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[174814_at] chromodomain-helicase-DNA-biniding protein

Description CEK087F5R_rc /REP_DB=TREMBL Accession /GB=D64728 /CHR=1 /FEA=Genomic Cluster /DEF=C.elegans cDNA clone yk87f5 : 3prime end, single read.
Cluster 6grp_highest_10_10 > 63      6grp_high1_10_10 > 36      4grp_highest_8_8 > 51      4grp_high_8_8 > 24      6grp_highest_nonorm > 40      6grp_total > 36      4grp_total > 39      6grp_highest_sub > Cu      6grp_high1_sub > Cu      6grp_total_sub > Cup      4grp_rule_based > L1      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 633
1 2 3 4 range
A 986.5
(3)
P 		353.1
(-3)
P 		398.2
(-2.6)
P 		406.4
(-2.5)
P 		633
B 867
(3)
P 		407.9
(-2.8)
P 		392.4
(-3)
P 		591.9
(-0.5)
P 		475
C 899.5
(3)
P 		414.2
(-3)
P 		477.6
(-2.2)
P 		468.6
(-2.3)
P 		485
avr 917.7
(3) 		391.7
(-3) 		422.7
(-2.6) 		489
(-1.9) 		526

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 472
1 2 3 4 5 6 range
A 708.5
(1.9)
P 		754.6
(3)
P 		543.6
(-2)
P 		499.6
(-3)
P 		502.2
(-2.9)
P 		570.3
(-1.3)
P 		255
B 835.9
(3)
P 		683.4
(0.4)
P 		604.1
(-1)
P 		644.9
(-0.3)
P 		490.5
(-3)
P 		638.3
(-0.4)
P 		345
C 707.2
(2.9)
P 		688.5
(2.6)
P 		625.2
(1.5)
P 		710.8
(3)
P 		364.1
(-3)
P 		712.4
(3)
P 		348
avr 750.5
(3) 		708.8
(2.2) 		591
(-0.2) 		618.4
(0.3) 		452.3
(-3) 		640.3
(0.8) 		298
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 300
1 2 3 4 range
A 359.2
(3)
P 		76.7
(-2.7)
P 		104.1
(-2.1)
P 		59.5
(-3)
P 		300
B 276.5
(3)
P 		100.8
(-2.7)
P 		90.9
(-3)
P 		126.1
(-1.9)
P 		186
C 297.8
(3)
P 		119.1
(-1.9)
P 		166.5
(-0.6)
P 		79
(-3)
P 		219
avr 311.2
(3) 		98.9
(-2.7) 		120.5
(-2.1) 		88.2
(-3) 		223

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 173
1 2 3 4 5 6 range
A 130.6
(-2.5)
P 		268.4
(3)
P 		118.4
(-3)
P 		126.7
(-2.7)
P 		151.5
(-1.7)
P 		138.9
(-2.2)
P 		150
B 290.8
(3)
P 		227.5
(0.4)
P 		146.7
(-3)
P 		170.8
(-2)
P 		199.3
(-0.8)
P 		238
(0.8)
P 		144
C 262.1
(3)
P 		210.1
(0.8)
P 		159.1
(-1.3)
P 		143
(-2)
P 		117.8
(-3)
P 		238.5
(2)
P 		144
avr 227.8
(2.5) 		235.3
(3) 		141.4
(-3) 		146.8
(-2.7) 		156.2
(-2.1) 		205.1
(1.1) 		94
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 174814_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.20412
Sequence Type Exemplar sequence
Representative Public ID CEK087F5R NCBI
Target Description CEK087F5R_rc /REP_DB=TREMBL Accession /GB=D64728 /CHR=1 /FEA=Genomic Cluster /DEF=C.elegans cDNA clone yk87f5 : 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_059593(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_059593 NCBI Caenorhabditis elegans H06O01.2 (H06O01.2) mRNA, complete cds. 11/11 None
H06O01.2 ENSEMBL cdna:known chromosome:CEL140:I:7017275:7023340:-1 gene:H06O01.2 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
chrI:7017245-7017581(-) 100.0 100.0
Public Domain and Genome References
Gene Title chromodomain-helicase-DNA-biniding protein
Ensembl H06O01.2
Entrez Gene 172432 Entrez gene
SwissProt O17909 EMBL-EBI
WormBase CE32454 Wormbase
Functional Annotations
Ortholog
ID Title Organism
ATGENOME1:12298_AT chromodomain-helicase-DNA-binding family protein / CHD family protein at
ATH1-121501:263349_AT chromodomain-helicase-DNA-binding family protein / CHD family protein at
CANINE:1598766_AT similar to Chromodomain-helicase-DNA-binding protein 2 (CHD-2) cfa
CANINE_2:CFA.18812.1.S1_AT similar to Chromodomain-helicase-DNA-binding protein 2 (CHD-2) cfa
CANINE_2:CFAAFFX.17145.1.S1_AT similar to Chromodomain-helicase-DNA-binding protein 2 (CHD-2) cfa
CANINE_2:CFAAFFX.17289.1.S1_S_AT similar to Chromodomain-helicase-DNA-binding protein 2 (CHD-2) cfa
DROSOPHILA_2:1639816_AT Chromodomain-helicase-DNA-binding protein dm
DROSGENOME1:151704_S_AT Chromodomain-helicase-DNA-binding protein dm
DROSGENOME1:142858_AT Chromodomain-helicase-DNA-binding protein dm
HG-U133_PLUS_2:203461_AT chromodomain helicase DNA binding protein 2 hs
HG-U133A:203461_AT chromodomain helicase DNA binding protein 2 hs
HG-FOCUS:203461_AT chromodomain helicase DNA binding protein 2 hs
HG-U133A_2:203461_AT chromodomain helicase DNA binding protein 2 hs
U133_X3P:G4557448_3P_AT chromodomain helicase DNA binding protein 2 hs
U133_X3P:HS2.36787.2.A1_3P_S_AT chromodomain helicase DNA binding protein 2 hs
U133_X3P:HS.36787.1.S1_3P_AT chromodomain helicase DNA binding protein 2 hs
HG-U133_PLUS_2:1554014_AT chromodomain helicase DNA binding protein 2 hs
HG-U133_PLUS_2:1554015_A_AT chromodomain helicase DNA binding protein 2 hs
HG-U133_PLUS_2:228999_AT chromodomain helicase DNA binding protein 2 hs
HG-U133B:228999_AT chromodomain helicase DNA binding protein 2 hs
HG-U95AV2:35700_AT chromodomain helicase DNA binding protein 2 hs
HG-U95C:63705_F_AT chromodomain helicase DNA binding protein 2 hs
HG-U95C:63906_F_AT chromodomain helicase DNA binding protein 2 hs
HG-U95E:72228_AT chromodomain helicase DNA binding protein 2 hs
HG-U95E:72230_G_AT chromodomain helicase DNA binding protein 2 hs
HG-U133_PLUS_2:243751_AT Chromodomain helicase DNA binding protein 2 hs
HG-U133B:243751_AT Chromodomain helicase DNA binding protein 2 hs
HG-U95C:63630_AT Chromodomain helicase DNA binding protein 2 hs
HG-U95E:71620_AT Chromodomain helicase DNA binding protein 2 hs
HG-U95E:85176_AT Chromodomain helicase DNA binding protein 2 hs
HG-U95D:86628_AT Chromodomain helicase DNA binding protein 2 hs
HU35KSUBB:RC_H53564_AT Chromodomain helicase DNA binding protein 2 hs
HU35KSUBA:RC_AA447110_AT Chromodomain helicase DNA binding protein 2 hs
HU35KSUBC:RC_N29696_AT Chromodomain helicase DNA binding protein 2 hs
HU35KSUBD:RC_H51039_AT Chromodomain helicase DNA binding protein 2 hs
U133_X3P:HS.140963.0.A1_3P_AT Chromodomain helicase DNA binding protein 2 hs
MOUSE430_2:1445843_AT chromodomain helicase DNA binding protein 2 mm
MOE430B:1445843_AT chromodomain helicase DNA binding protein 2 mm
MU11KSUBB:MSA.29330.0_S_AT chromodomain helicase DNA binding protein 2 mm
MOE430B:1444246_AT chromodomain helicase DNA binding protein 2 mm
MOUSE430_2:1444246_AT chromodomain helicase DNA binding protein 2 mm
RAE230B:1381683_AT chromodomain helicase DNA binding protein 2 (predicted) rn
RAT230_2:1381683_AT chromodomain helicase DNA binding protein 2 (predicted) rn
RAT230_2:1371675_AT Chromodomain helicase DNA binding protein 2 (predicted) rn
RAE230A:1371675_AT Chromodomain helicase DNA binding protein 2 (predicted) rn
RAE230B:1379830_AT Chromodomain helicase DNA binding protein 2 (predicted) rn
RAT230_2:1379830_AT Chromodomain helicase DNA binding protein 2 (predicted) rn
RAE230B:1397779_AT Chromodomain helicase DNA binding protein 2 (predicted) rn
RAT230_2:1397779_AT Chromodomain helicase DNA binding protein 2 (predicted) rn
RG-U34A:RC_AA893193_AT Chromodomain helicase DNA binding protein 2 (predicted) rn
RG-U34B:RC_AI030599_AT Chromodomain helicase DNA binding protein 2 (predicted) rn
YEAST_2:1776167_AT Nucleosome remodeling factor that functions in regulation of transcription elongation; contains a chromo domain, a helicase domain and a DNA-binding domain; component of both the SAGA and SILK complexes Sc
Gene Ontology
GO Biological Process (view graph)
ID Description Evidence Links
6333 chromatin assembly or disassembly inferred from electronic annotation QuickGO AmiGO
GO Cellular Component (view graph)
ID Description Evidence Links
785 chromatin inferred from electronic annotation QuickGO AmiGO
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
3682 chromatin binding 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
Protein Similarities
Method ID Description E-Value
blast CAB07481 Hypothetical protein H06O01.2 [Caenorhabditis elegans] ref|NP_491994.2| H06O01.2 [Caenorhabditis elegans] 0.0
blast CAE65711 Hypothetical protein CBG10790 [Caenorhabditis briggsae] 0.0
blast XP_859429 PREDICTED: similar to Chromodomain-helicase-DNA-binding protein 2 (CHD-2) isoform 14 [Canis familiaris] 0.0
Protein Domains
Database ID Description E-Value
Pfam IPR000330 EMBL-EBI SNF2 related domain 2.3E-120
Pfam IPR000953 EMBL-EBI Chromo 2.6E-11
Pfam IPR000953 EMBL-EBI Chromo 3.0E-11
Pfam IPR001650 EMBL-EBI Helicase, C-terminal 6.7E-25
Sequence
Target Sequence 
>C. ELEGANS:174814_AT
cgccgacattagtctaactccatcttttcgtctacctgcacacactacactcacgggttc
ttcgtaaactgcgatataatttccatcatcccgtttctctttccccaaaacatgtcaatt
tttagttttcaaattcgttgttgataaatagaaattcttattcatttctaaatgatataa
tcctaattttgtccgtttatttgccattccttatccatctagctcgatttcttttcctgt
tttctttggtcgggtttacttttttttgtttttatttcaaatgtttatcacatttcatct
ttttt

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
CGCCGACATTAGTCTAACTCCATCT 320 257 14 Antisense
CATTAGTCTAACTCCATCTTTTCGT 525 213 20 Antisense
TACACTCACGGGTTCTTCGTAAACT 81 629 59 Antisense
ACGGGTTCTTCGTAAACTGCGATAT 451 89 66 Antisense
GATATAATTTCCATCATCCCGTTTC 705 425 86 Antisense
TTCTCTTTCCCCAAAACATGTCAAT 224 687 108 Antisense
GATATAATCCTAATTTTGTCCGTTT 436 421 187 Antisense
TAATTTTGTCCGTTTATTTGCCATT 290 635 197 Antisense
ATTCCTTATCCATCTAGCTCGATTT 141 9 219 Antisense
TATCCATCTAGCTCGATTTCTTTTC 140 659 225 Antisense
ATGTTTATCACATTTCATCTTTTTT 665 47 294 Antisense
Sequence Source Affymetrix Proprietary Database