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[174400_s_at] transcription factor IIH subunit

Description C53125_rc /REP_DB=TREMBL Accession /GB=C53125 /CHR=3 /FEA=Genomic Cluster /DEF=C.elegans cDNA clone yk294a4 : 3prime end, single read.
Cluster 6grp_highest_10_10 > 97      6grp_high1_10_10 > 78      4grp_highest_8_8 > 47      4grp_high_8_8 > 11      6grp_highest_nonorm > 83      6grp_total > 69      4grp_total > 13      6grp_highest_sub > Cu      6grp_high1_sub > Cu      6grp_total_sub > Cup      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 161
1 2 3 4 range
A 342
(-1.6)
P 		370.3
(0.1)
P 		319.3
(-3)
P 		419.1
(3)
P 		100
B 402.1
(-0.2)
P 		347.2
(-2.5)
P 		334.2
(-3)
P 		480
(3)
P 		146
C 395.8
(3)
P 		330.1
(-3)
P 		361.9
(-0.1)
P 		353.5
(-0.9)
P 		66
avr 380
(0.2) 		349.2
(-2.2) 		338.5
(-3) 		417.5
(3) 		79

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 361
1 2 3 4 5 6 range
A 453.1
(-1.7)
P 		396.9
(-2.8)
P 		385.6
(-3)
P 		440.7
(-1.9)
P 		529.3
(-0.2)
P 		688.4
(3)
P 		303
B 463.9
(-0.1)
P 		380.3
(-1.9)
P 		327.5
(-3)
P 		431.4
(-0.8)
P 		462.4
(-0.1)
P 		607.2
(3)
P 		280
C 454
(-0.8)
P 		329.9
(-3)
P 		429.8
(-1.2)
P 		369.1
(-2.3)
P 		547.3
(0.9)
P 		661.9
(3)
P 		332
avr 457
(-1.1) 		369
(-3) 		381
(-2.7) 		413.7
(-2.1) 		513
(0) 		652.5
(3) 		284
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 71
1 2 3 4 range
A 124.5
(3)
P 		80.4
(-1.2)
P 		83.5
(-0.9)
P 		61.3
(-3)
P 		63
B 128.2
(3)
P 		85.8
(-2)
P 		77.4
(-3)
P 		102.3
(-0.1)
P 		51
C 131
(3)
P 		94.9
(-0)
P 		126.1
(2.6)
P 		59.6
(-3)
P 		71
avr 127.9
(3) 		87
(-1.6) 		95.7
(-0.6) 		74.4
(-3) 		54

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 152
1 2 3 4 5 6 range
A 83.5
(-3)
P 		141.1
(1.1)
P 		84
(-3)
P 		111.8
(-1)
P 		159.7
(2.4)
P 		167.6
(3)
P 		84
B 161.4
(0.3)
P 		126.6
(-1.1)
P 		79.5
(-3)
P 		114.3
(-1.6)
P 		187.9
(1.4)
P 		226.4
(3)
P 		147
C 168.3
(0.8)
P 		100.7
(-1.9)
P 		109.4
(-1.6)
P 		74.2
(-3)
P 		177.1
(1.2)
P 		221.6
(3)
P 		147
avr 137.7
(-0.5) 		122.8
(-1.3) 		91
(-3) 		100.1
(-2.5) 		174.9
(1.4) 		205.2
(3) 		114
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 174400_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.21074
Sequence Type Exemplar sequence
Representative Public ID C53125 NCBI
Target Description C53125_rc /REP_DB=TREMBL Accession /GB=C53125 /CHR=3 /FEA=Genomic Cluster /DEF=C.elegans cDNA clone yk294a4 : 3prime end, single read.
Cluster Evidence This cluster is supported by a Genomic 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_066838(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_066838 NCBI Caenorhabditis elegans T16H12.4 (T16H12.4) mRNA, complete cds. 11/11 None
SNAP00000013069 ENSEMBL cdna:SNAP chromosome:CEL140:III:10087294:10090667:-1 11/11 None
GENEFINDER00000013080 ENSEMBL cdna:GeneFinder chromosome:CEL140:III:10088742:10090667:-1 11/11 None
T16H12.4.1 ENSEMBL cdna:known chromosome:CEL140:III:10088652:10090682:-1 gene:T16H12.4 11/11 None
T16H12.4.2 ENSEMBL cdna:known chromosome:CEL140:III:10088710:10090673:-1 gene:T16H12.4 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:10088715-10089044(-) 100.0 100.0
Public Domain and Genome References
Gene Title transcription factor IIH subunit
Ensembl T16H12.4
Entrez Gene 176421 Entrez gene
SwissProt P34567 EMBL-EBI
WormBase CE29053 Wormbase
Functional Annotations
Ortholog
ID Title Organism
ATH1-121501:265218_AT basic transcription factor 2, 44kD subunit-related at
ATGENOME1:13369_AT basic transcription factor 2, 44kD subunit-related at
CANINE:1588532_AT similar to TFIIH basal transcription factor complex p44 subunit (Basic transcription factor 2 44 kDa subunit) (BTF2-p44) (General transcription factor IIH polypeptide 2) cfa
CANINE_2:CFA.15007.1.A1_AT similar to TFIIH basal transcription factor complex p44 subunit (Basic transcription factor 2 44 kDa subunit) (BTF2-p44) (General transcription factor IIH polypeptide 2) cfa
CANINE_2:CFA.20989.1.S1_AT similar to TFIIH basal transcription factor complex p44 subunit (Basic transcription factor 2 44 kDa subunit) (BTF2-p44) (General transcription factor IIH polypeptide 2) cfa
CANINE_2:CFA.20989.1.S1_S_AT similar to TFIIH basal transcription factor complex p44 subunit (Basic transcription factor 2 44 kDa subunit) (BTF2-p44) (General transcription factor IIH polypeptide 2) cfa
CANINE_2:CFAAFFX.12531.1.S1_AT similar to TFIIH basal transcription factor complex p44 subunit (Basic transcription factor 2 44 kDa subunit) (BTF2-p44) (General transcription factor IIH polypeptide 2) cfa
CANINE_2:CFAAFFX.12531.1.S1_S_AT similar to TFIIH basal transcription factor complex p44 subunit (Basic transcription factor 2 44 kDa subunit) (BTF2-p44) (General transcription factor IIH polypeptide 2) cfa
DROSOPHILA_2:1638161_AT dm
DROSGENOME1:152186_AT dm
CHICKEN:GGAAFFX.1572.1.S1_AT similar to TFIIH basal transcription factor complex p44 subunit (Basic transcription factor 2 44 kDa subunit) (BTF2-p44) (General transcription factor IIH polypeptide 2) gga
CHICKEN:GGAAFFX.1597.1.S1_AT similar to TFIIH basal transcription factor complex p44 subunit (Basic transcription factor 2 44 kDa subunit) (BTF2-p44) (General transcription factor IIH polypeptide 2) gga
HG-U95AV2:33715_R_AT general transcription factor IIH, polypeptide 2, 44kDa hs
HG-U133A:221540_X_AT general transcription factor IIH, polypeptide 2, 44kDa hs
HG-U133_PLUS_2:221540_X_AT general transcription factor IIH, polypeptide 2, 44kDa hs
HG-FOCUS:221540_X_AT general transcription factor IIH, polypeptide 2, 44kDa hs
HG-U133A_2:221540_X_AT general transcription factor IIH, polypeptide 2, 44kDa hs
HU35KSUBB:RC_Z38155_AT general transcription factor IIH, polypeptide 2, 44kDa hs
HU35KSUBD:RC_AA281797_S_AT general transcription factor IIH, polypeptide 2, 44kDa hs
HUGENEFL:U80017_RNA1_AT general transcription factor IIH, polypeptide 2, 44kDa hs
HG-U133B:223758_S_AT general transcription factor IIH, polypeptide 2, 44kDa hs
HG-U133_PLUS_2:223758_S_AT general transcription factor IIH, polypeptide 2, 44kDa hs
U133_X3P:G5531808_3P_X_AT general transcription factor IIH, polypeptide 2, 44kDa hs
U133_X3P:G5531808_3P_AT general transcription factor IIH, polypeptide 2, 44kDa hs
U133_X3P:G13529148_3P_AT general transcription factor IIH, polypeptide 2, 44kDa hs
U133_X3P:221540_3P_X_AT general transcription factor IIH, polypeptide 2, 44kDa hs
HG-U95E:89507_AT general transcription factor IIH, polypeptide 2, 44kDa hs
HG-U133_PLUS_2:215470_AT General transcription factor IIH, polypeptide 2, 44kDa hs
HG-U133A_2:215470_AT General transcription factor IIH, polypeptide 2, 44kDa hs
HG-U133A:215470_AT General transcription factor IIH, polypeptide 2, 44kDa hs
HU35KSUBB:RC_R99606_S_AT General transcription factor IIH, polypeptide 2, 44kDa hs
U133_X3P:HS.14658.0.A1_3P_AT General transcription factor IIH, polypeptide 2, 44kDa hs
HG-U95AV2:40194_AT General transcription factor IIH, polypeptide 2, 44kDa hs
HG-U95D:67745_AT General transcription factor IIH, polypeptide 2, 44kDa hs
HU35KSUBC:RC_N58276_AT General transcription factor IIH, polypeptide 2, 44kDa hs
MG-U74BV2:108558_AT general transcription factor II H, polypeptide 2 mm
MOE430A:1450701_A_AT general transcription factor II H, polypeptide 2 mm
MOUSE430A_2:1450701_A_AT general transcription factor II H, polypeptide 2 mm
MOUSE430_2:1450701_A_AT general transcription factor II H, polypeptide 2 mm
MU19KSUBA:TC16832_AT General transcription factor II H, polypeptide 2, mRNA (cDNA clone MGC:28787 IMAGE:4488798) mm
MU19KSUBA:TC17041_AT General transcription factor II H, polypeptide 2, mRNA (cDNA clone MGC:28787 IMAGE:4488798) mm
MU19KSUBA:TC17041_G_AT General transcription factor II H, polypeptide 2, mRNA (cDNA clone MGC:28787 IMAGE:4488798) mm
RG-U34B:RC_AA957770_AT general transcription factor II H, polypeptide 2 (predicted) rn
RAE230B:1382030_AT general transcription factor II H, polypeptide 2 (predicted) rn
RAT230_2:1382030_AT general transcription factor II H, polypeptide 2 (predicted) rn
RAE230B:1385803_AT general transcription factor II H, polypeptide 2 (predicted) rn
RAT230_2:1385803_AT general transcription factor II H, polypeptide 2 (predicted) rn
RAE230B:1395837_AT General transcription factor II H, polypeptide 2 (predicted) rn
RAT230_2:1395837_AT General transcription factor II H, polypeptide 2 (predicted) rn
YEAST_2:1779548_AT Component of the core form of RNA polymerase transcription factor TFIIH, which has both protein kinase and DNA-dependent ATPase/helicase activities and is essential for transcription and nucleotide excision repair; interacts with Tfb4p Sc
Gene Ontology
GO Biological Process (view graph)
ID Description Evidence Links
6281 DNA repair inferred from electronic annotation QuickGO AmiGO
45449 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
3676 nucleic acid binding inferred from electronic annotation QuickGO AmiGO
3700 transcription factor activity inferred from electronic annotation QuickGO AmiGO
8270 zinc ion binding inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast CAA83139 Hypothetical protein T16H12.4 [Caenorhabditis elegans] ref|NP_499239.1| T16H12.4 [Caenorhabditis elegans] sp|P34567|TF2H2_CAEEL Probable TFIIH basal transcription factor complex p44 subunit (General transcription factor IIH polypeptide 2) 0.0
blast CAE65046 Hypothetical protein CBG09887 [Caenorhabditis briggsae] 0.0
Protein Domains
Database ID Description E-Value
Pfam IPR007198 EMBL-EBI Ssl1-like 1.0E-126
Sequence
Target Sequence 
>C. ELEGANS:174400_S_AT
tcactgctcgattccagctgaatgcccggtttgcaaacttacacttgtcgcagctccaca
gcttgctcgagcgtttcgacatcttcagccgctgtcagcttttgagcaaattgaagtgac
acgaggattctgctacgcatgtgaaactcgtctatctggtgaaggttttcgctgtgg

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
TCACTGCTCGATTCCAGCTGAATGC 704 625 16 Antisense
TTCCAGCTGAATGCCCGGTTTGCAA 389 697 27 Antisense
GAATGCCCGGTTTGCAAACTTACAC 336 317 35 Antisense
TGCAAACTTACACTTGTCGCAGCTC 470 575 47 Antisense
TTGCTCGAGCGTTTCGACATCTTCA 479 703 78 Antisense
TCTTCAGCCGCTGTCAGCTTTTGAG 313 617 97 Antisense
AGCCGCTGTCAGCTTTTGAGCAAAT 528 83 102 Antisense
TGACACGAGGATTCTGCTACGCATG 84 569 132 Antisense
GCTACGCATGTGAAACTCGTCTATC 395 303 147 Antisense
GTGAAACTCGTCTATCTGGTGAAGG 139 483 156 Antisense
TATCTGGTGAAGGTTTTCGCTGTGG 641 655 168 Antisense
Sequence Source Affymetrix Proprietary Database