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[174089_s_at]

Description CEC8916 /REP_DB=TREMBL Accession /GB=C13891 /CHR=3 /FEA=Genomic Cluster /DEF=C.elegans cDNA clone yk189g3 : 5prime end, single read.
Cluster 6grp_highest_10_10 > 79      6grp_high1_10_10 > 98      4grp_highest_8_8 > 57      4grp_high_8_8 > 34      6grp_highest_nonorm > 91      6grp_total > 98      4grp_total > 45      6grp_highest_sub > In      6grp_high1_sub > In      6grp_total_sub > Increase      6grp_rule_based > S6      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 112
1 2 3 4 range
A 281
(3)
P 		227.2
(0.1)
P 		194.2
(-1.6)
P 		168.7
(-3)
P 		112
B 237
(3)
P 		204.1
(-0.5)
P 		179.8
(-3)
P 		188.5
(-2.1)
P 		57
C 226.6
(-3)
P 		244.1
(3)
P 		228.6
(-2.3)
P 		240.7
(1.8)
P 		18
avr 248.2
(3) 		225.1
(0.2) 		200.9
(-2.8) 		199.3
(-3) 		49

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 223
1 2 3 4 5 6 range
A 132.2
(-3)
P 		194.8
(-0.9)
P 		218
(-0.1)
P 		178
(-1.5)
P 		253.2
(1.1)
P 		310.7
(3)
P 		179
B 232.3
(-2.5)
P 		241.9
(-2)
P 		220.1
(-3)
P 		264.6
(-1)
P 		319.3
(1.4)
P 		355.4
(3)
P 		135
C 204.5
(-1.9)
P 		170.3
(-3)
P 		209.1
(-1.7)
P 		178.6
(-2.7)
P 		332.6
(2.4)
P 		349.4
(3)
P 		179
avr 189.7
(-3) 		202.3
(-2.5) 		215.7
(-2) 		207.1
(-2.3) 		301.7
(1.5) 		338.5
(3) 		149
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 78
1 2 3 4 range
A 102.3
(3)
P 		49.3
(-1.1)
P 		50.8
(-1)
P 		24.7
(-3)
P 		78
B 75.6
(3)
P 		50.4
(-1.3)
P 		41.7
(-2.7)
P 		40.2
(-3)
P 		35
C 75
(2.3)
P 		70.2
(1.5)
P 		79.7
(3)
P 		40.6
(-3)
P 		39
avr 84.3
(3) 		56.6
(-0.4) 		57.4
(-0.3) 		35.2
(-3) 		49

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 108
1 2 3 4 5 6 range
A 24.4
(-3)
P 		69.3
(2.2)
P 		47.5
(-0.3)
P 		45.1
(-0.6)
P 		76.4
(3)
P 		75.6
(2.9)
P 		52
B 80.8
(-0.9)
P 		80.5
(-0.9)
P 		53.5
(-3)
P 		70.1
(-1.7)
P 		129.7
(2.8)
P 		132.5
(3)
P 		79
C 75.8
(-0)
P 		51.9
(-1.8)
P 		53.2
(-1.7)
P 		35.9
(-3)
P 		107.6
(2.3)
P 		117
(3)
P 		81
avr 60.3
(-2) 		67.2
(-1.3) 		51.4
(-2.9) 		50.4
(-3) 		104.6
(2.6) 		108.4
(3) 		58
NetAffx Links Cluster Members
Consensus/Exemplar
Group Members
GeneChip Array Information
Probe Set ID 174089_s_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.21099
Sequence Type Exemplar sequence
Representative Public ID CEC8916 NCBI
Target Description CEC8916 /REP_DB=TREMBL Accession /GB=C13891 /CHR=3 /FEA=Genomic Cluster /DEF=C.elegans cDNA clone yk189g3 : 5prime 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_067086(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_067086 NCBI Caenorhabditis elegans Y66D12A.15 (Y66D12A.15) mRNA, complete cds. 11/11 None
SNAP00000020812 ENSEMBL cdna:SNAP chromosome:CEL140:III:11526558:11534316:1 10/11 None
GENEFINDER00000020835 ENSEMBL cdna:GeneFinder chromosome:CEL140:III:11526558:11552219:1 9/11 None
Y66D12A.15 ENSEMBL cdna:known chromosome:CEL140:III:11526248:11534462:1 gene:Y66D12A.15 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:11533391-11534448(+) 100.0 100.0
Public Domain and Genome References
Gene Title
Ensembl Y66D12A.15
Entrez Gene 176584 Entrez gene
SwissProt Q95PZ4 EMBL-EBI
WormBase CE28998 Wormbase
Functional Annotations
Ortholog
ID Title Organism
ATH1-121501:249307_S_AT DNA repair protein and transcription factor, putative (XPB2) at
CANINE_2:CFA.2806.1.A1_AT similar to TFIIH basal transcription factor complex helicase XPB subunit (Basic transcription factor 2 89 kDa subunit) (BTF2-p89) (TFIIH 89 kDa subunit) (DNA-repair protein complementing XP-B cells) (Xeroderma pigmentosum group B complementing prot... cfa
CANINE_2:CFAAFFX.7709.1.S1_S_AT similar to TFIIH basal transcription factor complex helicase XPB subunit (Basic transcription factor 2 89 kDa subunit) (BTF2-p89) (TFIIH 89 kDa subunit) (DNA-repair protein complementing XP-B cells) (Xeroderma pigmentosum group B complementing prot... cfa
DROSOPHILA_2:1641306_AT haywire dm
DROSGENOME1:155043_AT haywire dm
CHICKEN:GGAAFFX.12180.1.S1_S_AT excision repair cross-complementing rodent repair deficiency, complementation group 3 (xeroderma pigmentosum group B complementing) gga
HG-U95AV2:1885_AT excision repair cross-complementing rodent repair deficiency, complementation group 3 (xeroderma pigmentosum group B complementing) hs
HC-G110:1885_AT excision repair cross-complementing rodent repair deficiency, complementation group 3 (xeroderma pigmentosum group B complementing) hs
HG-U133A:202176_AT excision repair cross-complementing rodent repair deficiency, complementation group 3 (xeroderma pigmentosum group B complementing) hs
HG-U133_PLUS_2:202176_AT excision repair cross-complementing rodent repair deficiency, complementation group 3 (xeroderma pigmentosum group B complementing) hs
HG-U133A_2:202176_AT excision repair cross-complementing rodent repair deficiency, complementation group 3 (xeroderma pigmentosum group B complementing) hs
HG-FOCUS:202176_AT excision repair cross-complementing rodent repair deficiency, complementation group 3 (xeroderma pigmentosum group B complementing) hs
HUGENEFL:M31899_AT excision repair cross-complementing rodent repair deficiency, complementation group 3 (xeroderma pigmentosum group B complementing) hs
U133_X3P:G4557562_3P_AT excision repair cross-complementing rodent repair deficiency, complementation group 3 (xeroderma pigmentosum group B complementing) hs
MU11KSUBB:MSA.18514.0_S_AT excision repair cross-complementing rodent repair deficiency, complementation group 3 mm
MU11KSUBB:MSA.37995.0_S_AT excision repair cross-complementing rodent repair deficiency, complementation group 3 mm
MU11KSUBB:MSA.11962.0_AT excision repair cross-complementing rodent repair deficiency, complementation group 3 mm
MG-U74AV2:102346_AT excision repair cross-complementing rodent repair deficiency, complementation group 3 mm
MG-U74BV2:114429_AT excision repair cross-complementing rodent repair deficiency, complementation group 3 mm
MOE430A:1448497_AT excision repair cross-complementing rodent repair deficiency, complementation group 3 mm
MOUSE430A_2:1448497_AT excision repair cross-complementing rodent repair deficiency, complementation group 3 mm
MOUSE430_2:1448497_AT excision repair cross-complementing rodent repair deficiency, complementation group 3 mm
MU19KSUBA:TC18769_AT Excision repair cross-complementing rodent repair deficiency, complementation group 3, mRNA (cDNA clone IMAGE:4974086) mm
MU19KSUBA:TC21966_AT Excision repair cross-complementing rodent repair deficiency, complementation group 3, mRNA (cDNA clone IMAGE:4974086) mm
RAE230A:1374011_AT excision repair cross-complementing rodent repair deficiency, complementation group 3 (predicted) rn
RAT230_2:1374011_AT excision repair cross-complementing rodent repair deficiency, complementation group 3 (predicted) rn
RAE230B:1380926_AT Excision repair cross-complementing rodent repair deficiency, complementation group 3 (predicted) rn
RAT230_2:1380926_AT Excision repair cross-complementing rodent repair deficiency, complementation group 3 (predicted) rn
RAE230B:1391723_AT Excision repair cross-complementing rodent repair deficiency, complementation group 3 (predicted) rn
RAT230_2:1391723_AT Excision repair cross-complementing rodent repair deficiency, complementation group 3 (predicted) rn
RAE230B:1395147_AT Excision repair cross-complementing rodent repair deficiency, complementation group 3 (predicted) rn
RAT230_2:1395147_AT Excision repair cross-complementing rodent repair deficiency, complementation group 3 (predicted) rn
RG-U34B:RC_AA899152_AT Excision repair cross-complementing rodent repair deficiency, complementation group 3 (predicted) rn
YEAST_2:1770149_AT Component of the holoenzyme form of RNA polymerase transcription factor TFIIH, has DNA-dependent ATPase/helicase activity and is required, with Rad3p, for unwinding promoter DNA; involved in DNA repair; homolog of human ERCC3 Sc
Gene Ontology
GO Biological Process (view graph)
ID Description Evidence Links
6289 nucleotide-excision repair inferred from electronic annotation QuickGO AmiGO
9307 DNA restriction-modification system 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
3677 DNA binding inferred from electronic annotation QuickGO AmiGO
4003 ATP-dependent DNA helicase activity inferred from electronic annotation QuickGO AmiGO
4386 helicase activity inferred from electronic annotation QuickGO AmiGO
5524 ATP binding inferred from electronic annotation QuickGO AmiGO
8026 ATP-dependent helicase activity inferred from electronic annotation QuickGO AmiGO
15668 type III site-specific deoxyribonuclease activity inferred from electronic annotation QuickGO AmiGO
Protein Similarities
Method ID Description E-Value
blast CAC70144 Hypothetical protein Y66D12A.15 [Caenorhabditis elegans] ref|NP_499487.1| Y66D12A.15 [Caenorhabditis elegans] 0.0
blast CAE67700 Hypothetical protein CBG13269 [Caenorhabditis briggsae] 0.0
blast XP_882866 PREDICTED: similar to TFIIH basal transcription factor complex helicase XPB subunit (Basic transcription factor 2 89 kDa subunit) (BTF2-p89) (TFIIH 89 kDa subunit) (DNA-repair protein complementing XP-B cells) (Xeroderma pigmentosum group B complementing prot... iso [Bos taurus] 0.0
blast CAC70135 Hypothetical protein Y66D12A.14 [Caenorhabditis elegans] ref|NP_499488.1| Y66D12A.14 [Caenorhabditis elegans] 0.0
Protein Families
Method ID Description E-Value
ec 4CL1_ARATH (Q42524) 4-coumarate--CoA ligase 1 (EC 6.2.1.12) (4CL 1) (4-coumaroyl-CoA synthase 1) 2.0E-18
ec 4CL1_ARATH (Q42524) 4-coumarate--CoA ligase 1 (EC 6.2.1.12) (4CL 1) (4-coumaroyl-CoA synthase 1) 4.2
Protein Domains
Database ID Description E-Value
Pfam IPR001650 EMBL-EBI Helicase, C-terminal 7.5E-13
Pfam IPR001242 EMBL-EBI Condensation domain 4.2E-7
Pfam IPR005828 EMBL-EBI General substrate transporter 1.3E-10
Pfam IPR005828 EMBL-EBI General substrate transporter 4.5E-7
Pfam IPR000873 EMBL-EBI AMP-dependent synthetase and ligase 3.9E-34
Pfam IPR000873 EMBL-EBI AMP-dependent synthetase and ligase 5.9E-11
Pfam IPR000873 EMBL-EBI AMP-dependent synthetase and ligase 2.3E-53
Pfam IPR001650 EMBL-EBI Helicase, C-terminal 7.5E-13
Pfam IPR006163 EMBL-EBI Phosphopantetheine-binding domain 6.2E-7
Pfam IPR006163 EMBL-EBI Phosphopantetheine-binding domain 1.6E-14
Pfam IPR006163 EMBL-EBI Phosphopantetheine-binding domain 2.6E-8
Trans Membrane
ID Number Of Domains Domain Boundaries
GENEFINDER00000020835 9 3958-3975,3982-4004,4014-4036,4043-4062,4132-4154,4161-4183,4198-4220,4227-4249,4288-4310
Sequence
Target Sequence 
>C. ELEGANS:174089_S_AT
cgacttcggatgctgatgctgaagaggaggatgttaaggaagagcttgccgacggtacaa
ttcgaatctctcgccgcgaggcaacaatggcgtcaatgtcgggtggccagggagcacagt
accattcgaaagccaaagcgattgccgaacgacatccattgttcaaacgattccggcagt
gaattggata

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
CGACTTCGGATGCTGATGCTGAAGA 701 251 32 Antisense
TAAGGAAGAGCTTGCCGACGGTACA 533 635 66 Antisense
GACGGTACAATTCGAATCTCTCGCC 504 377 82 Antisense
GAATCTCTCGCCGCGAGGCAACAAT 101 329 95 Antisense
GAGGCAACAATGGCGTCAATGTCGG 614 403 109 Antisense
CAATGTCGGGTGGCCAGGGAGCACA 282 181 125 Antisense
GGGAGCACAGTACCATTCGAAAGCC 456 495 141 Antisense
GAAAGCCAAAGCGATTGCCGAACGA 658 355 159 Antisense
CGATTGCCGAACGACATCCATTGTT 593 247 170 Antisense
ATCCATTGTTCAAACGATTCCGGCA 199 39 185 Antisense
AACGATTCCGGCAGTGAATTGGATA 705 139 197 Antisense
Sequence Source Affymetrix Proprietary Database