transcription factor TFIIF dm
CHICKEN:GGA.9598.1.S1_AT general transcription factor IIF, polypeptide 2, 30kDa gga
HG-FOCUS:209595_AT general transcription factor IIF, polypeptide 2, 30kDa hs
HG-U133_PLUS_2:209595_AT general transcription factor IIF, polypeptide 2, 30kDa hs
HG-U133A:209595_AT general transcription factor IIF, polypeptide 2, 30kDa hs
HG-U133A_2:209595_AT general transcription factor IIF, polypeptide 2, 30kDa hs
HU35KSUBA:X16901_AT general transcription factor IIF, polypeptide 2, 30kDa hs
HUGENEFL:X16901_AT general transcription factor IIF, polypeptide 2, 30kDa hs
U133_X3P:G12804688_3P_X_AT general transcription factor IIF, polypeptide 2, 30kDa hs
U133_X3P:G12804688_3P_S_AT general transcription factor IIF, polypeptide 2, 30kDa hs
U133_X3P:209595_3P_AT general transcription factor IIF, polypeptide 2, 30kDa hs
HG-U95AV2:36510_AT general transcription factor IIF, polypeptide 2, 30kDa hs
HG-U95C:62279_AT General transcription factor IIF, polypeptide 2, 30kDa hs
HU35KSUBB:RC_T96919_AT General transcription factor IIF, polypeptide 2, 30kDa hs
HU35KSUBD:RC_N62995_AT General transcription factor IIF, polypeptide 2, 30kDa hs
MU11KSUBB:MSA.26333.0_S_AT general transcription factor IIF, polypeptide 2 mm
MG-U74AV2:103651_R_AT general transcription factor IIF, polypeptide 2 mm
MOE430A:1426626_AT general transcription factor IIF, polypeptide 2 mm
MOUSE430A_2:1426626_AT general transcription factor IIF, polypeptide 2 mm
MOUSE430_2:1426626_AT general transcription factor IIF, polypeptide 2 mm
MOE430B:1441801_AT General transcription factor IIF, polypeptide 2, mRNA (cDNA clone MGC:18965 IMAGE:3986466) mm
MOUSE430_2:1441801_AT General transcription factor IIF, polypeptide 2, mRNA (cDNA clone MGC:18965 IMAGE:3986466) mm
RG-U34A:L01267_AT general transcription factor IIF, polypeptide 2 rn
RG-U34B:RC_AI028898_AT general transcription factor IIF, polypeptide 2 rn
RAE230A:1368233_AT general transcription factor IIF, polypeptide 2 rn
RAT230_2:1368233_AT general transcription factor IIF, polypeptide 2 rn
RAE230B:1396388_AT General transcription factor IIF, polypeptide 2 rn
RAT230_2:1396388_AT General transcription factor IIF, polypeptide 2 rn
YEAST_2:1773214_AT TFIIF (Transcription Factor II) middle subunit; involved in both transcription initiation and elongation of RNA polymerase II; homologous to human RAP30 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
5674 transcription factor TFIIF 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
5524 ATP binding inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast CAB61063 Hypothetical protein Y39B6A.39 [Caenorhabditis elegans] ref|NP_741658.1| Y39B6A.39 [Caenorhabditis elegans] 1.0E-169
blast CAD31828 Hypothetical protein Y39B6A.36 [Caenorhabditis elegans] ref|NP_741661.1| Y39B6A.36 [Caenorhabditis elegans] 1.0E-142
blast CAD31829 Hypothetical protein Y39B6A.37 [Caenorhabditis elegans] ref|NP_741660.1| Y39B6A.37 [Caenorhabditis elegans] 1.0E-137
blast CAE56105 Hypothetical protein CBG23703 [Caenorhabditis briggsae] 1.0E-107
blast EAA04044 ENSANGP00000015059 [Anopheles gambiae str. PEST] ref|XP_308768.2| ENSANGP00000015059 [Anopheles gambiae str. PEST] 9.0E-40
Protein Domains
Database ID Description E-Value
Pfam IPR003196 EMBL-EBI Transcription initiation factor IIF, beta subunit 1.9E-7
Pfam IPR003196 EMBL-EBI Transcription initiation factor IIF, beta subunit 7.9E-41
Pfam IPR003196 EMBL-EBI Transcription initiation factor IIF, beta subunit 1.9E-7
Pfam IPR003196 EMBL-EBI Transcription initiation factor IIF, beta subunit 7.9E-41
Sequence
Target Sequence 
>C. ELEGANS:183088_AT
agtgcccagatatttgtcagagctctgggatgccaacgagggaaatgttgttggaaaatt
gcagattggagcgcaggtcgagcttcacaccgccaaaggtctcattcatcccaaaccaaa
agagcccacagagggctcatcatctacagtaacccaaccagaagcctcggaaattccaac
agaatactcatttattcttcatgacgtcaaatctcaaacaatgagcgttttatccgaaga
taagcagggactcggtgcagatgctccaatcaaaactggaaaactggcaattgagggacg
aattatcaaaaaagcggaatgtcggccaccggccacgtcgaaatatatgaaaatgaagtt
ggcacatattgtgaaaaatactcaaccaaagaaaacggttaaaatgattgaaaaagcggc
tgtgaagtttaagcccgtgtctgtacat

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
AGTGCCCAGATATTTGTCAGAGCTC 61 61 84 Antisense
GTCAGAGCTCTGGGATGCCAACGAG 255 465 99 Antisense
AGATTGGAGCGCAGGTCGAGCTTCA 296 63 146 Antisense
TTCACACCGCCAAAGGTCTCATTCA 320 687 167 Antisense
CAAAGGTCTCATTCATCCCAAACCA 554 189 177 Antisense
ATCCCAAACCAAAAGAGCCCACAGA 315 37 191 Antisense
AGCCCACAGAGGGCTCATCATCTAC 400 83 206 Antisense
TAACCCAACCAGAAGCCTCGGAAAT 208 637 233 Antisense
TACTCATTTATTCTTCATGACGTCA 155 647 268 Antisense
ACTCGGTGCAGATGCTCCAATCAAA 380 97 333 Antisense
GAAGTTTAAGCCCGTGTCTGTACAT 497 335 507 Antisense
Sequence Source Affymetrix Proprietary Database